Open access

Introductory Chapter: DNA as Nanowires

Written By

Ruby Srivastava

Submitted: February 12th, 2019 Published: March 8th, 2019

DOI: 10.5772/intechopen.85172

Chapter metrics overview

1,229 Chapter Downloads

View Full Metrics

1. Introduction

The integration of nanotechnology with biology and bioengineering has produced many advances with the manipulation of well-defined structures at the nanoscale with high accuracy. DNA molecules can be used for the assembly of devices, for the interconnect joints, or as the device element itself. Sequence-specific DNA detection has been applied in the diagnosis of pathogenic and genetic diseases. The unique physical properties of dots or wires with the remarkable recognition capabilities of DNA could lead to the miniaturization of biological electronics and optical devices, which includes the biosensors and probes. Numerous advantages of nano- and micro-biodevices include the separation technologies, HPLC and capillary electrophoretic separation of DNA, nanopillar devices for the ultra-fast separation of DNA and proteins, nanoball materials for the fast separation of wide range of DNA fragments and the nanowire devices for ultra-fast separation of DNA, RNA, and proteins. The studies about these devices have been carried out by Prof. Yoshinobu Baba and the research group [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]. The nanopillar, nanowall, nanoslit, and nanopore structures were designed by the top down or semiconductor nano-fabrication technology, while the nanoball, nanowire, nanoparticles and the quantum dot structures are designed by the use of bottom up or self-assembled nano-fabrication technology. These devices are shown in Figure 1.

Figure 1.

(a) Device design of nanopillar and (b) nanobiodevices with nanopore, nanopillar, nanowire and nanowell. Adapted from Ref. [1].

DNA exhibits many other properties; as high stability, adjustable conductance, vast information storage, self-organising capability and programmability. So it is considered as an ideal material for the applications of nanodevices, nanoelectronics and molecular computing. There are several advantages to use DNA for these device designs. The first step of the DNA-based nanotechnology is to attach DNA molecules to the surfaces. It can be done by three different methods: by electrostatic interaction between DNA and a substrate, covalent binding of a chemical group attached to the DNA end and the binding of protein attached at the DNA end to the corresponding antibody immobilized at the surface. Seeman and co-workers [13] have exploited the properties of DNA’s molecular recognition to design complex mesoscopic structures based solely on DNA. They used the branched DNA to form stick figures by properly choosing the sequence of the complementary strands. Further macrocycles, DNA quadrilateral, DNA knots, Holliday junctions, and other periodic crystal structures were also designed. DNA-mediated self-assembly of nanostructures has been extended to metallic nanowires [14, 15, 16]. In a study, DNA as a template was used to grow conducting silver nanowires [14]. The fabrication of gold and silver wires was used with the DNA as a template or skeleton [15]. Nguyen et al. developed an approach for the attachment of DNA to oxidatively open the ends of multiwall carbon nanotube arrays [17]. The carbon wall nanotubes can be used as electrodes to transmit electrical signals or as sensors to detect the concentration of chemical or biological materials [18, 19, 20]. Efficient DNA delivery is vital for the gene therapy, DNA vaccination and the advancement of other clinical therapies. Molecular devices are highly desirable as they can rapidly accumulate and displace electrons/charges within the nanoscale structures, and are sensitive to the changes in the physicochemical and biological environments. DNA logic gates can also constructed from the concepts based on the DNA tweezers [21]. Molecular wires and/or machines resemble electronic memory units can be made by cost-effective and low-energy technologies, so that they can provide the environmental friendly solutions. DNA origami has gained much attention recently because of its potential to direct the formation of predefined 2D or 3D DNA structures at the nanoscale [22].

DNA nanomachines can also be fuelled by enzymes or DNA [23, 24]. An enzyme-operated DNA-switch was proposed recently [24]. DNA-protein conjugates were widely applied in the development of immunoassays, biosensors, micro-chips and molecular devices [25]. A field effect transistor was also designed, based on the DNA base deoxyguanosine derivative [26]. The replacement of the natural bases can be carried out by the artificial nucleosides or nucleoside mimics [27]. Metal ions (Cu2+, Pd2+, and Ag+) have been successfully incorporated as artificial DNA bases into the oligonucleotides [28]. Ni-DNA nanowires exhibit the characteristics of memristors, find potential application in mass information storage system [12]. The Ni-DNA device structure is given in Figure 2.

Figure 2.

Ni-DNA nanobiodevice structure. Adapted from Ref. [12].

Assembling the biomolecules and microorganisms into a desired architecture has offered new routes to the fabrication of nanomaterials [29, 30]. DNA nanowires can be used as a template to fabricate functional nanomaterials and as a platform for genetic analysis [31, 32, 33]. These nanowires associate with an aqueous solution of DNA molecules, where capillary forces of the solution at a receding meniscus act to stretch and immobilize the molecules on a solid surface [34]. Yet the widespread use is still hindered due to the limited control over the size, geometry, and alignment of the nanowires. Hence to manipulate the size, geometry, and alignment of nanowires, efforts has been needed to control the evaporation of the solutions by adjusting the experimental parameters, such as: concentration and temperature, or by applying external forces that move the droplets in the desired direction [35, 36, 37].

Advertisement

2. Electrical characterization of DNA-based metallic nanowires

Novel conductive DNA-based nanomaterial, DNA-peptide wire composed of a DNA core and a peripheral peptide layer, is used for the wide variety of nano electronic and biosensor applications. The electrical conductivity of these wires is higher than the native double-stranded DNA (dsDNA). These wires produce high conductivity and better resistance to the mechanical deformations caused by the interactions between the substrate and electrode surface. Porath et al. [38] has studied the electrical transport through short (10 nm) dsDNA molecules deposited between platinum nanoelectrodes at different temperatures, confirming the reproducible semiconducting behavior with a gap [39, 40].

Electrical studies indicate that the charge transport in DNA is dominated by holes due to the position of the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) levels of DNA with respect to the Fermi energy of the coinage metal contacts (e.g., Au and Pt), though the photo physical studies indicate the transportation of both hole and electron in DNA [41]. As a result, DNA molecule behaves as a p-type nanowire [42]. The representation of conductive silver nanowires and nanoparticles NPs attached on the DNA origami are given in Figure 3.

Figure 3.

(a) The construction of conductive silver nanowires, (b) PVD metal deposition on the alignment of DNA NW, (c) RNA functionalized AuNPs and (d) (1) DNA origami molds with Au nanoparticles and (2) nanoparticles NPs attached on the DNA origami. Adapted from Ref. [40].

The charge transport is explained by three main mechanisms: single-step-electron-tunnelling, thermal hopping, and domain hopping [43]. The charge transport in DNA occurs predominantly through the guanine bases due to their lowest electrochemical oxidation potential. When the DNA is absorbed on the surface, the conformations are affected by the van der Waals, electrostatic, and hydrophobic interactions within the substrate. Further the behaviour of DNA is affected by the DNA sequences, substrate and contact properties, temperature and humidity [44, 45, 46]. Recently, studies were conducted on the electrical measurements on guanine quadruplex DNA (G4-DNA), which is uniform in composition, consist of only G-nucleotides and it was observed that G4-DNA exhibit a greater bending rigidity compared to the dsDNA. Several techniques have been developed for contacting the nanowires with the combination of bottom-up and top-down strategies. These are:

  1. Lithographically defined contacts and in situ/ex situ I–V measurements

  2. Conductive AFM measurements

  3. DNA Origami-based metal nanostructures

Advertisement

3. Conclusion

DNA acts as a promising material for biomolecular nanotechnology due to its unique recognition capabilities, physicochemical stability, mechanical rigidity and high precision processibility. Significant progress has been made in this field, but it is still in the early stages. The catalytic, electrical, magnetic, and electrochemical properties of such structures can be systematically investigated and will represent the new frontiers in this field. Various DNA-based nanostructures, including DNA itself, DNA functionalized with metal and semiconductor nanoparticles, DNA-directed nanowires, and DNA-functionalized carbon nanotubes are used in wider application for biological and medical applications. Due to the present applicability of DNA structures, these properties should be properly studied to provide an access to the new and useful electronic and photonic materials. The development of DNA nanowires has recently focussed its attention in three aspects: (1) customising the sequence of nucleic acids for better electrical conductivity with reduced mismatch pair complexes, (2) stacking targeted double-helical backbone for stable and rigid nanowires, and (3) interconnection of discrete DNA origami structures [47]. Though researches have been carried out for the achievement of these targets, the cost of experimental synthesis need to be address in near future.

Advertisement

Acknowledgments

RS acknowledges the financial assistance by the DST WOS-A (SR/WOS-A/CS-69/2018). RS is also thankful to her mentor Dr. Shrish Tiwari, Bioinformatics Department, CSIR—Centre for Cellular and Molecular Biology, Hyderabad for the support.

References

  1. 1. Baba Y. Nano- and microbiodevices for high-performance separation of biomolecules. Chromatography. 2004;22:1360-1361. DOI: 10.15583/jpchrom.2015.030
  2. 2. Yasui T, Kaji N, Reza Mohamadi M, Okamoto Y, Tokeshi M, Horiike Y, et al. Electroosmotic flow in microchannels with nanostructures. ACS Nano. 2011;5:7775-7780. DOI: 10.1021/nn2030379
  3. 3. Serag MF, Braeckmans K, Habuchi S, Kaji N, Bianco A, Baba Y. Spatiotemporal visualization of subcellular dynamics of carbon nanotubes. Nano Letters. 2012;12:6145-6151. DOI: 10.1021/nl3029625
  4. 4. Yasui T, Inoue Y, Naito T, Okamoto Y, Kaji N, Tokeshi M, et al. Inkjet injection of DNA droplets for microchannel array electrophoresis. Analytical Chemistry. 2012;84:9282-9286. DOI: 10.1021/ac3020565
  5. 5. Hirano K, Ichikawa M, Ishido T, Ishikawa M, Baba Y, Yoshikawa K. How environmental solution conditions determine the compaction velocity of single DNA molecules. Nucleic Acids Research. 2012;40:284-289. DOI: 10.1093/nar/gkr712
  6. 6. Hirano K, Yamamoto YS, Ishido T, Murase N, Ichikawa M, Yoshikawa K, et al. Plasmonic imaging of brownian motion of single DNA molecules spontaneously binding to Ag nanoparticles. Nano Letters. 2013;13:1877-1882. DOI: 10.1021/nl304247n
  7. 7. Yasui T, Rahong S, Motoyama K, Yanagida T, Wu Q , Kaji N, et al. DNA manipulation and separation in sublithographic-scale nanowire array. ACS Nano. 2013;7:3029-3030. DOI: 10.1021/nn4002424
  8. 8. Rahong S, Yasui T, Yanagida T, Nagashima K, Kanai M, Klamchuen A, et al. Ultrafast and wide range analysis of DNA molecules using rigid network structure of solid nanowires. Scientific Reports. 2014;4:5252. DOI: 10.1038/srep05252
  9. 9. Wang J, Aki M, Onoshima D, Arinaga K, Kaji N, Tokeshi M, et al. Electrochemical biosensors: Towards point-of-care cancer diagnostics. Biosensors & Bioelectronics. 2014;51:280-285. DOI: 10.1016/j.bios.2013.07.058
  10. 10. Yasaki H, Onoshima D, Yasui T, Yukawa H, Kaji N, Baba Y. Microfluidic transfer of liquid interface for parallel stretching and stamping of terminal-unmodified single DNA molecules in zigzag-shaped microgrooves. Lab on a Chip. 2015;15:135-140. DOI: 10.1039/c4lc00990h
  11. 11. Yasui T, Kaji N, Ogawa R, Hashioka S, Tokeshi M, Horiike Y, et al. Arrangement of a nanostructure array to control equilibrium and nonequilibrium transports of macromolecules. Nano Letters. 2015;15:3445-3451. DOI: 10.1021/acs.nanolett.5b00783
  12. 12. Pandiana SRK, Yuana CJ, Lina CC, Wanga WH, Changa CC. DNA-based nanowires and nanodevices. Advances in Physics: X. 2017;2(1):22-34. DOI: 10.1080/23746149.2016.1254065
  13. 13. Seeman NC. Nucleic acid junctions and lattices. Journal of Theoretical Biology. 1982;99:237-247. DOI: 10.1016/0022-5193(82)90002-9
  14. 14. Braun E, Eichen Y, Sivan U, Ben-Yoseph G. DNA-templated assembly and electrode attachment of a conducting silver wire. Nature. 1998;391:775-778. DOI: 10.1038/35826
  15. 15. Martin BR, Dermody DJ, Reiss BD, Fang M, Lyon LA, Natan MJ, et al. Orthogonal self-assembly on colloidal gold-platinum nanorods. Advanced Materials. 1999;11:1021-1025. DOI: 10.1002/(SICI)1521-4095(199908)11:12<1021
  16. 16. Guo MX, Neuta IH, Madaboosi N, Nilsson M, and Wijngaart W. Efficient DNA-assisted synthesis of trans-membrane gold nanowires. Microsystems & Nanoengineering. 2018;4:17084-17092. DOI: 10.1038/micronano.2017.84
  17. 17. Nguyen CV, Delzeit L, Cassell AM, Li J, Han J, Meyyappan M. Preparation of nucleic acid functionalized carbon nanotube arrays. Nano Letters. 2002;2:1079-1081. DOI: 10.1021/nl025689f
  18. 18. Abu-Salah KM, Alrokyan SA, Khan MN, Ansari AA. Nanomaterials as analytical tools for genosensors. Sensors. 2010;10:963-993. DOI: 10.3390/s100100963
  19. 19. Behabtu N, Green MJ, Pasquali M. Carbon nanotube-based neat fibers. Nano Today. 2008;3(5-6):24-348. DOI: 10.1016/s1748-0132(08)70062-8
  20. 20. Wang J, Lin Y. Functionalized carbon nanotubes and nanofibers for biosensing applications. Trends in Analytical Chemistry. 2008;27(7):619-626. DOI: 10.1016/j.trac.2008.05.009
  21. 21. Li XY, Huang J, Jiang H-X, Du Y-C, Han G-M, Kong D-M. Molecular logic gates based on DNA tweezers responsive to multiplex restriction endonucleases. RSC Advances. 2016;6:38315-38320. DOI: 10.1039/C6RA05132D
  22. 22. Castro CE, Kilchherr F, Kim DN, Shiao EL, Wauer T, Wortmann P, et al. A primer to scaffolded DNA origami. Nature Methods. 2011;8:221-229. DOI: 10.1038/nmeth.1570
  23. 23. Yurke B, Turberfield AJ, Mills AP, Simmel FC, Neumann JL. A DNA-fuelled molecular machine made of DNA. Nature. 2000;406:605-608. DOI: 10.1038/35020524
  24. 24. Del Grosso E, Dallaire AM, Vallée-Bélisle A, Ricci F. Enzyme-operated DNA-based nanodevices. Nano Letters. 2015;15:8407-8411. DOI: 10.1021/acs.nanolett.5b04566
  25. 25. Niemeyer CM. Chemistry—A European Journal. 2001;7:3189-3195
  26. 26. Maruccio G, Visconti P, Arima V, D’Amico S, Biasco A, D'Amone E, et al. Field effect transistor based on a modified DNA base. Nano Letters. 2003;3:479-483. DOI: 10.1021/nl034046c
  27. 27. Kool ET. Replacing the nucleobases in DNA with designer molecules. Accounts of Chemical Research. 2002;35:927-936. DOI: 10.1021/ar000183u
  28. 28. Wagenknecht H-A. Metal-mediated DNA base pairing and metal arrays in artificial DNA: Towards new nanodevices. Angewandte Chemie, International Edition. 2003;42:3204-3206. DOI: 10.1002/anie.200301661
  29. 29. Mao C et al. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Science. 2004;303:213-217. DOI: 10.1126/science.1092740
  30. 30. Nguyen K et al. Synthesis of thin and highly conductive DNA-based palladium nanowires. Advanced Materials. 2008;20:1099-1104. DOI: 10.1002/adma.200701803
  31. 31. Watson SMD, Pike AR, Pate J, Houlton A, Horrocks BR. DNA-templated nanowires: Morphology and electrical conductivity. Nanoscale. 2014;6:4027-4037. DOI: 10.1039/C3NR06767J
  32. 32. Catherall T, Huskisson D, McAdams S, Vijayaraghavan A. Self-assembly of one dimensional DNA-templated structures. Journal of Materials Chemistry C. 2014;2:6895-6920. DOI: 10.1039/C4TC00460D
  33. 33. Michalet X et al. Dynamic molecular combing: Stretching the whole human genome for high-resolution studies. Science. 1997;277:1518-1523. PMID: 9278517
  34. 34. Bensimon A et al. Alignment and sensitive detection of DNA by a moving interface. Science. 1994;265:2096-2098. PMID:7522347
  35. 35. Li B et al. Macroscopic highly aligned DNA nanowires created by controlled evaporative self-assembly. ACS Nano. 2013;7:4326-4333. DOI: 10.1021/nn400840y
  36. 36. Li B, Zhang C, Jiang B, Han W, Lin Z. Flow-enabled self-assembly of large-scale aligned nanowires. Angewandte Chemie International Edition in English. 2015;54:4250-4254. DOI: 10.1002/anie.201412388
  37. 37. Deen J et al. Combing of genomic DNA from droplets containing picograms of material. ACS Nano. 2015;9:809-816. DOI: 10.1021/nn5063497
  38. 38. Porath D, Bezryadin A, de Vries S, Dekker C, De Vries S, Dekker C. Direct measurement of electrical transport through DNA molecules. Nature. 2000;403:635-638. DOI: 10.1038/35001029
  39. 39. Cohen H, Nogues C, Naaman R, Porath D. Direct measurement of electrical transport through single DNA molecules of complex sequence. Proceedings of the National Academy of Sciences of the United States of America. 2005;102:11589-11593. DOI: 10.1038/35001029
  40. 40. Bayrak T, Jagtap NS, Erbe A. Review of the electrical characterization of metallic nanowires on DNA templates. International Journal of Molecular Sciences. 2018;19:3019-3037. DOI: 10.3390/ijms19103019
  41. 41. Elias B, Shao F, Barton JK. Charge migration along the DNA duplex: Hole versus electron transport. Journal of the American Chemical Society. 2008;130:1152-1153. DOI: 10.1021/ja710358p
  42. 42. Takagi S, Takada T, Matsuo N, Yokoyama S, Nakamura M, Yamana K. Gating electrical transport through DNA molecules that bridge between silicon nanogaps. Nanoscale. 2012;4:1975-1977. DOI: 10.1039/C2NR12106A
  43. 43. Boon EM, Barton JK. Charge transport in DNA. Current Opinion in Structural Biology. 2002;12:320-329. PMID: 12127450
  44. 44. Heim T, Deresmes D, Vuillaume D. Conductivity of DNA probed by conducting-atomic force microscopy: Effects of contact electrode, DNA structure, and surface interactions. Journal of Applied Physics. 2004;96:2927-2936. DOI: 10.1063/1.1769606
  45. 45. Dong HH, Nham H, Yoo K-HH, So HM, Lee H-YY, Kawai T. Humidity effects on the conductance of the assembly of DNA molecules. Chemical Physics Letters. 2002;355:405-409. DOI: 10.3390/nano7060128
  46. 46. Yamahata C, Collard D, Takekawa T, Kumemura M, Hashiguchi G, Fujita H. Humidity dependence of charge transport through DNA revealed by silicon-based nanotweezers manipulation. Biophysical Journal. 2008;94:63-70. DOI: 10.1529/biophysj.107.115980
  47. 47. Eidelshtein G, Kotlyar A, Hashemi M, Gurevich L. Aligned deposition and electrical measurements on single DNA molecules. Nanotechnology. 2015;26:475102. DOI: 10.1088/0957-4484/26/47/475102

Written By

Ruby Srivastava

Submitted: February 12th, 2019 Published: March 8th, 2019