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Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport. Symmetry (Basel) 2019. [DOI: 10.3390/sym11080968] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This review is devoted to tight-binding (TB) modeling of nucleic acid sequences like DNA and RNA. It addresses how various types of order (periodic, quasiperiodic, fractal) or disorder (diagonal, non-diagonal, random, methylation et cetera) affect charge transport. We include an introduction to TB and a discussion of its various submodels [wire, ladder, extended ladder, fishbone (wire), fishbone ladder] and of the process of renormalization. We proceed to a discussion of aperiodicity, quasicrystals and the mathematics of aperiodic substitutional sequences: primitive substitutions, Perron–Frobenius eigenvalue, induced substitutions, and Pisot property. We discuss the energy structure of nucleic acid wires, the coupling to the leads, the transmission coefficients and the current–voltage curves. We also summarize efforts aiming to examine the potentiality to utilize the charge transport characteristics of nucleic acids as a tool to probe several diseases or disorders.
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Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
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Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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Fu HH, Gu L, Wu DD, Zhang ZQ. Enhancement of the thermoelectric figure of merit in DNA-like systems induced by Fano and Dicke effects. Phys Chem Chem Phys 2015; 17:11077-87. [DOI: 10.1039/c4cp04382k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a theoretical study highlighting the thermoelectric properties of biological and synthetic DNA molecules.
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Affiliation(s)
- Hua-Hua Fu
- College of Physics and Wuhan National High Magnetic field center
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
| | - Lei Gu
- College of Physics and Wuhan National High Magnetic field center
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
| | - Dan-Dan Wu
- College of Physics and Wuhan National High Magnetic field center
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
| | - Zu-Quan Zhang
- College of Physics and Wuhan National High Magnetic field center
- Huazhong University of Science and Technology
- Wuhan 430074
- People's Republic of China
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Applications of biomaterials to liquid crystals. Molecules 2013; 18:4703-17. [PMID: 23603952 PMCID: PMC6270325 DOI: 10.3390/molecules18044703] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/10/2013] [Accepted: 04/17/2013] [Indexed: 11/23/2022] Open
Abstract
Nowadays, chemically synthesized proteins and peptides are attractive building blocks and have potential in many important applications as biomaterials. In this review, applications of biomaterials to thermotropic liquid crystals are discussed. The review covers the improvement of the performance of liquid crystal displays using liquid crystal physical gels consisting of a liquid crystal and amino acid-based gelators, and also new functionalization of liquid crystals. Moreover, the influence of DNA, which is one of the more attractive biomaterials, dispersed in thermotropic liquid crystals and its potential use in the liquid crystal industry is described. In addition, we found interesting results during electrooptical measurements of liquid crystals doped with DNA, and explain them from the point of view of biological applications. These recent approaches suggest that these biomaterials may be applicable in the electronic device industry and should be considered as an interesting material with their physical properties having the potential to create or refine an industrial product.
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Juhaniewicz J, Sek S. Peptide molecular junctions: Distance dependent electron transmission through oligoprolines. Bioelectrochemistry 2012; 87:21-7. [DOI: 10.1016/j.bioelechem.2011.11.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 11/13/2011] [Accepted: 11/28/2011] [Indexed: 11/16/2022]
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Unique synthesis of graphene-based materials for clean energy and biological sensing applications. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-012-5128-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Agapito LA, Gayles J, Wolowiec C, Kioussis N. Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps. NANOTECHNOLOGY 2012; 23:135202. [PMID: 22418779 PMCID: PMC3305288 DOI: 10.1088/0957-4484/23/13/135202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green's function (NEGF) theory to determine the electrical response of graphene--base-pair--graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.
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Affiliation(s)
- Luis A Agapito
- Department of Physics and W M Keck Computational Materials Theory Center, California State University Northridge, Northridge, CA 91330, USA.
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Shapir E, Brancolini G, Molotsky T, Kotlyar AB, Di Felice R, Porath D. Energy gap reduction in DNA by complexation with metal ions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:4290-4294. [PMID: 21837629 DOI: 10.1002/adma.201101100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/29/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Errez Shapir
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
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D'Abramo M, Orozco M, Amadei A. Effects of local electric fields on the redox free energy of single stranded DNA. Chem Commun (Camb) 2010; 47:2646-8. [PMID: 21180762 DOI: 10.1039/c0cc04352d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Influence of external electric field as well as base substitution effects on the reduction/oxidation free energies of single stranded DNA suggest that base sequencing via measuring redox properties might be feasible under the conditions that (i) a difference of ∼ 230 kJ mol(-1) in the oxidation potentials is enough to discriminate between nucleobases conductance signals and (ii) the strand is long enough to reduce end effects.
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Affiliation(s)
- Marco D'Abramo
- Departamento de Bioquímica y Biología Molecular Universitat de Barcelona, Barcelona, Spain.
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Xu M, Fujita D, Hanagata N. Perspectives and challenges of emerging single-molecule DNA sequencing technologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2638-2649. [PMID: 19904762 DOI: 10.1002/smll.200900976] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The growing demand for analysis of the genomes of many species and cancers, for understanding the role of genetic variation among individuals in disease, and with the ultimate goal of deciphering individual human genomes has led to the development of non-Sanger reaction-based technologies towards rapid and inexpensive DNA sequencing. Recent advancements in new DNA sequencing technologies are changing the scientific horizon by dramatically accelerating biological and biomedical research and promising an era of personalized medicine for improved human health. Two single-molecule sequencing technologies based on fluorescence detection are already in a working state. The newly launched and emerging single-molecule DNA sequencing approaches are reviewed here. The current challenges of these technologies and potential methods of overcoming these challenges are critically discussed. Further research and development of single-molecule sequencing will allow researchers to gather nearly error-free genomic data in a timely and inexpensive manner.
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Affiliation(s)
- Mingsheng Xu
- International Center for Young Scientists National Institute for Materials Science, Tsukuba, Ibaraki, Japan.
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Jauregui LA, Salazar-Salinas K, Seminario JM. Transverse electronic transport in double-stranded DNA nucleotides. J Phys Chem B 2009; 113:6230-9. [PMID: 19402724 DOI: 10.1021/jp808790j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We calculate the transverse current through double-stranded DNA nucleotides using ab initio techniques in order to establish a protocol to recognize the type and sequence of double-stranded DNA nucleotides. The distinct current-voltage features between nucleotides are used as signatures for their characterization and sequencing. Extended bulk gold electrodes as well as extensions of the DNA backbones are tested as contacts for the electron transport, yielding currents 2 orders of magnitude larger for the former. The addition of Na or H positive counterions improves the signal levels, thus leading to a better discrimination, especially when sodium cations are added.
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Affiliation(s)
- Luis A Jauregui
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, USA
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12
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Tsukamoto T, Ishikawa Y, Sengoku Y, Kurita N. A combined DFT/Green's function study on electrical conductivity through DNA duplex between Au electrodes. Chem Phys Lett 2009; 474:362-365. [PMID: 20160924 PMCID: PMC2761638 DOI: 10.1016/j.cplett.2009.04.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Electrical conducting properties of DNA duplexes sandwiched between Au electrodes have been investigated by use of first-principles molecular simulation based on DFT and Green's function to elucidate the origin of their base sequence dependence. The theoretically simulated effects of DNA base sequence on the electrical conducting properties are in qualitative agreement with experiment. The HOMOs localized on Guanine bases have the major contribution to the electrical conductivity through DNA duplexes.
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Affiliation(s)
- Takayuki Tsukamoto
- Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yasuyuki Ishikawa
- Department of Chemistry, University of Puerto Rico, P. O. Box 23346, UPR Station, San Juan, PR 00931-3346, USA
| | - Yasuo Sengoku
- Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Noriyuki Kurita
- Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan
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Guo AM, Xiong SJ, Yang Z, Zhu HJ. Enhancement of transport in DNA-like systems induced by backbone disorder. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:061922. [PMID: 19256883 DOI: 10.1103/physreve.78.061922] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Indexed: 05/27/2023]
Abstract
We report a theoretical study highlighting the fundamental effects of backbone disorder which simulates the environmental complications on charge transport properties of biological and synthetic DNA molecules. Based on effective tight-binding models of duplex DNA, the Lyapunov coefficient and current-voltage characteristics are numerically calculated by varying the backbone disorder degree. In contrast to the localization picture that the conduction of duplex DNA becomes poorer when the backbone disorder degree is increased, we find that the backbone disorder can enhance the charge transport ability of the DNA molecules when the environment-induced disorder surpasses a critical value, giving rise to a semiconducting-metallic transition. The physical origin for this is traced back to the antiresonant effects. These results provide a scenario to interpret a variety of transport behaviors observed in DNA molecules and suggest perspectives for future experiments intending to control the charge transport through DNA-based nanodevices.
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Affiliation(s)
- Ai-Min Guo
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
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Xu M, Endres RG, Arakawa Y. The electronic properties of DNA bases. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:1539-43. [PMID: 17786897 DOI: 10.1002/smll.200600732] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Mingsheng Xu
- Nanoelectronics Collaborative Research Center, IIS, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan.
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Nogues C, Cohen SR, Daube S, Apter N, Naaman R. Sequence Dependence of Charge Transport Properties of DNA. J Phys Chem B 2006; 110:8910-3. [PMID: 16671692 DOI: 10.1021/jp060870o] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrical conduction through three short oligomers (26 base pairs, 8 nm long) with differing numbers of GC base pairs was measured. One strand is poly(A)-poly(T), which is entirely devoid of GC base pairs. Of the two additional strands, one contains 8 and the other 14 GC base pairs. The oligomers were adsorbed on a gold substrate on one side and to a gold nanoparticle on the other side. Conducting atomic force microscope was used for obtaining the current versus voltage curves. We found that in all cases the DNA behaves as a wide band-gap semiconductor, with width depending on the number of GC base pairs. As this number increases, the band-gap narrows. For applied voltages exceeding the band-gap, the current density rises dramatically. The rise becomes sharper with increasing number of GC base pairs, reaching more than 1 nA/nm2 for the oligomer containing 14 GC pairs.
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