Dr. Pletser’s experience includes 30 years of working with the European Space Agency as a Senior Physicist/Engineer and coordinating their parabolic flight campaigns, and he is the Guinness World Record holder for the most number of aircraft flown (12) in parabolas, personally logging more than 7,300 parabolas.
\\n\\n
Seeing the 5,000th book published makes us at the same time proud, happy, humble, and grateful. This is a great opportunity to stop and celebrate what we have done so far, but is also an opportunity to engage even more, grow, and succeed. It wouldn't be possible to get here without the synergy of team members’ hard work and authors and editors who devote time and their expertise into Open Access book publishing with us.
\\n\\n
Over these years, we have gone from pioneering the scientific Open Access book publishing field to being the world’s largest Open Access book publisher. Nonetheless, our vision has remained the same: to meet the challenges of making relevant knowledge available to the worldwide community under the Open Access model.
\\n\\n
We are excited about the present, and we look forward to sharing many more successes in the future.
\\n\\n
Thank you all for being part of the journey. 5,000 times thank you!
\\n\\n
Now with 5,000 titles available Open Access, which one will you read next?
Preparation of Space Experiments edited by international leading expert Dr. Vladimir Pletser, Director of Space Training Operations at Blue Abyss is the 5,000th Open Access book published by IntechOpen and our milestone publication!
\n\n
"This book presents some of the current trends in space microgravity research. The eleven chapters introduce various facets of space research in physical sciences, human physiology and technology developed using the microgravity environment not only to improve our fundamental understanding in these domains but also to adapt this new knowledge for application on earth." says the editor. Listen what else Dr. Pletser has to say...
\n\n\n\n
Dr. Pletser’s experience includes 30 years of working with the European Space Agency as a Senior Physicist/Engineer and coordinating their parabolic flight campaigns, and he is the Guinness World Record holder for the most number of aircraft flown (12) in parabolas, personally logging more than 7,300 parabolas.
\n\n
Seeing the 5,000th book published makes us at the same time proud, happy, humble, and grateful. This is a great opportunity to stop and celebrate what we have done so far, but is also an opportunity to engage even more, grow, and succeed. It wouldn't be possible to get here without the synergy of team members’ hard work and authors and editors who devote time and their expertise into Open Access book publishing with us.
\n\n
Over these years, we have gone from pioneering the scientific Open Access book publishing field to being the world’s largest Open Access book publisher. Nonetheless, our vision has remained the same: to meet the challenges of making relevant knowledge available to the worldwide community under the Open Access model.
\n\n
We are excited about the present, and we look forward to sharing many more successes in the future.
\n\n
Thank you all for being part of the journey. 5,000 times thank you!
\n\n
Now with 5,000 titles available Open Access, which one will you read next?
\n'}],latestNews:[{slug:"intechopen-partners-with-ehs-for-digital-advertising-representation-20210416",title:"IntechOpen Partners with EHS for Digital Advertising Representation"},{slug:"intechopen-signs-new-contract-with-cepiec-china-for-distribution-of-open-access-books-20210319",title:"IntechOpen Signs New Contract with CEPIEC, China for Distribution of Open Access Books"},{slug:"150-million-downloads-and-counting-20210316",title:"150 Million Downloads and Counting"},{slug:"intechopen-secures-indefinite-content-preservation-with-clockss-20210309",title:"IntechOpen Secures Indefinite Content Preservation with CLOCKSS"},{slug:"intechopen-expands-to-all-global-amazon-channels-with-full-catalog-of-books-20210308",title:"IntechOpen Expands to All Global Amazon Channels with Full Catalog of Books"},{slug:"stanford-university-identifies-top-2-scientists-over-1-000-are-intechopen-authors-and-editors-20210122",title:"Stanford University Identifies Top 2% Scientists, Over 1,000 are IntechOpen Authors and Editors"},{slug:"intechopen-authors-included-in-the-highly-cited-researchers-list-for-2020-20210121",title:"IntechOpen Authors Included in the Highly Cited Researchers List for 2020"},{slug:"intechopen-maintains-position-as-the-world-s-largest-oa-book-publisher-20201218",title:"IntechOpen Maintains Position as the World’s Largest OA Book Publisher"}]},book:{item:{type:"book",id:"5866",leadTitle:null,fullTitle:"Indigenous People",title:"Indigenous People",subtitle:null,reviewType:"peer-reviewed",abstract:"Indigenous peoples are the native ethnic groups, who are descended from and identified with the original inhabitants of a region, in contrast to groups that have settled, occupied, or colonized the area more recently. 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\r\n\tIdiopathic pulmonary fibrosis (IPF) is the most common and important type of Idiopathic interstitial pneumonia, characterized by progressive fibrosis. It is a serious disease of unknown etiology with a high fatality rate. Over the past two decades there has been a tremendous amount of research in this field, that has helped us better understand the epidemiology, risk factors, pathogenesis, diagnostic evaluation and management strategies of IPF. The incidence and prevalence of the disease increases with age.
\r\n
\r\n\tWorldwide IPF has known to affect more than 3 million people. In US the reported incidence of IPF is 6 to 94 cases per 100,000 person years and prevalence is 18-495 cases per 100,000 adults depending on the age of the cohort. IPF is a clinically heterogenous disease and the course and progression of IPF is highly variable with intermittent episodes of acute exacerbations with rapid decline in lung function. Patients present with dyspnea and hypoxemia which significantly affects their quality of life. IPF is an expensive disease and the direct treatment cost is around 25,000 USD per person year. The pathogenesis of the disease is complex, and it is important to rule out a number of other diseases that can lead to pulmonary fibrosis. The hallmark of this disease is usual interstitial pneumonia (UIP) pattern seen on HRCT and on histology.
\r\n
\r\n\tThe diagnosis requires a multidisciplinary team approach and several guidelines have been published in the recent years to help the clinicians diagnose this disease in a timely manner. After decades of research two antifibrotic drugs are now available which are not curative but has shown to significantly slow down the decline in lung function associated with this disease. There are newer and less invasive technologies, biomarkers that are being developed to diagnose IPF and novel targeted treatment strategies are on pipeline. Lung transplant still remains the cornerstone of management as despite the treatment with antifibrotic agents most of the patients with IPF will progress to advanced end-stage lung disease.
",isbn:"978-1-83969-240-6",printIsbn:"978-1-83969-239-0",pdfIsbn:"978-1-83969-241-3",doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!0,hash:"365bb9762ba33db2d07e677690af1772",bookSignature:"Dr. Salim Surani and Dr. Venkat Rajasurya",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/9816.jpg",keywords:"Pulmonary Fibrosis, Pathogenesis, Epidemiology, Lung Transplant, Interstitial Lung Disease, HRCT, Echocardiogram, Lung Biopsy, Respiratory Failure, Perfinodine, Ninetanib, Steroid",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:null,numberOfDimensionsCitations:null,numberOfTotalCitations:null,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"January 25th 2021",dateEndSecondStepPublish:"February 22nd 2021",dateEndThirdStepPublish:"April 23rd 2021",dateEndFourthStepPublish:"July 12th 2021",dateEndFifthStepPublish:"September 10th 2021",remainingDaysToSecondStep:"2 months",secondStepPassed:!0,currentStepOfPublishingProcess:3,editedByType:null,kuFlag:!1,biosketch:"Dr. Salim Surani has been instrumental in starting the Emergency Medicine residency program, Pharmacy residency program, and Pulmonary and critical care residency program. He serves as Thursday morning health segment for Channel III news Corpus Christi (ABC affiliate), and Honorary Co-Anchor for COVID, first edition in Kiii TV (an affiliate of ABC News). Dr. Surani is highly regarding among his peers and is very well respected as a mentor, clinician, and humanitarian.",coeditorOneBiosketch:"Dr. Venkat Rajasurya works as an Attending Pulmonary Critical Care physician at Novant Forsyth Medical Center in Winston-Salem, NC. He has played a key role in the training and education of medical and pharmacy residents as well as physician assistants throughout his career. He currently serves as a Co-investigator for a number of clinical trials at Southeastern Research Center in Winston Salem, NC. Dr. Rajasurya has authored and reviewed articles and serves as an editorial board member.",coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"15654",title:"Dr.",name:"Salim",middleName:null,surname:"Surani",slug:"salim-surani",fullName:"Salim Surani",profilePictureURL:"https://mts.intechopen.com/storage/users/15654/images/system/15654.jpeg",biography:"Dr. Salim Surani currently works as the Chair of Critical Care services at Corpus Christi Medical Center. He serves as Adjunct Clinical Professor of Medicine, department of Pulmonary, Critical Care & Sleep Medicine at Texas A&M University. He also serves as the program director for Pulmonary & Critical Care Fellowship Program at Bay Area Medical Center, Corpus Christi. He has done his fellowship in Pulmonary Medicine from Baylor College of Medicine, Houston Texas. Dr. Surani has done his Master in Public Health, & Epidemiology from Yale University and Masters in Health Management from University of Texas, Dallas. Dr. Surani also has served as board trustee and secretary of THE CHEST Foundation. He currently serves as chair for ACCP practice operations steering committee and steering committee member for the executive committee of networks of American College of CHEST Physicians. Dr. Surani has authored more than 250 articles in the peer review journals and has written several books and book chapters. He is involved in teaching residents for more than two decades. He has been instrumental in starting Emergency Medicine residency program, Pharmacy residency program and pulmonary and critical care residency program. He has been named as faculty of the year award numerous times. He has established himself as Master Clinician who has trained significant numbers of practicing primary care, internal medicine and emergency physicians in the Coastal Bend region. He has served as an independent grant reviewer for Government of Australia, Government of Singapore, as well as European Nation via Rannis. He also serves as ad hoc reviewer for more than 20 journals. He has served as a speaker in several regional, national and international scientific conferences. His area of expertise includes critical care, sleep medicine, ICU infections and practice operations. Dr. Surani serves as Thursday morning health segment for Channel III news Corpus Christi (ABC affiliate), and Honorary Co-Anchor for COVID, first edition in Kiii TV (affiliate of ABC News). He has also served in committee for several national organizations and has received several communities and teaching awards, including Health Care Hero award, Humanitarian awards by American College of Physician, American College of Chest Physicians and Texas Medical Association. Dr. Surani is highly regarding among his peers and is very well respected as a mentor, clinician and humanitarian.",institutionString:"Texas A&M University – Central Texas",position:null,outsideEditionCount:0,totalCites:0,totalAuthoredChapters:"5",totalChapterViews:"0",totalEditedBooks:"1",institution:{name:"Texas A&M University – Central Texas",institutionURL:null,country:{name:"United States of America"}}}],coeditorOne:{id:"302059",title:"Dr.",name:"Venkat",middleName:null,surname:"Rajasurya",slug:"venkat-rajasurya",fullName:"Venkat Rajasurya",profilePictureURL:"https://s3.us-east-1.amazonaws.com/intech-files/0030O00002mZEV7QAO/Profile_Picture_1590050673470",biography:"Dr. Venkat Rajasurya currently works as an Attending Pulmonary Critical Care physician at Novant Forsyth Medical Center in Winston-Salem, NC. He has worked as a Clinical Assistant Professor at the Southern Illinois University program in Decatur, Illinois for 4 years and served as director of multiple clinical and leadership committees at Decatur Memorial Hospital, Decatur, Illinois. Dr. Rajasurya completed his Fellowship in Pulmonary Critical Care at Cook County/ Rush University Hospital in Chicago, Illinois. He served as the Medical Advisor for Illinois Society of Respiratory Care for 3 years. He has played a key role in the training and education of medical and pharmacy residents as well as physician assistants throughout his career. He currently serves as a Co-investigator for a number of clinical trials at Southeastern Research Center in Winston Salem, NC. Dr. Rajasurya has authored and reviewed articles and serves as an editorial board member for peer reviewed journals. He has given oral presentations at a number of national and international conferences. His area of interest includes obstructive airway diseases, interstitial lung diseases, lung cancer, sepsis, critical care management of acute conditions and resident education. He is an active member of American College of Chest Physicians and was awarded FCCP for his excellence, dedication and leadership in chest medicine. He is also actively involved in Society of Critical Care Medicine and American Thoracic Society. In addition to multiple teaching and research awards throughout his career, he was awarded the prestigious ‘Gold Doc’ award by Arnold P. Gold foundation for humanism in medicine. 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\n
1. Introduction
\n
More than 50 years ago, Biot [1, 2] proposed a semi-phenomenological theory which provides a rigorous description of the propagation of acoustic waves in porous media saturated by a compressible viscous fluid. Due to its very general and rather fundamental character, it has been applied in various fields of acoustics such as geophysics, underwater acoustics, seismology, ultrasonic characterization of bones, etc. Biot’s theory describes the motion of the solid and the fluid, as well as the coupling between the two phases. The loss of acoustic energy is due mainly to the viscosity of the fluid and the relative fluid-structure movement. The model predicts that the acoustic attenuation, as well as the speed of sound, depends on the frequency and elastic constants of the porous material, as well as porosity, tortuosity, permeability, etc. The theory predicts two compressional waves: a fast wave, where the fluid and solid move in phase, and a slow wave where fluid and solid move out of phase. Johnson et al. [3] introduced the concept of tortuosity or dynamic permeability which has better described the viscous losses between fluid and structure in both high and low frequencies.
\n
Air-saturated porous materials such as plastic foams or fibrous materials are widely used in passive control and noise reduction. These materials have interesting acoustic properties for sound absorption, and their use is quite common in the building trade and automotive and aeronautical fields. The determination of the physical parameters of the medium from reflected and transmitted experimental data is a classical inverse scattering problem.
\n
Pulse propagation in porous media is usually modeled by synthesizing the signal via a Fourier transform of the continuous wave results. On the other hand, experimental measurements are usually carried out using pulses of finite bandwidth. Therefore, direct modeling in the time domain is highly desirable [4–10]. The temporal and frequency approaches are complementary for studying the propagation of acoustic signals. For transient signals, the temporal approach is the most appropriate because it is closer to the experimental reality and the finite duration of the signal. However, for monochromatic harmonic signals, the frequency approach is the most suitable [11].
\n
Fractional calculus has been used in the past by many authors as an empirical method to describe the viscoelastic properties of materials (e.g., see Caputo [12] and Bagley and Torvik [13]). The fact that acoustic attenuation, stiffness, and damping in porous materials are proportional to the fractional powers of frequency [4, 5, 7, 9, 10] suggests that fractional-order time derivatives could describe the propagation of acoustic waves in these materials.
\n
In this chapter, acoustic wave propagation in porous media is studied in the high- and the low-frequency range. The direct and inverse scattering problems are solved for the mechanical characterization of the medium. The general Biot model applied to porous materials having elastic structure is treated, and also the equivalent fluid model, used for air-saturated porous materials (\nFigures 1\n and \n2\n).
\n
Figure 1.
Air-saturated plastic foam.
\n
Figure 2.
Human cancellous bone sample.
\n
\n
\n
2. Porous materials with elastic frame
\n
In porous media, the equations of motion of the frame and fluid are given by the Euler equations applied to the Lagrangian density. Here, \n\nu\n\n and \n\nU\n\n are the displacements of the solid and fluid phases. The equations of motion are given by [1, 2]
where \n\nP\n\n, \n\nQ\n\n, and \n\nR\n\n are the generalized elastic constants, \n\nφ\n\n is the porosity, \n\n\nK\nf\n\n\n is the bulk modulus of the pore fluid, \n\n\nK\ns\n\n\n is the bulk modulus of the elastic solid, and \n\n\nK\nb\n\n\n is the bulk modulus of the porous skeletal frame. \n\nN\n\n is the shear modulus of the composite as well as that of the skeletal frame. The equations which explicitly relate \n\nP\n\n, \n\nQ\n\n, and \n\nR\n\n to \n\nφ\n\n, \n\n\nK\nf\n\n\n, \n\n\nK\ns\n\n\n, \n\n\nK\nb\n\n\n, and \n\nN\n\n are given by
The Young modulus and the Poisson ratio of the solid \n\n\nE\ns\n\n\n and \n\n\nν\ns\n\n\n and of the skeletal frame \n\n\nE\nb\n\n\n and \n\n\nν\nb\n\n\n depend on the generalized elastic constant \n\nP\n\n, \n\nQ\n\n, and \n\nR\n\n via the relations:
where \n\n\nα\n∞\n\n\n is the tortuosity of the medium. The damping of the acoustic wave in porous material is essentially due to the viscous exchanges between the fluid and the structure. To express the viscous losses, the dynamic tortuosity is introduced [3] \n\nα\n\nω\n\n\n given by
where \n\n\nj\n2\n\n=\n−\n1\n\n, \n\nω\n\n is the angular frequency, \n\nσ\n\n is the fluid resistivity, \n\n\nk\n0\n\n\n is the viscous permeability, and \n\nΛ\n\n is the viscous characteristic length given by Johnson et al. [3]. The ratio of the sizes of the pores to the viscous skin depth thickness \n\nδ\n=\n\n\n\n2\nη\n/\n\nωρ\n0\n\n\n\n\n1\n/\n2\n\n\n\n gives an estimation of the parts of the fluid affected by the viscous exchanges. In this domain of the fluid, the velocity distribution is perturbed by the frictional forces at the interface between the viscous fluid and the motionless structure. At high frequencies, the viscous skin thickness is very thin near the radius of the pore \n\nr\n\n. The viscous exchanges are concentrated in a small volume near the surface of the frame \n\nδ\n/\nr\n≪\n1\n\n. The expression of the dynamic tortuosity \n\nα\n\nω\n\n\n is given by [3]
The range of frequencies such that viscous skin thickness \n\nδ\n=\n\n\n\n2\nη\n/\n\nωρ\n0\n\n\n\n\n1\n/\n2\n\n\n\n is much larger than the radius of the pores \n\nr\n\n\n
\n
\n\n\nδ\nr\n\n≫\n1\n\nE8
\n
is called the low-frequency range. For these frequencies, the viscous forces are important everywhere in the fluid. When \n\nω\n→\n0\n\n, the expression of the dynamic tortuosity becomes
where \n\nv\n\nr\n\n\n is the microscopic velocity. The angle brackets represent the average of the random variable over the sample of material. In the time domain, and in the high-frequency domain, the dynamic tortuosity (Eq. 7) \n\nα\n\nω\n\n\n acts as the operator, and its expression is given by [8]
\n\n\nδ\n\nt\n\n\n is the Dirac function. In this model the time convolution of \n\n\nt\n\n−\n1\n/\n2\n\n\n\n with a function is interpreted as a semi-derivative operator according to the definition of the fractional derivative of order \n\nν\n\n given by Samko et al. [16]:
where \n\n0\n≤\nν\n<\n1\n\n and \n\nΓ\n\nx\n\n\n is the gamma function. A fractional derivative acts as a convolution integral operator and no longer represents the local variations of the function. The properties of fractional derivatives and fractional calculus are given by Samko et al. [16].
\n
The introduction of the tortuosity operator \n\n\nα\n˜\n\n\nt\n\n\n (Eq. 11) in Biot’s Eqs. (1) and (2) to describe the inertial and viscous interactions between fluid and structure will express the propagation equations in the time domain. When \n\n\nα\n˜\n\n\nt\n\n\n is used instead of \n\n\nα\n∞\n\n\n in Eqs. (1) and (2), the equations of motion (1) and (2) will be written as [17]
In these equations, the temporal operators \n\n\n\nρ\n˜\n\n11\n\n\nt\n\n\n, \n\n\n\nρ\n˜\n\n12\n\n\nt\n\n\n, and \n\n\n\nρ\n˜\n\n22\n\n\nt\n\n\n represent the mass coupling operators between the fluid and solid phases and are given by
where \n\n\nα\n˜\n\n\nt\n\n\n is given by Eq. (11).
\n
The wave equations of dilatational and rotational waves can be obtained using scalar and vector displacement potentials, respectively. Two scalar potentials for the frame and the fluid, \n\n\nΦ\ns\n\n\n and \n\n\nΦ\nf\n\n\n, are defined for compressional waves giving
where \n\nA\n=\n\n\n2\n\nφρ\nf\n\n\nα\n∞\n\n\nΛ\n\n\n\nη\n\nρ\nf\n\n\n\n\n, \n\nΔ\n\n is the Laplacian, and \n\n\n\n∂\n\n3\n/\n2\n\n\n\n∂\n\nt\n\n3\n/\n2\n\n\n\n\n\n represents the fractional derivative following the definition given by Eq. (12).
\n
Two distinct longitudinal modes called fast and slow waves are obtained by the resolution of the eigenvalue problem of the matrix of Biot (Eq. (14)). On a basis of fast and slow waves \n\n\nΦ\n1\n\n\nt\n\n\n and \n\n\nΦ\n2\n\n\nt\n\n\n, one can have
where \n\n\n\nλ\n˜\n\n1\n\n\nt\n\n\n and \n\n\n\nλ\n˜\n\n2\n\n\nt\n\n\n are the “eigenvalue operators” of the Biot matrix (Eq. (14)). Their expressions are given by
where Eq. (18) is a fractional propagation equations [17] in time domain of the fast and slow waves, respectively. These equations describe the attenuation and the spreading of the temporal signal propagating inside the porous material. These fractional propagation equations have been solved and well-studied in the case of rigid porous materials using the equivalent fluid model.
\n
\n
\n
3. Porous materials with rigid frame
\n
In the acoustics of porous media, two situations can be distinguished: elastic and rigid frame materials. In the first case, the Biot [1, 2] theory is best suited. In the second case, the acoustic wave cannot vibrate the structure. The equivalent fluid model is then used, in which the acoustic wave propagates inside the saturating fluid [8, 11]. The equations for the acoustics in the equivalent fluid model are given by
In these relations, \n\np\n\n is the acoustic pressure. The first equation is the Euler equation, and the second one is a constitutive equation obtained from the equation of mass conservation associated with the behavior (or adiabatic) equation. These equations can be obtained from the Biot Eqs. (1, 2) by canceling the solid displacement. Assuming that the porous medium studied is homogeneous and has a linear elasticity, we obtain easily the following wave equation (propagation along the \n\nx\n\n axis) for the acoustic pressure in a lossless porous material:
In Eq. (20), the viscous and thermal losses that contribute to the sound damping in acoustic materials are not described. The thermal exchanges are generally negligible near viscous effects in the porous materials obeying to the Biot theory, this is not the case for air-saturated porous materials using the equivalent fluid model. To take into account the fluid-structure exchanges, the density and compressibility of the fluid are “renormalized” by the dynamic tortuosity \n\nα\n\nω\n\n\n and the dynamic compressibility \n\nβ\n\nω\n\n\n, via the relations \n\nρ\n→\nρα\n\nω\n\n\n and \n\n\nK\nf\n\n→\n\nK\nf\n\n/\nβ\n\nω\n\n\n, giving the following wave equation in frequency domain (Helmholtz equation) for a lossy porous material:
The thermal exchanges to the fluid compressions-dilatations are produced by the wave motion. The parts of the fluid affected by the thermal exchanges can be estimated by the ratio of a microscopic characteristic length of thermal skin depth thickness \n\n\nδ\n′\n\n=\n\n\n\n2\nη\n/\nωρ\n\nP\nr\n\n\n\n\n1\n/\n2\n\n\n\n (\n\nη\n\n is the fluid viscosity; \n\n\nP\nr\n\n\n is the Prandtl number).
\n
The expression of the dynamic compressibility is given by
where \n\nγ\n\n is the adiabatic constant, the magnitude \n\n\nk\n0\n′\n\n\n introduced by Lafarge [14] called thermal permeability by analogy to the viscous permeability, and \n\n\nΛ\n′\n\n\n is the thermal characteristic length. The low-frequency approximation of \n\nβ\n\nω\n\n\n [14] is given by
where \n\n\nk\n0\n′\n\n\n, which has the same size (area) that of Darcy’s permeability of \n\n\nk\n0\n\n\n, is a parameter analogous to the parameter \n\n\nk\n0\n\n\n but is adapted to the thermal problem.
\n
In a high-frequency limit, Allard and Champoux [18] showed the following behavior of \n\nβ\n\nω\n\n\n:
Replacing \n\nα\n\nω\n\n\n and \n\nβ\n\nω\n\n\n given by Eqs (18) in Eq. (21), we obtain the following lossy equation for porous materials in the high-frequency domain:
In this equation, the term \n\n\n\n\n∂\n\n3\n/\n2\n\n\np\n\nx\nt\n\n\n\n∂\n\nt\n\n3\n/\n2\n\n\n\n\n\n is interpreted as a semi-derivative operator following the definition of the fractional derivative of order \n\nν\n\n, given by Samko and coll. [16]. The solution of the wave Eq. (26) with suitable initial and boundary conditions is by using the Laplace transform. \n\nF\n\n is the medium’s Green function [9] given by
Let us consider a homogeneous porous material which occupies the region \n\n0\n≤\nx\n≤\nL\n\n; the expressions of the reflection and transmission coefficients in the frequency domain are given by
These expressions are simplified by taking into account the reflections at the interfaces \n\nx\n=\n0\n\n and \n\nx\n=\nL\n\n; the expressions of the reflection and transmission operators are given in time domain by
where \n\nδ\n\nt\n\n\n is the Dirac function and \n\nF\n\n is the Green function of the medium given by Eq. (27). In the next sections, we will use the reflected and transmitted waves for solving the inverse problem in order to characterize the porous materials.
\n
\n
3.1. Ultrasonic measurement of porosity, tortuosity, and viscous and thermal characteristic lengths via transmitted waves
\n
The experimental setup consists of two transducers broadband Ultran NCT202 with a central frequency of 190 kHz in air and a bandwidth of 6 dB extending from 150 to 230 kHz [19]. A pulser/receiver 5058PR Panametrics sends pulses of 400 V. The high-frequency noise is avoided by filtering the received signals above 1 MHz. Electronic interference is eliminated by 1000 acquisition averages. The experimental setup is shown in \nFigure 3\n. The inverse problem is to find the parameters \n\n\nα\n∞\n\n\n, \n\nφ\n\n, \n\nΛ\n\n, and \n\n\nΛ\n′\n\n\n which minimize numerically the discrepancy function \n\nU\n\n\nα\n∞\n\nφ\nΛ\n\nΛ\n′\n\n\n=\n\n∑\n\ni\n=\n1\n\n\ni\n=\nN\n\n\n\n\n\n\np\nexp\nt\n\n\nx\n\nt\ni\n\n\n−\n\np\nt\n\n\nx\n\nt\ni\n\n\n\n\n2\n\n,\n\n wherein \n\n\np\nexp\nt\n\n\n\nx\n\nt\ni\n\n\n\ni\n=\n1\n,\n2\n,\n…\nn\n\n\n\n is the discrete set of values of the experimental transmitted signal and \n\n\np\nt\n\n\n\nx\n\nt\ni\n\n\n\ni\n=\n1\n,\n2\n,\n…\nn\n\n\n\n is the discrete set of values of the simulated transmitted signal predicted from Eq. (33). The least squares method is used for solving the inverse problem using the simplex search method (Nelder-Mead) [20] which does not require numerical or analytic gradients.
\n
Figure 3.
Experimental setup of the ultrasonic measurements.
\n
Consider a sample of plastic foam M1, of thicknesses \n\n0.8\n±\n0.01\n\ncm\n\n. Sample M1 was characterized using classic methods [21–31] and gave the following physical parameters \n\nφ\n=\n0.85\n±\n0.05\n\n, \n\n\nα\n∞\n\n=\n1.45\n±\n0.05\n\n, \n\nΛ\n=\n\n\n30\n±\n1\n\n\n\nμm\n\n, and \n\n\nΛ\n′\n\n=\n\n\n60\n±\n3\n\n\n\nμm\n\n. \nFigure 4\n shows the experimental incident signal (dashed line) generated by the transducer and the experimental transmitted signal (solid line). After solving the inverse problem simultaneously for the porosity \n\nφ\n\n, tortuosity \n\n\nα\n∞\n\n\n, and viscous and thermal characteristic lengths \n\nΛ\n\n and \n\n\nΛ\n′\n\n\n, we find the following optimized values: \n\nφ\n=\n0.87\n±\n0.01\n\n, \n\n\nα\n∞\n\n=\n1.45\n±\n0.01\n\n, \n\nΛ\n=\n\n\n32.6\n±\n0.5\n\n\n\nμm\n\n, and \n\n\nΛ\n′\n\n=\n\n\n60\n±\n0.5\n\n\n\nμm\n\n. The values of the inverted parameters are close to those obtained by conventional methods [21–31]. We present in \nFigures 5\n and \n6\n the variation of the minimization function \n\nU\n\n with the porosity, tortuosity, viscous characteristic length, and the ratio between \n\n\nΛ\n′\n\n\n and \n\nΛ\n\n. In \nFigure 7\n, we show a comparison between an experimental transmitted signal and simulated transmitted signal for the optimized values of \n\nφ\n\n, \n\n\nα\n∞\n\n\n, \n\nΛ\n\n, and \n\n\nΛ\n′\n\n\n. The difference between the two curves is small, which leads us to conclude that the optimized values of the physical parameters are correct.
\n
Figure 4.
Experimental incident signal (solid line) and experimental transmitted signal (dashed line).
\n
Figure 5.
Variation of the minimization function \n\nU\n\n with porosity and tortuosity.
\n
Figure 6.
Variation of the cost function \n\nU\n\n with the viscous characteristic length \n\nΛ\n\n and the ratio \n\n\nΛ\n′\n\n/\nΛ\n\n.
\n
Figure 7.
Comparison between the experimental transmitted signal (black dashed line) and the simulated transmitted signals (black line) using the reconstructed values of \n\nϕ\n\n, \n\n\nα\n∞\n\n\n, \n\nΛ\n\n, and \n\n\nΛ\n′\n\n\n.
\n
\n
\n
3.2. Measuring flow resistivity of porous material via acoustic reflected waves at low-frequency domain
\n
In the low-frequency domain, the viscous forces are important everywhere in all the fluid saturating the porous material. The thermal exchanges between fluid and structure are favored by the slowness of the cycle of expansion and compression in the material. The temperature of the frame is practically unchanged by the passage of the sound wave because of the high value of its specific heat: the frame acts as a thermostat; the isothermal compressibility is directly applicable. In this domain, the viscous skin thickness \n\nδ\n=\n\n\n\n2\nη\n/\n\nωρ\n0\n\n\n\n\n1\n/\n2\n\n\n\n is much larger than the radius of the pores \n\nr\n\n\n
\n\n\nδ\nr\n\n≫\n1\n.\n\nE34
\n\n
We consider the low-frequency approximations of the response factor \n\nα\n\nω\n\n\n and \n\nβ\n\nω\n\n\n. When \n\nω\n→\n0\n\n, Eqs. (22) and (6), respectively, become
\n
\n\nα\n\nω\n\n=\n\nσφ\niωρ\n\n,\n\nE35
\n
\n\nβ\n\nω\n\n=\nγ\n.\n\nE36
\n
For a wave traveling along the direction \n\nox\n\n, the generalized forms of the basic Eqs. (19) in the time domain are now
where the Euler equation is reduced to Darcy’s law which defines the static flow resistivity \n\nσ\n=\nη\n/\n\nk\n0\n\n\n. The wave equation in time domain is given by
The expression of the reflection coefficient \n\nR\n\nz\n\n\n in Laplace domain (put \n\nz\n=\njω\n\n for obtaining the frequency domain of \n\nR\n\nω\n\n\n), is given by [32]
The multiple reflections in the material are taken into account in these expressions. As the attenuation is high in the porous materials, the multiple reflection effects are negligible. Let us consider the reflections at the interfaces \n\nx\n=\n0\n\n and \n\nx\n=\nL\n\n:
Consider a sample of porous material having a physical parameters that correspond to quite common acoustic materials, as follows: thickness \n\nL\n=\n4\n\ncm\n\n, porosity \n\nφ\n=\n0.9\n\n, flow resistivity \n\nσ\n=\n30000\n\nN\n\n\nm\n\n−\n4\n\n\ns\n\n, and radius of the pore \n\nr\n=\n70\n\nμm\n\n. Let us study the sensitivity of the main parameters using numerical simulations of waves reflected by a porous material. Fifty percent variation is applied to the physical parameters (flow resistivity \n\nσ\n\n and porosity \n\nφ\n\n).
\n
To obtain the simulated reflected waves, we use the incident signal given in \nFigure 8\n (dashed line). The result (reflected wave) is the wave given in the same figure (\nFigure 8\n) in solid line. The spectra of the two waves (incident and reflected) are given in \nFigure 9\n. From \nFigure 8\n, we can see that there is just an attenuation of the reflected wave without dispersion, since the two waves have the same spectral bandwidth (\nFigure 9\n). \nFigure 8\n shows the results obtained after reducing flow resistivity by \n\n50\n%\n\n of its initial value. The wave in dashed line corresponds to the simulated reflected signal for \n\nσ\n=\n30000\n\nN\n\n\nm\n\n−\n4\n\n\ns\n\n and the second one (solid line) to \n\nσ\n=\n15000\nN\n\n\nm\n\n−\n4\n\n\ns\n\n. The values of the porosity \n\nφ\n=\n0.9\n\n and thickness \n\nL\n=\n4\n\ncm\n\n have been kept constant. When the flow resistivity is reduced, the amplitude of reflected wave decreases by 30% of its initial value. Physically, by reducing the flow resistivity, the medium is less resistive, since the viscous effects become less important in the porous material, and thus the amplitude of the reflected wave decreases. No change is observed in the reflected wave when reducing the porosity by \n\n50\n%\n\n of its initial value. We can conclude that the porosity has no significant sensitivity in reflected mode.
\n
Figure 8.
Incident signal (dashed line) and simulated reflected signal (solid line).
\n
Figure 9.
Spectrum of incident signal (dashed line) and spectrum of reflected signal (solid line).
\n
For the propagation of transient signals at low frequency, a guide (pipe) [32], having a diameter of 5 cm and of length 50 m, is chosen. The pipe can be rolled without perturbations on experimental signals (the cutoff frequency of the tube \n\n\nf\nc\n\n∼\n4\n\nkHz\n\n). The same microphone (Brüel & Kjær, 4190) is used for measuring the incident and reflected signals. Burst is provided by synthesized function generator Stanford Research Systems model DS345-30 MHz. A sound source driver unit “Brand” constituted by loudspeaker Realistic 40-9000 is used. The incident signal is measured by putting a total reflector in the same position than the porous sample. The experimental setup is shown in \nFigure 10\n. Consider a cylindrical sample of plastic foam M1 of flow resistivity value \n\nσ\n=\n40000\n±\n6000\n\n\nNm\n\n‐\n4\n\n\ns\n\n. This value is obtained using the method of Bies and Hansen [33]. The sample M1 has a diameter of 5 cm and a thickness of 3 cm. \nFigure 11\n shows the experimental incident wave (solid line) generated by the loudspeaker in the frequency bandwidth (35–75) Hz, and the experimental reflected signal (dashed line), with their spectra. There is no dispersion, since the two signals have practically the same bandwidth. The minimization of the function \n\nU\n\n gives the solution if the inverse problem:
where \n\n\np\nexp\nr\n\n\n\nx\n\nt\ni\n\n\n\ni\n=\n1\n,\n2\n,\n…\nN\n\n\n\n and \n\n\np\nr\n\n\n\nx\n\nt\ni\n\n\n\ni\n=\n1\n,\n2\n,\n…\nN\n\n\n\n represent the discrete set of values of the experimental reflected signal and of the simulated reflected signal, respectively. The optimized value of \n\nσ\n=\n40500\n±\n2000\n\n\nNm\n\n‐\n4\n\n\ns\n\n is obtained by solving the inverse problem. The variation of the minimization function \n\nU\n\n with the flow resistivity \n\nσ\n\n is given in \nFigure 12\n. A comparison between experiment and theory is given in \nFigure 13\n. The difference between theory and experiment is slight, which leads us to conclude that the optimized value of the flow resistivity is good.
\n
Figure 10.
Experimental setup of acoustic measurements.
\n
Figure 11.
Experimental incident signal (solid line) and experimental reflected signal (dashed line), and their spectra, respectively.
\n
Figure 12.
Variation of the minimization function \n\nU\n\n with flow resistivity \n\nσ\n\n.
\n
Figure 13.
Comparison between experimental reflected signal (dashed line) and simulated reflected signal (solid line) for the sample M1.
\n
This alternative acoustic method has the advantage of being simple and effective since it requires the use of only one microphone and therefore no calibration problem. In addition, this approach is different from conventional methods (Bies and Hansen [33]) that involve the use of fluid flow measurement techniques and pressure differences. The mathematical analysis of the reflected wave at low frequency is quite simple, because this wave is not propagative in the medium but simply diffusive (having the same frequency band with the incident signal). The wave reflected by the resistive materials has the advantage of being easily detectable experimentally compared to the transmitted wave.
\n
\n
\n
\n
\n
4. Conclusion
\n
Acoustic propagation in porous media involves a large number of physical parameters when the structure is elastic. This number is reduced when the structure is rigid, because the mechanical part does not intervene and thus remains only the acoustic part. The study of high and low frequencies separately solves the inverse problem and characterizes the porous materials in the domain of influence of the physical parameters. The proposed methods are simple and effective and allow an acoustic characterization of porous materials using transmitted or reflected experimental waves.
\n
\n\n',keywords:"acoustic porous materials, porosity, tortuosity, viscous and thermal charactertistic lengths, fractional derivatives",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/58101.pdf",chapterXML:"https://mts.intechopen.com/source/xml/58101.xml",downloadPdfUrl:"/chapter/pdf-download/58101",previewPdfUrl:"/chapter/pdf-preview/58101",totalDownloads:1027,totalViews:458,totalCrossrefCites:0,totalDimensionsCites:2,hasAltmetrics:0,dateSubmitted:"June 7th 2017",dateReviewed:"November 6th 2017",datePrePublished:"December 20th 2017",datePublished:"January 4th 2018",dateFinished:"December 9th 2017",readingETA:"0",abstract:"This chapter provides different models for the acoustic wave propagation in porous materials having a rigid and an elastic frames. The direct problem of reflection and transmission of acoustic waves by a slab of porous material is studied. The inverse problem is solved using experimental reflected and transmitted signals. Both high- and low-frequency domains are studied. Different acoustic methods are proposed for measuring physical parameters describing the acoustic propagation as porosity, tortuosity, viscous and thermal characteristic length, and flow resistivity. Some advantages and perspectives of this method are discussed.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/58101",risUrl:"/chapter/ris/58101",book:{slug:"computational-and-experimental-studies-of-acoustic-waves"},signatures:"Zine El Abiddine Fellah, Mohamed Fellah, Claude Depollier, Erick\nOgam and Farid G. Mitri",authors:[{id:"143693",title:"Dr.",name:"Zine El Abiddine",middleName:null,surname:"Fellah",fullName:"Zine El Abiddine Fellah",slug:"zine-el-abiddine-fellah",email:"fellah@lma.cnrs-mrs.fr",position:null,institution:{name:"Laboratory of Mechanics and Acoustics",institutionURL:null,country:{name:"France"}}},{id:"144519",title:"Prof.",name:"Claude",middleName:null,surname:"Depollier",fullName:"Claude Depollier",slug:"claude-depollier",email:"claude.depollier@univ-lemans.fr",position:null,institution:null},{id:"178778",title:"Prof.",name:"Mohamed",middleName:null,surname:"Fellah",fullName:"Mohamed Fellah",slug:"mohamed-fellah",email:"mfellah@usthb.dz",position:null,institution:null},{id:"209074",title:"Dr.",name:"Erick",middleName:null,surname:"Ogam",fullName:"Erick Ogam",slug:"erick-ogam",email:"ogam@lma.cnrs-mrs.fr",position:null,institution:null},{id:"227468",title:"Dr.",name:"Farid G",middleName:null,surname:"Mitri",fullName:"Farid G Mitri",slug:"farid-g-mitri",email:"F.G.Mitri@ieee.org",position:null,institution:null}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Porous materials with elastic frame",level:"1"},{id:"sec_3",title:"3. Porous materials with rigid frame",level:"1"},{id:"sec_3_2",title:"3.1. Ultrasonic measurement of porosity, tortuosity, and viscous and thermal characteristic lengths via transmitted waves",level:"2"},{id:"sec_4_2",title:"3.2. Measuring flow resistivity of porous material via acoustic reflected waves at low-frequency domain",level:"2"},{id:"sec_4_3",title:"3.2.1. Acoustic parameter sensitivity",level:"3"},{id:"sec_7",title:"4. Conclusion",level:"1"}],chapterReferences:[{id:"B1",body:'\nBiot MA. The theory of propagation of elastic waves in fluid-saturated porous solid. I. Low frequency range. The Journal of the Acoustical Society of America. 1956;28:168\n'},{id:"B2",body:'\nBiot MA. The theory of propagation of elastic waves in fluid-saturated porous solid. I. Higher frequency range. The Journal of the Acoustical Society of America. 1956;28:179\n'},{id:"B3",body:'\nJohnson DL, Koplik J, Dashen R. Theory of dynamic permeability and tortuosity in fluid-saturated porous media. Journal of Fluid Mechanics. 1987;176:379-402\n'},{id:"B4",body:'\nSzabo TL. Time domain wave equations for lossy media obeying a frequency power law. The Journal of the Acoustical Society of America. 1994;96:491\n'},{id:"B5",body:'\nSzabo TL. Causal theories and data for acoustic attenuation obeying a frequency power law. Journal of the Acoustical Society of America. 1995;97:14\n'},{id:"B6",body:'\nNorton V, Novarini JC. Including dispersion and attenuation directly in time domain for wave propagation in isotropic media. The Journal of the Acoustical Society of America. 2003;113:3024\n'},{id:"B7",body:'\nChen W, Holm S. Modified Szabo’s wave equation models for lossy media obeying frequency power law. The Journal of the Acoustical Society of America. 2003;113:3024\n'},{id:"B8",body:'\nFellah ZEA, Depollier C. Transient acoustic wave propagation in rigid porous media: A time domain approach. The Journal of the Acoustical Society of America. 2000;107(2):683-688\n'},{id:"B9",body:'\nFellah ZEA, Fellah M, Lauriks W, Depollier C, Angel Y, Chapelon JY. Solution in time domain of ultrasonic propagation equation in porous material. Wave Motion. 2003;38:151-163\n'},{id:"B10",body:'\nFellah ZEA, Depollier C, Fellah M. Direct and inverse scattering problem in porous material having a rigid frame by fractional calculus based method. Journal of Sound and Vibration. 2001;244(2):359-366\n'},{id:"B11",body:'\nAllard JF. Propagation of Sound in Porous Media : Modeling Sound Absorbing Materials. London: Chapman and Hall; 1993\n'},{id:"B12",body:'\nCaputo M. Vibration of an infinite plate with a frequency dependent Q. The Journal of the Acoustical Society of America. 1976;60:634-639\n'},{id:"B13",body:'\nBagley RL, Torvik PJ. On the fractional calculus model of viscoelastic behavior. Journal of Rheology. 1983;30:133-155\n'},{id:"B14",body:'\nLafarge D, Lemarnier P, Allard JF, Tarnow V. Dynamic compressibility of air in porous structures at audible frequencies. Journal of the Acoustical Society of America. 1996;102:4\n'},{id:"B15",body:'\nNorris AN. On the viscodynamic operator in Biot’s equations of poroelasticity. Journal of Wave-Material Interaction. 1986;1:365-380\n'},{id:"B16",body:'\nSamko SG, Kilbas AA, Marichev OI. Fractional Integrals and Derivatives Theory and Applications. Amsterdam: Gordon and Breach Publishers; 1993\n'},{id:"B17",body:'\nFellah M, Fellah ZEA, Mitr FG, Ogam E, Depollier C. Transient ultrasound propagation in porous media using biot theory and fractional calculus: Application to human cancellous bone. The Journal of the Acoustical Society of America. 2013;133(4):683-688\n'},{id:"B18",body:'\nAllard JF, Champoux Y. New empirical equations for sound propagation in rigid frame fibrous materials. Journal of the Acoustical Society of America. 1992;91:3346-3353\n'},{id:"B19",body:'\nFellah ZEA, Sadouki M, Fellah M, Mitri FG, Ogam E, Depollier C. Simultaneous determination of porosity, tortuosity, viscous and thermal characteristic lengths of rigid porous materials. Journal of Applied Physics. 2013;114:204902-204905\n'},{id:"B20",body:'\nLagarias JC, Reeds JA, Wright MH, Wright PE. Convergence properties of the Nelder–mead simplex method in low dimensions. SIAM Journal on Optimization. 1998;9:112Ű147\n'},{id:"B21",body:'\nLeclaire P, Kelders L, Lauriks W, Glorieux C, Thoen J. Determination of the viscous characteristic length in air-filled porous materials by ultrasonic attenuation measurements. The Journal of the Acoustical Society of America. 1996;99:1944\n'},{id:"B22",body:'\nAyrault C, Moussatov A, Castagnède B, Lafarge D. Ultrasonic characterization of plastic foams via measurements with static pressure variations. Applied Physics Letters. 1999;74:3224\n'},{id:"B23",body:'\nMoussatov A, Ayrault C, Castagnède B. Porous material characterization ultrasonic method for estimation of tortuosity and characteristic length using a barometric chamber. Ultrasonics. 2001;39:195\n'},{id:"B24",body:'\nLeclaire P, Kelders L, Lauriks W, Brown NR, Melon M, Castagnède B. Determination of viscous and thermal characteristic lengths of plastic foams by ultrasonic measurements in helium and air. Journal of Applied Physics. 1996;80:2009\n'},{id:"B25",body:'\nFellah ZEA, Depollier C, Berger S, Lauriks W, Trompette P, Chapelon JY. Determination of transport parameters in air saturated porous materials via ultrasonic reflected waves. The Journal of the Acoustical Society of America. 2003;113(5):2561-2569\n'},{id:"B26",body:'\nFellah ZEA, Berger S, Lauriks W, Depollier C, Chapelon JY. Inverse problem in air-saturated porous media via reflected waves. Review of Scientific Instruments. 2003;74(5):2871\n'},{id:"B27",body:'\nFellah ZEA, Berger S, Lauriks W, Depollier C, Aristégui C, Chapelon JY. Measuring the porosity and the tortuosity of porous materials via reflected waves at oblique incidence. The Journal of the Acoustical Society of America. 2003;113(5):2424\n'},{id:"B28",body:'\nFellah ZEA, Berger S, Lauriks W, Depollier C, Trompette P, Chapelon JY. Ultrasonic measuring of the porosity and tortuosity of air- saturated random packings of beads. Journal of Applied Physics. 2003;93:9352\n'},{id:"B29",body:'\nFellah ZEA, Mitri FG, Depollier D, Berger S, Lauriks W, Chapelon JY. Characterization of porous materials having a rigid frame via reflected waves. Journal of Applied Physics. 2003;94:7914\n'},{id:"B30",body:'\nFellah ZEA, Berger S, Lauriks W, Depollier C, Fellah M. Measurement of the porosity of porous materials having a rigid frame via reflected waves : A time domain analysis with fractional derivatives. Journal of Applied Physics. 2003;93:296\n'},{id:"B31",body:'\nFellah ZEA, Mitri FG, Fellah M, Ogam E, Depollier C. Ultrasonic characterization of porous absorbing materials: Inverse problem. Journal of Sound and Vibration. 2007;302:746-759\n'},{id:"B32",body:'\nSebaa N, Fellah ZEA, Fellah M, Lauriks W, Depollier C. Measuring flow resistivity of porous material via acoustic reflected waves. Journal of Applied Physics. 2005;98:084901\n'},{id:"B33",body:'\nBies DA, Hansen CH. Flow resistance information for acoustical design. Applied Acoustics. 1980;13:357-391\n'}],footnotes:[],contributors:[{corresp:"yes",contributorFullName:"Zine El Abiddine Fellah",address:"Fellah@lma.cnrs-mrs.fr",affiliation:'
LMA, CNRS, UPR 7051, Aix-Marseille Univ, Centrale Marseille, France
LMA, CNRS, UPR 7051, Aix-Marseille Univ, Centrale Marseille, France
'},{corresp:null,contributorFullName:"Farid G. Mitri",address:null,affiliation:'
Chevron, Area 52 - ETC, United States
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1. Introduction
DNA information is stored in the form of a code that constitutes four chemical bases namely: cytosine (C), adenine (A), thymine (T), and, lastly, guanine (G). The human DNA has approximately 3 billion bases, and not <99% of these bases are similar in all individuals. The sequence of these bases governs the available information for maintaining and building an organism, similar to the manner in which alphabetical letters are arranged to form sentences and words [1].
The chemical bases in a DNA pair up (C with G and A with T), in order to produce units known as base pairs. In addition, each base is attached to a phosphate molecule and a sugar molecule. Together, a phosphate, sugar, and base are referred to as a nucleotide. The nucleotides are organized in two long strands thereby forming a spiral known as a double helix. A double helix’s structure resembles a ladder, with the phosphate and sugar molecules forming the ladder’s vertical sidepieces. On the other hand, the base pairs form the rungs of the ladder.
Many anticancer drugs in clinical use interact with DNA through intercalation, which can be defined as the process by which compounds containing planar aromatic or heteroaromatic ring systems are inserted between adjacent base pairs perpendicularly to the axis of the helix and without disturbing the overall stacking pattern due to Watson-Crick hydrogen bonding [2, 3].
2. Structural features of DNA
DNA consists of two complementary anti-parallel sugar phosphate poly-deoxyribonucleotide strands that are associated with specific hydrogen bonding between nucleotide bases. The two strands are held together primarily through Watson-Crick hydrogen bonds where A forms two hydrogen bonds with T and C forms three hydrogen bonds with G (Figure 1). The structure of these paired strands defines the helical grooves, within which the edges of the heterocyclic bases are exposed. The biologically relevant B-form of the DNA double helix is characterized by a shallow-wide major groove and a deep-narrow minor groove. The chemical structure (feature) of the molecular surfaces in a given DNA sequence is well known in either groove. This forms the basis for molecular recognition of duplex DNA by small molecules and proteins [4, 5].
Figure 1.
Watson-Crick pairing between purine and pyrimidine bases in complementary DNA strand.
3. Anticancer drug-DNA interaction
DNA as carrier of genetic information is a major target for anticancer drug interaction because of the ability to interfere with transcription and DNA replication, a major step in cell growth and division. There are three principally different ways of anticancer drug binding. First is through control of transcription factors and polymerases. Here, the anticancer drugs interact with the proteins that bind directly to DNA. Second is through RNA binding to DNA double helices to form nucleic acid triple helical structures or RNA hybridization to exposed DNA single strand regions that will be forming DNA-RNA hybrids and it may interfere with transcriptional activity. Third is through small aromatic ligand molecules that bind to DNA double helical structures through non-covalent interaction either by intercalating binder or by minor groove binders (Figure 2) [6, 7]. Therefore, intercalation can be defined as the process by which compounds containing planar aromatic or heteroaromatic ring systems are inserted between adjacent base pairs perpendicularly to the axis of the helix and without disturbing the overall stacking pattern due to Watson-Crick hydrogen bonding [8]. In addition, intercalation binding involves the insertion of a planar molecule between DNA base pairs, which results in a decrease in the DNA helical twist and lengthening of the DNA. While groove binding, unlike intercalation, does not induce large conformational changes in DNA and may be considered similar to standard lock-and-key models for ligand-macromolecular binding. In addition, Groove binders are usually crescent-shaped molecules that bind to the minor groove of DNA [7].
Figure 2.
Groove binding to the minor groove of DNA (left) and the intercalation into DNA (right).
In order to accommodate the binder (like intercalation binder), DNA must undergo a conformational change to create a cavity for the incoming chromophore. The double helix is therefore partially unwound, which leads to distortions of the sugar-phosphate backbone and changes in the twist angle between successive base pairs (Figure 3) [8]. Once the drug has been sandwiched between the DNA base pairs, several non-covalent interactions such as Van der Waals interaction and hydrogen bonding optimizes the stability of the complex.
Figure 3.
Deformation of DNA by an intercalating agent.
4. Types of drug-DNA interactions
The study of interaction between drug molecules and DNA is very exciting and significant not only in understanding the mechanism of interaction, but also for the design of new drugs. However, the mechanism of interactions between them is still relatively little known. By understanding the mechanism of interaction between them, designing of new DNA-targeted drugs and the screening of these in vitro will be possible [9]. Many of the most valuable anticancer drugs currently used in therapy interact with DNA either by a covalent or non-covalent mechanism. Unfortunately, several of them show a considerable toxicity when the DNA molecular target is present in both normal and tumor cells [10]. The covalent type of binding of drug-DNA is irreversible and invariably causes the complete inhibition of DNA processes and subsequent cell death. A major advantage of covalent binders is the high binding strength. However, covalent bulky adducts can cause DNA backbone distortion, which affect both transcription and replication (disrupting protein complex recruitment). The covalent binders are also called alkylating agents due to adduct formation because they are used in cancer treatment to attach an alkyl group (CnH2n+1) to DNA [11]. Table 1 lists the different types of drug-DNA interactions with suitable examples. In addition, some important examples of a cross-linking agent covalent and non-covalent binder were shown in Figure 4 [5, 12].
No.
Type of interaction
Example
1
Covalent bonding
Nitrogen mustard, carboplatin and cyclophosphamide
2
Non-covalent bonding
Ethidium bromide and quinacrine
Table 1.
Listing the different types of drug-DNA interactions with suitable examples.
Figure 4.
Chemical structure of some covalent and non-covalent binders of DNA.
Non-covalent DNA interacting agents (groove, intercalators, and external binders) are generally considered less cytotoxic than agents producing covalent DNA adducts and other DNA damage. The non-covalent binding type is reversible and is typically preferred over covalent adduct formation keeping the drug metabolism and toxic side effects in mind. In addition, non-covalent DNA interacting agents can changes DNA conformation, DNA torsional tension, interrupt protein-DNA interaction, and potentially lead to DNA strand breaks [11].
5. Modeling of hairpin minor groove binders
Hairpin minor grove binding molecules have been identified and synthesized that bind to G-C reach nucleotide sequences. Hairpin polyamides are linked systems that exploit a set of simple recognition rules for DNA base pairs through specific orientation of imidazole (Im) and pyrrole (Py) rings (Figure 5) [13]. They originated from the discovery of the three-ring Im-Py-Py molecule that bound to minor groove DNA as an antiparallel side by side dimer.
Figure 5.
Structure of hairpin polyamide Im-Py-Py.
The solid phase synthesis of polyamides of variable length has produced efficient ligands. The advantage of polyamide ligand design has been reached with finding structures able to recognize DNA sequences of specific genes. Moreover, a new strategy of rational drug design exploits the combination of polyamides with bis-intercalating structures. The new synthetic compound showed a resistant against multidrug resistance in which small aromatic compounds are efficiently expelled from the cell-by-cell membrane transport proteins that commonly referred to as ABC transporters or ATP binding cassette proteins [14].
6. Rational for drug design
When a compound intercalates into nucleic acids, there are changes, which occur in both the DNA and the compound during complex formation that can be used to study the ligand DNA interaction. The binding is of course an equilibrium process because no covalent bond formation is involved. The binding constant can be determined by measuring the free and DNA bound form of the ligand. In addition, DNA double helix structures are found to be more stable with intercalating agents present and show a reduced heat denaturation. Correlating these biophysical parameters with cytotoxicity is used to support the antitumor activity of these drugs as based on their ability to intercalate in DNA double helical structures. [15].
Improvement of anticancer drugs based on intercalating activity is not only focused on DNA-ligand interaction, but also on tissue distribution and toxic side effects on the heart (cardiac toxicity) due to redox reduction of the aromatic rings and subsequent free radical formation. Free radical species are thought to induce destructive cellular events such as enzyme inactivation, DNA strand cleavage and membrane lipid peroxidation [16, 17].
7. Cisplatin-DNA interactions
Cisplatin (cis-[PtCl2(NH3)2]) is the most widely used anticancer drug today. Since the development of cisplatin became one of the main biological targets for the antitumor compounds. It is used against ovarian, cervical, head and neck, esophageal and non-small cell lung cancer. However, chemotherapy treatment by cisplatin comes with a price of severe side effects including nausea, vomiting and ear damage, as cisplatin not only attacks cancer cells, but also healthy cells. It is therefore important to elucidate the details of the cisplatin mode of action to design new cisplatin analogs that specifically target cancer cells. Furthermore, most cancer cells are insensitive towards cisplatin or develop resistance. There is therefore, also a need for cisplatin analogues with a broader range of cytotoxicity. The search for new analogues and the elucidation of the complete mode of action have been going on for more than 40 years and there is an enormous amount of data available for researchers. Still, the picture of how cisplatin works is incomplete [11, 18].
Cellular DNA has been shown to be the primary target for cisplatin, although cisplatin can react with several other cellular components. In the cell, the salt concentration is significantly lower (~20 mM) and cis-[PtCl2(NH3)2] is hydrolyzed by high salt concentration (>100 mM) to the probable active species cis-[PtCl(OH2)(NH3)2]+. The hydrolyzed product binds to DNA and preferentially to guanine N7> > adenine N7 > cytosine N3, first as a monoadduct, then forming a bidentate adduct. The primary products are 1,2-intrastrand cross-links of GpG (60–65%) or ApG (20–25%) sequences. A smaller amount corresponds to 1,3-intrastrand or G N7–G N7 interstrand adducts. The most common binding sites on the nucleobases for Pt are shown in Figure 6 [18]. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to be removed before Pt association.
Figure 6.
The structure of the most common binding sites on the nucleobases for Pt. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to be removed before Pt association.
The formation of these 1,2-intrastrand cross-links alters the duplex conformation. The most dramatic effect is unwinding of the two strands and bending of the DNA double helix (several values for the bend angle are reported in the range 20–80°). The platinated adducts are assumed to be recognized by proteins, followed either by stabilization of the distorted DNA structure or removal of the lesion through repair [18]. The deformation of the DNA structure can interfere with the normal functions of DNA, such as replication and transcription, leading to cellular death by apoptosis or necrosis. The ineffective isomer of cisplatin, transplatin (trans-[PtCl2(NH3)2]), is not able to form 1,2-intrastrand cross-links [19]. Transplatin forms only 1,3-intrastrand and interstrand cross-links and this might be the reason why transplatin is antitumor inactive [18].
In addition, a sensing system based on the photoinduced electron transfer of quantum dots (QDs) was also designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. The MTX adsorbed on the surface of QDs and this, can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process, then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs.
Cisplatin-DNA sequence selectivity has been given great attention from the research community. Several studies show that cisplatin first binds monofunctionally to guanine N7 and is particularly reactive towards Gn-runs (n ≥ 2) (Figure 7) [18, 20, 21]. The high nucleophilicity of Gn-runs attracts the positively charged cisplatin monoaqua specie. The lifetime of the monoadduct is relatively long and it has therefore been suggested that the initial monoadduct is crucial for the type of cross-linked adduct formed and thus for the cytotoxic properties of the Pt complex. The main factors influencing the mono-functional binding affinity in DNA are thought to be [18] the type of bound nucleotide and of the adjacent residues, the steric effects of the Pt complex, the hydrogen binding properties of the Pt-DNA adduct and the DNA conformation.
Figure 7.
Assumed mechanism for the formation of cisplatin-DNA adducts.
8. Sequence specific structural perturbation
The formation of a cisplatin adduct with the GpG bases requires a significant tilting of the bases leading to a perturbation of the regular B-DNA conformation. The structural perturbation has been shown to be specifically recognized by a number of cellular proteins, including proteins with high-mobility group (HMG) binding domains and the TATA box binding protein [22]. It is believed that (some of) these recognition proteins mediate the cellular response which finally induces cell death by apoptosis or necrosis. In some cases, relatively subtle changes in the adduct structure can affect the recognition and the biological effects in a major way. This is exemplified by the cisplatin analogue oxaliplatin which forms similar G*G*-Pt adducts as cisplatin [18]. However, the oxaliplatin-G*G adducts differ in repair efficiency, mutagenesis and translesion synthesis, believed to be related to the differential activity of the two drugs (oxaliplatin is used, in combination with 5-fluorouracil, for the treatment of colorectal cancers against which cisplatin is inactive). The evaluation of the structural details of the platinum-DNA adducts and of their effects on protein, recognition can therefore help to understand why the biological activities of two similar platinum compounds (e.g., cisplatin versus oxaliplatin) are different. So far only nine cisplatin-DNA adducts have been characterized by NMR and/or x-ray crystallography. These structures were extensively reviewed by Ano et al. and found to be basically similar in structure. The cisplatin-GG adduct kinks the double helix approx. Approximately 60 towards the major groove and induces N sugar pucker for X of 5′ XG*, 5′ G* and the C complementary to 3′ G* [18].
This metal-based compound or coordination compounds that bind to DNA have been an active area of research since the discovery of cisplatin and the platinum-based drugs. The transition-metal compounds bind to DNA through several ways and different factors that promote it, such as the intercalant ligand and the nature and position of the substituent over it. Several techniques to follow metal-based drugs interactions with DNA are used as a powerful tool in order to reach a deep knowledge of the parameters involved in the stabilization of coordination compound-DNA adduct.
9. Methods for elucidation of DNA-anticancer drug interactions
DNA damaging agents (drugs that interfere with DNA function by chemically modifying specific nucleotides) includes mitomycin-C and echinomycin.
9.1 Mitomycin-C
Mitomycin-C is a well-characterized antitumor antibiotic that forms a covalent interaction with DNA after reductive activation (Figure 8). The activated antibiotic forms a cross-linking structure between guanine bases on adjacent strands of DNA therefore inhibiting single strand formation [8].
Figure 8.
Schematic interaction between DNA and mitomycin-C.
9.2 Echinomycin
Several studies have proved that both echinomycin quinoxaline rings bisintercalate into DNA, with CG selectivity, while the inner part of the depsipeptide establishes H-bonds with the DNA bases of the minor groove region of the two base pairs comprised between the chromophores (Figure 9) [8].
Figure 9.
Schematic interaction between DNA and echinomycin.
10. Mechanisms of anticancer drug-DNA interaction
The addition of anticancer drugs to a DNA molecule creates a new bond. Some examples for these mechanisms include intercalating agents, intercalating reagents (II), and bleomycins.
10.1 Intercalating agent
This agent contains planar aromatic or heteroaromatic ring systems (dactinomycin as an example), binding to sugar phosphate backbone by cyclic peptide or by NH3. The planar systems slip between the layers of nucleic acid pairs and disrupt the shape of the helix. The preference is often shown for the minor or major groove. The intercalation prevents replication and transcription. In addition, the intercalation inhibits topoisomerase II (an enzyme that relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand). Another example is the intercalation of the flat part of the molecule of Adriamycin into DNA, presenting the local unwinding of the helical structure (Figure 10) [23].
Figure 10.
Diagrammatic model illustrating intercalation of the flat part of the molecule of adriamycin (in black) into DNA, presenting the local unwinding of the helical structure.
10.2 Intercalating reagents (II)
During replication, supercoiled DNA is unwound by the helicase. The thereby created tension is removed by the topoisomerase II (topo II) that cuts and rejoins the DNA strands. When doxorubicin is bound to the DNA it stabilizes the DNA-topo (II) complex at the point where the enzyme is covalently bound (Figure 11) [1, 24].
Figure 11.
Stabilizations of DNA-topo (II) complex.
10.3 Bleomycin A2
The bleomycin A2 intercalate via the bithiazole moiety (DNA-binding domain) (Figure 12). The bithiazole moiety intercalates into the double helix and the attached side chain containing a sulfonium ion is attracted to the phosphodiester backbone. In addition, the N-atoms of the primary amines, pyrimidine ring and imidazole ring chelate Fe, which is involved in the formation of superoxide radicals, which subsequently act to cut DNA between purine and pyrimidine nucleotides [25].
Figure 12.
The intercalating region (in blue color) of bleomycin A2 via the bithiazole moiety to DNA.
11. Techniques for studying drug-DNA interactions
Various analytical techniques have been used for studying drug-DNA interactions (interaction between DNA and small ligand molecules that are potentially of pharmaceutical importance). Several instrumental techniques (emission and absorption spectroscopic) such as infrared (IR), UV-visible, nuclear magnetic resonance (NMR) spectroscopies, circular dichroism, atomic force microscopy (AFM), electrophoresis, mass spectrometry, viscosity measurements (viscometry), UV thermal denaturation studies, and cyclic, square wave and differential pulse voltammetry, etc., were used to study such interactions. These techniques have been used as a major tool to characterize the nature of drug-DNA complexation and the effects of such interaction on the structure of DNA. In addition, these techniques are regularly applied to monitor interactions of drugs with DNA because these optical properties are easily measured and tend to be quite sensitive to the environment. Moreover, these techniques provide various types of information (qualitative or quantitative) and at the same time complement each other to provide full picture of drug-DNA interaction and aid in the development of new drugs. In addition, the information gained from this part might be useful for the development of potential survey for DNA structure and new therapeutic reagents for tumors and other diseases. In this part of the chapter, we will focus on FT-IR, UV-Visible, NMR, AFM and viscosity measurements [5].
11.1 Fourier transform infrared spectroscopy
Fourier transform infrared (FT-IR) spectroscopy is a widely used technique to study interactions of nucleic acids (DNA and RNA) and proteins with anticancer drugs and other cytotoxic agents in solutions [26, 27]. In addition, it can generate structural information of the whole molecule in a single spectrum as a photograph of all conformations present in the sample that can distinguish among A-, B- and Z-forms of DNA, triple stranded helices, and other structural patterns. In addition, it is a powerful tool to study interactions of DNA with drugs and the effects of such interactions in the structure of DNA, and providing some insights about the mechanism of drug action. The technique is ideal for systematic studies of nucleic acids (e.g., sequence variations, covalent modifications), since it is fast, nondestructive, and requires only small amount of sample [28].
IR spectrum can be divided into four characteristic spectral ranges. The region between 1800 and 1550 cm−1 corresponds to the in-plane double bond vibrations of the nucleic bases (C〓O, C〓N, C〓C and N▬H bending vibrations of bases). These bands are sensitive to changes in the base stacking and base pairing interactions. Bands occurring in the interval 1500–1250 cm−1 assigned to vibrations of the bases and base-sugar connections are strongly related to the conformational changes of the backbone chain and glycosidic bond rotation. The range 1250–1000 cm−1 involves sugar phosphate vibrations, such as, PO2 symmetric and asymmetric stretching vibrations and C▬O stretching vibrations. These vibrations show high sensitivity to conformational changes in the backbone. The range 1000–800 cm−1 is characteristic for bands associated with vibrations of sugars which correlate with the various nucleic acid sugar puckering modes (C2’-endo and C3’-endo) [29, 30].
Due to interfering absorption bands of water at 1650 cm−1 and below 950 cm−1, spectra are generally recorded also in D2O, where these bands move to 1200 cm−1, and below 750 cm−1. Combination of results from both spectra allows obtaining a complete spectrum. The use of D2O also causes shifts in nucleic acid absorptions, resulting from deuterium exchange of labile NH protons, and these can be used to monitor H–D exchange processes. A method to remove water signals in the spectra is water subtraction, using a sodium chloride (NaCl) solution as reference. D2O is used to allow shifts in the absorption of nucleic acid in order to monitor H–D exchange processes. Four regions, each having marker bands showing either nucleic acid interactions or conformations, are presented in Figure 13 [31, 32].
Figure 13.
The characteristics IR bands of DNA and aqueous solvents. (a) 1800–1500 cm-1 region is sensitive to effects of base pairing and base stacking; (b) 1500–1250 cm-1 region is sensitive to glycosidic bond rotation, backbone conformation, and sugar pucker; (c) 1250–1000 cm-1 region is sensitive to backbone conformation; and (d) 1000–800 cm-1 region is sensitive to sugar conformation.
The ring vibrations of nitrogenous bases (C〓O, C〓N stretching), PO2 stretching vibrations (symmetric and asymmetric) and deoxyribose stretching of DNA backbone are confined in the spectral region between 1800 and 700 cm−1. The vibrational bands of DNA at 1710, 1662, 1613 and 1492 cm−1 are assigned to guanine (G), thymine (T), adenine (A) and cytosine (C) nitrogenous bases, respectively. Bands at 1228 and 1087 cm−1 denote phosphate asymmetric and symmetric vibrations, respectively. These are the prominent bands of pure DNA, which are monitored during carboplatin-DNA interaction at different ratios. Changes in these bands are shown in Figure 14 [33]. After carboplatin addition to DNA solution, G-band at 1710 shifts to 1702–3, T-band at 1662 shifts to 1655 and A-band at 1613 shifts towards lower wave number 1609–10 cm−1. These shifting can be attributed to direct platin binding to G (N7), T (O2), and A (N7) of DNA bases. No major shifting is observed for phosphate asymmetric and symmetric vibrations indicating no external binding. The plots of the relative intensity (R i) of several peaks of DNA in-plane vibrations related to A–T, G–C base pairs and the PO2− stretching vibrations such as 1717 (G), 1663 (T), 1609 (A), 1492 (C), and 1222 cm−1 (PO2− groups), against the compound concentrations can be obtained after peak normalization using formula (1) [5, 34]:
Figure 14.
Intensity ratio variations for DNA as a function of different carboplatin/DNA molar ratios.
Ri=Iil968E1
where Ri is the relative intensity, Ii is the intensity of absorption peak for pure DNA and DNA in the complex with i concentration of compound, and l968 is the intensity of the 968 cm−1 peak (internal reference) [35].
Similarly, Raman spectroscopy, which also depends on characteristic group vibrational frequencies, can be used together with infrared spectra to study vibrations in DNA. It is useful because Raman and IR spectroscopy provide complementary information.
11.2 UV-visible spectroscopy
UV-visible absorption spectroscopy can be utilized to detect the DNA-ligand interaction by measuring the changes in the absorption properties of the DNA molecules or the ligand. The UV-vis absorption spectrum of DNA displays a broad band in the range of 200–350 nm in the UV region, with a maximum situated at 260 nm. The maximum is due to the chromophoric groups in pyrimidine and purine moieties responsible for the electronic transitions. The utilization of this simple and versatile technique enables an accurate estimation of the DNA molar concentration based on absorbance measurement at 260 nm. To measure the interaction between ligands and DNA, a hypochromic shift is utilized because the monitoring of the values of absorbance enables studying of the melting action of DNA. Apart from versatility, other major advantages of UV-vis absorption spectroscopy include simplicity, reproducibility, and good sensitivity [36, 37].
11.3 Nuclear magnetic resonance spectroscopy
Binding between ligands and the molecules of DNA causes a significant change in the chemical shift of the values presented in Table 2 [32]. For example, applying thermal denaturing in order to un-stack the base-pair double-helical DNA to form two ss-DNAs is often accompanied by the 1H resonances’ downfield shift for non-exchangeable protons.
Proton type
Expected chemical shifta (ppm)
Proton type
Expected chemical shifta (ppm)
T5 (CH3)
1.00–2.00
A 2 (CH); A 8 (CH); G 8 (CH) T 6 (CH) C 6 (CH)
6.50–8.20
Sugar 2′ (CH2)
2.00–3.00
Sugar 5′ terminal (CH2)
3.70
Sugar 5′ (CH2); 4’(CH)
4.00–4.50
C 4 (NH2) (H-1)b
6.40–6.80
Sugar 3′ (CH)
4.50–5.20
C 4 (NH2) (H-2)b
8.30–8.50 ppm
Sugar 1′ (CH)
5.30–6.20
G 1 (NH)
12.50–13.00 ppm
C 5 (CH)
5.30–6.20
T 3 (NH)
13.50–14.00 ppm
Table 2.
Typical ranges of chemical shifts for 1H NMR spectra of nucleic acids.
a Chemical shifts relative to internal TSP (3-(trimethylsilyl)propionic acid).
b For Watson-Crick base pairs (CG).
The broadening of 1H NMR resonances of DNA upon addition of an appropriate minor groove binding compound is one type of evidence of complex formation in DNA 31P-NMR spectroscopy has also been used to provide important information concerning the binding of intercalators to DNA. The 31P chemical shifts are sensitive DNA conformational changes, and hence intercalating drugs cause downfield shift, while divalent cations causes up field shifts in the 31P signal [38].
11.4 Mass spectrometry
Mass spectrometry (MS) has become one of the most common techniques adopted to study interactions between DNA and small ligand molecules. The ability of mass spectrometry to investigate drug-DNA interactions have been reviewed recently. The binding stoichiometry, the relative binding affinities and the binding constants for DNA double helices of various sequences may be determined. Electrospray ionization (ESI) is the most common ionization method used in the study of biomolecules due to its soft ionization. Using ESI techniques, biomolecules can be transferred from the solution to the mass spectrometer with minimal fragmentation and, so, both the mass of the DNA and the mass of the DNA-ligand complex can be determined, as the non-covalent interactions that formed the complex are not altered during the electrospray process [39, 40, 41]. Focusing on the use of ESI-MS to study complexes, MS gives a signal for each species with a different mass and so it is very straightforward to establish the stoichiometry of the complexes. ESI-MS signals enable several calculations to be performed. The number of DNA strands involved, the number of bound cations (if present) and the number of bound ligands, among others. Taking into account the structure of the nucleic acids, ESI-MS studies are performed using negative polarity. It is well known that the phosphodiester backbone of DNA is fully deprotonated under usual working conditions. In general, in order to preserve their structure, nucleic acid solutions are prepared with monovalent ions. Perylene derivatives, such as, N,N-bis-(2-(dimethylamino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide, favor π-π interactions with the G-tetrad surface. Moreover, 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21H,23H-porphine is an effective telomerase inhibitor, also binds to the G-quadruplex in the c-myc promoter [42].
11.5 Atomic force microscopy
Atomic force microscopy (AFM) can be used to distinguish proteins bound to nucleic acid templates. One of the great advantages of the atomic force microscope, particularly with respect to the imaging of biological specimens, is that it can work in fluid, so that experiments can be performed under near physiological conditions and allowing the imaging of interactions and transactions between molecules in real time [43]. AFM techniques will play a larger role in studying interactions between biological specimens, such as ligand-receptor and protein-DNA systems, and can be applied to the study of drug interactions with a variety of biological specimens [5].
Drug-DNA complexes have been studied with AFM to determine the binding force between them. This is of considerable interest since nucleic acid ligands are commonly used as anticancer drugs and in the treatment of genetic diseases. However, determining whether they bind to DNA by intercalation within major and/or minor grooves, by normal modes, or by a combination of these modes can often be difficult. AFM was used to study drug binding mode, affinity, and exclusion number by comparing the length of DNA fragments that have and have not been exposed to the drug. It is well known that if intercalative binding is occurring, the DNA strand increases in length. Moreover, the degree of lengthening is informative in determining the binding affinity and the site-exclusion number. AFM was shown to be an effective means of seeing and measuring any changes in the DNA strand. For example, when it exposed to ethidium, the DNA strand was shown through AFM to have increased in length from 3300 to 5250 nm, this indicating the intercalative mode of binding. Similarly, AFM intercalative binding studies showed the increase in the DNA strand, from 3300 to 4670 nm, upon exposure to daunomycin. This technique has also successfully been applied to new drugs in which the mode of binding was unclear. For example, exposure of 2,5-bis(4-amidinophenyl) (APF), did not produce lengthening of the DNA strands, indicating that the drug binds by non-intercalative modes. The different structural changes and binding processes of the DNA occur because of interactions with these two components [5].
11.6 Viscosity measurements
DNA viscosity is sensitive to DNA length change, for this reason, its measurement upon the addition of a compound is often concerned as the least ambiguous and most critical method to clarify the interaction mode of a compound with DNA and this will provide reliable evidence for the intercalative binding mode. Relative viscosity measurements have proved to be a reliable method for the assignment of the mode of binding compounds to DNA. In the case of classical intercalation, DNA base pairs are separated in order to host the bound compound resulting in the lengthening of the DNA helix and subsequently increased DNA viscosity. On the other side, the binding of a compound exclusively in DNA grooves by means of partial and/or non-classic intercalation, under same conditions, causes a bend or kink in the DNA helix and reducing its effective length and, as a result, DNA solution viscosity is decreased, or it remains unchanged.
Figure 15 show the interaction of three Schiff base compounds of N′-substituted benzohydrazide and sulfonohydrazide derivatives: (1) N′-(2-hydroxy-3-methoxybenzylidene)-4-tert-butylbenzohydrazide, (2) N′-(5-bromo-2 hydroxy-benzylidene)-4-tert-butylbenzohydrazide and (3) N′-(2-hydroxy-3-methoxy-benzylide-ne)-4-methylbenzenesulfonohydrazide with SS-DNA [44]. This can be explained by the insertion of the compounds in between the DNA base pairs, leading to an increase in the separation of base pairs at intercalation sites and, thus, an increase in DNA length [45].
Figure 15.
Effects of increasing amount of compounds (1–3) on relative viscosity of SS-DNA at 25 ± 0.1°C. [DNA] = 7.2 μM, r = 0, 6.9, 13.9, 20.8, 27.8.
The viscosity data show that there are at least two phases of binding between the complex and CT-DNA. At lower concentration of the complex, the viscosity first decreases and then increases at higher concentration of complex. This slow increase in viscosity is an indication of groove binding [11].
Figure 16 indicate that with increasing amount of (3-(3,5 dimethyl-phenylimino)methyl)benzene-1,2-diol (HL), the relative viscosity of DNA first remains constant and then increases [46]. This observation supports that HL bind through intercalation mode but with different affinity, i.e., also show some affinity for binding with grooves of DNA through hydrogen bonding, typically to N3 of adenine and O2 of thymine. However, strong binding is presumably due to intercalation with DNA [11].
Figure 16.
Effects of increasing amount of HL on relative viscosity of CT-DNA at 25 ± 0.1°C. [DNA] = 2.37 × 10−5 M.
Figure 17 [47] and Figure 18 [48] shows the electrostatic binding mode of nickel and organotin(IV) complexes with DNA, respectively. The viscosity of DNA remains essentially unchanged on the addition of the nickel complexes while it decreases in case of organotin(IV) complexes [11].
Figure 17.
(1) Effect of increasing amount of the complexes [Ni(hhmh)2], (2) [Ni(bhmh)2], (3) [Ni(ihmh)2], (4) [Ni(PPh3)(hpeh)], (5) [Ni(PPh3)(bpeh)] and (6) [Ni(PPh3)(ipeh)] on the relative viscosity of HS-DNA at 16(±0.L)°C.
Figure 18.
(1) Effects of increasing amount of tri-n-butyltin (IV) 3-[(3′,5’dimethylphenylamino)] propanoate and (2) triphenyltin(IV) 3-[(3′,5’dimethylphenylamino)]propanoate on relative viscosity of SS-DNA at 25 ± 0.1°C, [DNA] = 1.86 × 10−4 M.
12. Conclusions
This chapter has focused on drug-DNA interactions and their study by various analytical techniques such as IR spectroscopy, viscosity measurements, MS and AFM. These techniques are used to evaluate the binding mode as well as binding strength of the complex formed between drug and DNA. The study should be useful for the development of potential survey for DNA structure and new therapeutic reagents for tumors and other diseases. Fundamentally, drugs interact with DNA through two different ways, covalent and/or non-covalent modes. Covalent binders act as alkylating agents as they alkylate the nucleotides of DNA, while, the non-covalent binders interact by three different ways: (i) intercalation, (ii) groove binding, and (iii) external binding (on the outside of the helix). Different spectroscopic techniques are generally, powerful tools to study interactions of DNA with drugs and the effects of such interactions in the structure of DNA, providing some insights about the mechanism of drug action. The binding stoichiometry, the relative binding affinities and the binding constants for DNA double helices of various sequences.
\n',keywords:"anticancer drugs, DNA, interactions, proteins, hydrogen bond",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/70000.pdf",chapterXML:"https://mts.intechopen.com/source/xml/70000.xml",downloadPdfUrl:"/chapter/pdf-download/70000",previewPdfUrl:"/chapter/pdf-preview/70000",totalDownloads:614,totalViews:0,totalCrossrefCites:0,dateSubmitted:"September 30th 2018",dateReviewed:"March 12th 2019",datePrePublished:"November 11th 2019",datePublished:"February 19th 2020",dateFinished:"November 9th 2019",readingETA:"0",abstract:"The deoxyribonucleic acid (DNA) is the molecule of life that controls all the chemical changes that take place in cells. The interaction of drugs with DNA is among the most important aspects of biological studies in drug discovery and pharmaceutical development processes. Moreover, the knowledge of specific targets in rational design of chemotherapeutics is a fundamental factor, principally, for the design of molecules that can be used in the treatment of oncologic diseases. Observing the pre- and postsigns of drug-DNA interaction provides good evidence for the interaction mechanism to be elucidated. Also, this interaction could be used for the quantification of drugs and for the determination of new drugs targeting DNA. Approaches can provide new insight into rational drug design and would lead to further understanding of the interaction mechanism between anticancer drugs and DNA. The intention of this chapter is to provide several examples of anticancer drugs, DNA interaction, and the mechanisms of interaction in order to understand the influence of several interaction factors in the capacity and selectivity of the anticancer drugs to interact with DNA. In addition, different experimental and theoretical approaches to detect and to evaluate the anticancer drugs’ interactions with DNA were also discussed.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/70000",risUrl:"/chapter/ris/70000",signatures:"Saad Hmoud Alotaibi and Awad Abdalla Momen",book:{id:"6897",title:"Biophysical Chemistry",subtitle:"Advance Applications",fullTitle:"Biophysical Chemistry - Advance Applications",slug:"biophysical-chemistry-advance-applications",publishedDate:"February 19th 2020",bookSignature:"Mohammed A. A. Khalid",coverURL:"https://cdn.intechopen.com/books/images_new/6897.jpg",licenceType:"CC BY 3.0",editedByType:"Edited by",isbn:"978-1-78984-048-3",printIsbn:"978-1-78984-047-6",pdfIsbn:"978-1-83880-138-0",editors:[{id:"137240",title:"Prof.",name:"Mohammed",middleName:null,surname:"Khalid",slug:"mohammed-khalid",fullName:"Mohammed Khalid"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"}},authors:[{id:"277977",title:"Dr.",name:"Saad",middleName:null,surname:"Alosaimi",fullName:"Saad Alosaimi",slug:"saad-alosaimi",email:"alosaimi.sr@gmail.com",position:null,institution:null},{id:"277982",title:"Dr.",name:"Awad",middleName:null,surname:"Momen",fullName:"Awad Momen",slug:"awad-momen",email:"aamomena@yahoo.com",position:null,institution:null}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Structural features of DNA",level:"1"},{id:"sec_3",title:"3. Anticancer drug-DNA interaction",level:"1"},{id:"sec_4",title:"4. Types of drug-DNA interactions",level:"1"},{id:"sec_5",title:"5. Modeling of hairpin minor groove binders",level:"1"},{id:"sec_6",title:"6. Rational for drug design",level:"1"},{id:"sec_7",title:"7. Cisplatin-DNA interactions",level:"1"},{id:"sec_8",title:"8. Sequence specific structural perturbation",level:"1"},{id:"sec_9",title:"9. Methods for elucidation of DNA-anticancer drug interactions",level:"1"},{id:"sec_9_2",title:"9.1 Mitomycin-C",level:"2"},{id:"sec_10_2",title:"9.2 Echinomycin",level:"2"},{id:"sec_12",title:"10. Mechanisms of anticancer drug-DNA interaction",level:"1"},{id:"sec_12_2",title:"10.1 Intercalating agent",level:"2"},{id:"sec_13_2",title:"10.2 Intercalating reagents (II)",level:"2"},{id:"sec_14_2",title:"10.3 Bleomycin A2",level:"2"},{id:"sec_16",title:"11. Techniques for studying drug-DNA interactions",level:"1"},{id:"sec_16_2",title:"11.1 Fourier transform infrared spectroscopy",level:"2"},{id:"sec_17_2",title:"11.2 UV-visible spectroscopy",level:"2"},{id:"sec_18_2",title:"11.3 Nuclear magnetic resonance spectroscopy",level:"2"},{id:"sec_19_2",title:"11.4 Mass spectrometry",level:"2"},{id:"sec_20_2",title:"11.5 Atomic force microscopy",level:"2"},{id:"sec_21_2",title:"11.6 Viscosity measurements",level:"2"},{id:"sec_23",title:"12. Conclusions",level:"1"}],chapterReferences:[{id:"B1",body:'Wang JC. Nature reviews. Cellular roles of DNA topoisomerases: A molecular perspective. Molecular and Cellular Biology. 2002;3:430-440'},{id:"B2",body:'Guerra CF, Bickelhaupt FM. Watson-Crick hydrogen bonds: Nature and role in DNA replication. Modern Methods for Theoretical Physical Chemistry of Biopolymers. 2006;19:79-97'},{id:"B3",body:'Langkjæra N, Wengela J, Pasternak A. Watson–Crick hydrogen bonding of unlocked nucleic acids. 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Binding of a hairpin polyamide in the minor groove of DNA: Sequence-specific enthalpic discrimination. Proceedings of the National Academy of Sciences of the United States of America. 1996;93:8306-8311'},{id:"B14",body:'Mrksich M, Parks ME, Dervan PB. Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA. Journal of the American Chemical Society. 1994;116:7983-7988'},{id:"B15",body:'Vollmer M, Nägele E, Hörth P. Differential proteome analysis: Two-dimensional nano–LC/MS of E. coli proteome grown on different carbon sources. Journal of Biomolecular Technology. 2003;21:289-307'},{id:"B16",body:'Mandal S, Moudgil M, Mandal S. Rational drug design. European Journal of Pharmacology. 2009;625(1-3):90-100'},{id:"B17",body:'Newlands ES, Stevens MFG, Wedge SR, Wheelhouse RT, Brock C. Temozolomide: A review of its discovery, chemical properties, pre-clinical development and clinical trials. Cancer Treatment Reviews. 1997;23:35-61'},{id:"B18",body:'Skauge T. Antibacterial and anticancer drugs—Interaction with DNA (i) antibacterial fluoroquinolones (ii) anticancer cis–platinum(II) complexes [PhD thesis]. Department of Chemistry, Faculty of Science, University of Bergen; 2006'},{id:"B19",body:'Eastman A, Jennerwein MM, Nagel DL. Characterization of bifunctional adducts produced in DNA by trans–diamminedichloroplatinum(II). Chemico-Biological Interactions. 1988;67:71-80'},{id:"B20",body:'Davies M, Berners-Price SJ, Hambley TW. Slowing of cisplatin aquation in the presence of DNA but not in the presence of phosphate: Improved understanding of sequence selectivity and the roles of monoaquated and diaquated species in the binding of cisplatin to DNA. Inorganic Chemistry. 2000;39:5603-5613'},{id:"B21",body:'Legendre F, Bas V, Kozelka J, Chottard J. 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A library of IR bands of nucleic acids in solution. Biophysical Chemistry. 2003;104(2):477-488'},{id:"B32",body:'González-Ruiz V, Olives A, Martín M, Ribelles P, Ramos M, Menéndez J. An overview of analytical techniques employed to evidence drug–DNA interactions. Applications to the design of genosensors. In: Biomedical Engineering, Trends, Research and Technologies. 2011. pp. 65-90'},{id:"B33",body:'Nafisi S, Saboury AA, Keramat N, Neault JF, Tajmir-Riahi HA. Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue. Journal of Molecular Structure. 2007;827(1-3):35-43'},{id:"B34",body:'Nafisi S, Bonsaii M, Alexis V, Glick J. Binding of 2–acetylaminofluorene to DNA. DNA and Cell Biology. 2011;30(11):955-962'},{id:"B35",body:'Andrushchenko V., Leonenko Z., Cramb D., van de Sande H, Wieser H. VCD and AFM study of DNA interaction with Cr3+ ions, VCD and AFM evidence of DNA condensation. 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Experimental methods for studying the interactions between G–quadruplex structures and ligands. Current Pharmaceutical Design. 2012;18(14):1900-1916'},{id:"B41",body:'Rosu F, De Pauw E, Gabelica V. Electrospray mass spectrometry to study drug–nucleic acids interactions. Biochimie. 2008;90:1074-1087'},{id:"B42",body:'Li H, Liu Y, Lin S, Yuan G. Spectroscopy probing of the formation, recognition, and conversion of a G–quadruplex in the promoter region of the bcl-2 oncogene chemistry. A European Journal. 2009;15(10):2445-2452'},{id:"B43",body:'Edwardson J, Henderson RM. Atomic force microscopy and drug discovery. Research Focus/Reviews. 2004;9(2):64-71'},{id:"B44",body:'Sirajuddin M, Uddin N, Ali S, Tahir MN. Potential bioactive Schiff base compounds: synthesis, characterization, X-ray structures, biological screenings and interaction with Salmon sperm DNA. Spectrochimica Acta Part A. 2013;116:111-121'},{id:"B45",body:'Dimiza F, Perdih F, Tangoulis V, Turel I, Kessissoglou D, Psomas G. 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Department of Chemistry, Turabah University College, Taif University, Saudi Arabia
Department of Chemistry, College of Industrial and Applied Science, University of Bahri, Sudan
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The Open Access model is applied to all of our publications and is designed to eliminate subscriptions and pay-per-view fees. This approach ensures free, immediate access to full text versions of your research.
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The Open Access Publishing Fee (OAPF) is payable only after your full chapter, monograph or Compacts monograph is accepted for publication.
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If a manuscript requires Heavy Editing or Language Polishing, this will incur additional fees.
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Open Access Funding
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To explore funding opportunities and learn more about how you can finance your IntechOpen publication, go to our Open Access Funding page. IntechOpen offers expert assistance to all of its Authors. We can support you in approaching funding bodies and institutions in relation to publishing fees by providing information about compliance with the Open Access policies of your funder or institution. We can also assist with communicating the benefits of Open Access in order to support and strengthen your funding request and provide personal guidance through your application process. You can contact us at oapf@intechopen.com for further details or assistance.
\n\n
For Authors who are still unable to obtain funding from their institutions or research funding bodies for individual projects, IntechOpen does offer the possibility of applying for a Waiver to offset some or all processing feed. Details regarding our Waiver Policy can be found here.
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Added Value of Publishing with IntechOpen
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Indexing and listing across major repositories, see details ...
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Long-term archiving
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Visibility on the world's strongest OA platform
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Live Performance Metrics to track readership and the impact of your chapter
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Dissemination and Promotion
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Proven world leader in Open Access book publishing with over 10 years experience
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Personal support during every step of the publication process
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+146,150 citations in Web of Science databases
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Currently strongest OA platform with over 150 million downloads
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