DNA-based nanowires and nanodevices

Pandian, Sureshbabu Ram Kumar; Yuan, Chiun‐Jye; Lin, Chih-Kuang; Wang, Wen Hung; Chang, Chia-Ching

doi:10.1080/23746149.2016.1254065

Cited by 4 publications

(3 citation statements)

References 53 publications

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“…The double helix’s ability to transfer charge follows directly from the base-pair stacking interaction [ 48 ]. Since the 1990s, ds-oligo has been perceived as a nanowire [ 49 ]. As discussed previously, the ds-DNA structure and electronic properties are influenced by the presence of Iz and Oz as part of a CDL.…”

Section: Resultsmentioning

confidence: 99%

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

Karwowski

2024

Molecules

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The genome—the source of life and platform of evolution—is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent–solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

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Section: Resultsmentioning

confidence: 99%

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

Karwowski

2024

Molecules

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“…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.…”

mentioning

confidence: 99%

“…Metal ions (Cu 2+ , Pd 2+ , 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.…”

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confidence: 99%

Introductory Chapter: DNA as Nanowires

Srivastava¹

2019

Bio-Inspired Technology [Working Title]

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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. Sequencespecific 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.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 con...

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