1
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Demir B, Akin Gultakti C, Koker Z, Anantram MP, Oren EE. Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations. J Phys Chem B 2024; 128:4646-4654. [PMID: 38712954 PMCID: PMC11103695 DOI: 10.1021/acs.jpcb.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
DNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations. We use four separate single strand DNAs, each having 8 bases (4 × G4C4 and 4 × A4T4), to form two different DNA nanostructures, each having two helices bundled together with one crossover. We also generated double-stranded DNAs to compare electronic properties to decipher the effects of crossovers and bundle formations. We demonstrate that density of states and band gap of DNA origami depend on its sequence and structure. The crossover regions could reduce the conductance due to a lack of available states near the HOMO level. Furthermore, we reveal that, despite having the same sequence, the two helices in the DNA origami structure could exhibit different electronic properties, and electrode position can affect the resulting conductance values. Our study provides better understanding of the electronic properties of DNA origamis and enables us to tune these properties for electronic applications such as nanowires, switches, and logic gates.
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Affiliation(s)
- Busra Demir
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Caglanaz Akin Gultakti
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - Zeynep Koker
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - M. P. Anantram
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
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2
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Gupta N, Wilkinson EA, Karuppannan SK, Bailey L, Vilan A, Zhang Z, Qi DC, Tadich A, Tuite EM, Pike AR, Tucker JHR, Nijhuis CA. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions. J Am Chem Soc 2021; 143:20309-20319. [PMID: 34826219 PMCID: PMC8662729 DOI: 10.1021/jacs.1c09549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.
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Affiliation(s)
- Nipun
Kumar Gupta
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Edward A. Wilkinson
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Senthil Kumar Karuppannan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Lily Bailey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ziyu Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Dong-Chen Qi
- Centre
for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Anton Tadich
- Australian
Synchrotron Clayton, 800 Blackburn Rd, Clayton, Victoria 3168, Australia
| | - Eimer M. Tuite
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Andrew R. Pike
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Christian A. Nijhuis
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science and Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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3
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Valdiviezo J, Clever C, Beall E, Pearse A, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions. Biochemistry 2021; 60:1368-1378. [PMID: 33870693 DOI: 10.1021/acs.biochem.1c00072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a G-block structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even-odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA-electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Caleb Clever
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Edward Beall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Pearse
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yookyung Bae
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| | - David H Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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4
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Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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5
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Aggarwal A, Bag S, Venkatramani R, Jain M, Maiti PK. Multiscale modelling reveals higher charge transport efficiencies of DNA relative to RNA independent of mechanism. NANOSCALE 2020; 12:18750-18760. [PMID: 32970051 DOI: 10.1039/d0nr02382e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we compare the charge transport properties of multiple double-stranded (ds)RNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA : RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in the coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has a smaller end-to-end length relative to that of dsDNA.
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Affiliation(s)
- Abhishek Aggarwal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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6
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Mukhopadhyay A, Bernard B, Liu K, Paulino V, Liu C, Donley C, Olivier JH. Molecular Strategies to Modulate the Electrochemical Properties of P-Type Si(111) Surfaces Covalently Functionalized with Ferrocene and Naphthalene Diimide. J Phys Chem B 2019; 123:11026-11041. [DOI: 10.1021/acs.jpcb.9b09812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Arindam Mukhopadhyay
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Brianna Bernard
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Kaixuan Liu
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Victor Paulino
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Chuan Liu
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Carrie Donley
- Chapel Hill Analytical and Nanofabrication Laboratory, Department of Applied Physical Sciences, University of North Carolina, 243 Chapman Hall, Chapel Hill, North Carolina 27599, United States
| | - Jean-Hubert Olivier
- Department of Chemistry, University of Miami, Cox Science Center, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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7
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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8
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Moneo A, González-Orive A, Bock S, Fenero M, Herrer IL, Milan DC, Lorenzoni M, Nichols RJ, Cea P, Perez-Murano F, Low PJ, Martin S. Towards molecular electronic devices based on 'all-carbon' wires. NANOSCALE 2018; 10:14128-14138. [PMID: 29999063 DOI: 10.1039/c8nr02347f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nascent molecular electronic devices based on linear 'all-carbon' wires attached to gold electrodes through robust and reliable C-Au contacts are prepared via efficient in situ sequential cleavage of trimethylsilyl end groups from an oligoyne, Me3Si-(C[triple bond, length as m-dash]C)4-SiMe3 (1). In the first stage of the fabrication process, removal of one trimethylsilyl (TMS) group in the presence of a gold substrate, which ultimately serves as the bottom electrode, using a stoichiometric fluoride-driven process gives a highly-ordered monolayer, Au|C[triple bond, length as m-dash]CC[triple bond, length as m-dash]CC[triple bond, length as m-dash]CC[triple bond, length as m-dash]CSiMe3 (Au|C8SiMe3). In the second stage, treatment of Au|C8SiMe3 with excess fluoride results in removal of the remaining TMS protecting group to give a modified monolayer Au|C[triple bond, length as m-dash]CC[triple bond, length as m-dash]CC[triple bond, length as m-dash]CC[triple bond, length as m-dash]CH (Au|C8H). The reactive terminal C[triple bond, length as m-dash]C-H moiety in Au|C8H can be modified by 'click' reactions with (azidomethyl)ferrocene (N3CH2Fc) to introduce a redox probe, to give Au|C6C2N3HCH2Fc. Alternatively, incubation of the modified gold substrate supported monolayer Au|C8H in a solution of gold nanoparticles (GNPs), results in covalent attachment of GNPs on top of the film via a second alkynyl carbon-Au σ-bond, to give structures Au|C8|GNP in which the monolayer of linear, 'all-carbon' C8 chains is sandwiched between two macroscopic gold contacts. The covalent carbon-surface bond as well as the covalent attachment of the metal particles to the monolayer by cleavage of the alkyne C-H bond is confirmed by surface-enhanced Raman scattering (SERS). The integrity of the carbon chain in both Au|C6C2N3HCH2Fc systems and after formation of the gold top-contact electrode in Au|C8|GNP is demonstrated through electrochemical methods. The electrical properties of these nascent metal-monolayer-metal devices Au|C8|GNP featuring 'all-carbon' molecular wires were characterised by sigmoidal I-V curves, indicative of well-behaved junctions free of short circuits.
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Affiliation(s)
- Andrea Moneo
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain.
| | - Alejandro González-Orive
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain. and Instituto de Nanociencia de Aragón (INA) and Laboratorio de Microscopías Avanzadas (LMA), edificio i+d Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain
| | - Sören Bock
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Marta Fenero
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain. and Instituto de Nanociencia de Aragón (INA) and Laboratorio de Microscopías Avanzadas (LMA), edificio i+d Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain
| | - I Lucía Herrer
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain. and Instituto de Nanociencia de Aragón (INA) and Laboratorio de Microscopías Avanzadas (LMA), edificio i+d Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain
| | - David C Milan
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Matteo Lorenzoni
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Richard J Nichols
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, UK
| | - Pilar Cea
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain. and Instituto de Nanociencia de Aragón (INA) and Laboratorio de Microscopías Avanzadas (LMA), edificio i+d Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain
| | - Francesc Perez-Murano
- Instituto de Microelectrónica de Barcelona (IMB-CNM, CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Paul J Low
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Santiago Martin
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Spain. and Instituto de Ciencias de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, 50009 Zaragoza, Spain
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9
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Maitarad A, Poomsuk N, Vilaivan C, Vilaivan T, Siriwong K. Insight into a conformation of the PNA-PNA duplex with (2′R,4′R)- and (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbones. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Beall E, Ulku S, Liu C, Wierzbinski E, Zhang Y, Bae Y, Zhang P, Achim C, Beratan DN, Waldeck DH. Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes. J Am Chem Soc 2017; 139:6726-6735. [PMID: 28434220 DOI: 10.1021/jacs.7b02260] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G0, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.
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Affiliation(s)
- Edward Beall
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Selma Ulku
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Chaoren Liu
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Emil Wierzbinski
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Yuqi Zhang
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Yookyung Bae
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Peng Zhang
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - Catalina Achim
- Chemistry Department, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - David N Beratan
- Chemistry Department, Duke University , Durham, North Carolina 27708, United States
| | - David H Waldeck
- Chemistry Department, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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11
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Seth C, Kaliginedi V, Suravarapu S, Reber D, Hong W, Wandlowski T, Lafolet F, Broekmann P, Royal G, Venkatramani R. Conductance in a bis-terpyridine based single molecular breadboard circuit. Chem Sci 2017; 8:1576-1591. [PMID: 28451287 PMCID: PMC5359913 DOI: 10.1039/c6sc03204d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/03/2016] [Indexed: 12/30/2022] Open
Abstract
Controlling charge flow in single molecule circuits with multiple electrical contacts and conductance pathways is a much sought after goal in molecular electronics. In this joint experimental and theoretical study, we advance the possibility of creating single molecule breadboard circuits through an analysis of the conductance of a bis-terpyridine based molecule (TP1). The TP1 molecule can adopt multiple conformations through relative rotations of 7 aromatic rings and can attach to electrodes in 61 possible single and multi-terminal configurations through 6 pyridyl groups. Despite this complexity, we show that it is possible to extract well defined conductance features for the TP1 breadboard and assign them rigorously to the underlying constituent circuits. Mechanically controllable break-junction (MCBJ) experiments on the TP1 molecular breadboard show an unprecedented 4 conductance states spanning a range 10 -2G0 to 10 -7G0. Quantitative theoretical examination of the conductance of TP1 reveals that combinations of 5 types of single terminal 2-5 ring subcircuits are accessed as a function of electrode separation to produce the distinct conductance steps observed in the MCBJ experiments. We estimate the absolute conductance for each single terminal subcircuit and its percentage contribution to the 4 experimentally observed conductance states. We also provide a detailed analysis of the role of quantum interference and thermal fluctuations in modulating conductance within the subcircuits of the TP1 molecular breadboard. Finally, we discuss the possible development of molecular circuit theory and experimental advances necessary for mapping conductance through complex single molecular breadboard circuits in terms of their constituent subcircuits.
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Affiliation(s)
- Charu Seth
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400 005 , India .
| | - Veerabhadrarao Kaliginedi
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3, CH-3012 , Bern , Switzerland .
| | - Sankarrao Suravarapu
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3, CH-3012 , Bern , Switzerland .
| | - David Reber
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3, CH-3012 , Bern , Switzerland .
| | - Wenjing Hong
- Department of Chemical and Biochemical Engineering , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Thomas Wandlowski
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3, CH-3012 , Bern , Switzerland .
| | - Frédéric Lafolet
- Université Grenoble Alpes , Département de Chimie Moléculaire , UMR CNRS-5250 , Institut de Chimie Moléculaire de Grenoble , FR CNRS-2607 , BP 53 , 38041 Grenoble Cedex 9 , France .
| | - Peter Broekmann
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3, CH-3012 , Bern , Switzerland .
| | - Guy Royal
- Université Grenoble Alpes , Département de Chimie Moléculaire , UMR CNRS-5250 , Institut de Chimie Moléculaire de Grenoble , FR CNRS-2607 , BP 53 , 38041 Grenoble Cedex 9 , France .
| | - Ravindra Venkatramani
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400 005 , India .
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12
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Liu C, Beratan DN, Zhang P. Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise. J Phys Chem B 2016; 120:3624-33. [DOI: 10.1021/acs.jpcb.6b01018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chaoren Liu
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Departments
of Biochemistry and Physics, Duke University, Durham, North Carolina 27708, United States
| | - Peng Zhang
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
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13
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Amdursky N, Sepunaru L, Raichlin S, Pecht I, Sheves M, Cahen D. Electron Transfer Proteins as Electronic Conductors: Significance of the Metal and Its Binding Site in the Blue Cu Protein, Azurin. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2015; 2:1400026. [PMID: 27980928 PMCID: PMC5115354 DOI: 10.1002/advs.201400026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/08/2015] [Indexed: 05/07/2023]
Abstract
Electron transfer (ET) proteins are biomolecules with specific functions, selected by evolution. As such they are attractive candidates for use in potential bioelectronic devices. The blue copper protein azurin (Az) is one of the most-studied ET proteins. Traditional spectroscopic, electrochemical, and kinetic methods employed for studying ET to/from the protein's Cu ion have been complemented more recently by studies of electrical conduction through a monolayer of Az in the solid-state, sandwiched between electrodes. As the latter type of measurement does not require involvement of a redox process, it also allows monitoring electronic transport (ETp) via redox-inactive Az-derivatives. Here, results of macroscopic ETp via redox-active and -inactive Az derivatives, i.e., Cu(II) and Cu(I)-Az, apo-Az, Co(II)-Az, Ni(II)-Az, and Zn(II)-Az are reported and compared. It is found that earlier reported temperature independence of ETp via Cu(II)-Az (from 20 K until denaturation) is unique, as ETp via all other derivatives is thermally activated at temperatures >≈200 K. Conduction via Cu(I)-Az shows unexpected temperature dependence >≈200 K, with currents decreasing at positive and increasing at negative bias. Taking all the data together we find a clear compensation effect of Az conduction around the Az denaturation temperature. This compensation can be understood by viewing the Az binding site as an electron trap, unless occupied by Cu(II), as in the native protein, with conduction of the native protein setting the upper transport efficiency limit.
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Affiliation(s)
- Nadav Amdursky
- Departments of Materials and Interfaces Weizmann Institute of Science Rehovot 76100 Israel; Departments of Organic Chemistry Weizmann Institute of Science Rehovot 76100 Israel
| | - Lior Sepunaru
- Departments of Materials and Interfaces Weizmann Institute of Science Rehovot 76100 Israel
| | - Sara Raichlin
- Departments of Materials and Interfaces Weizmann Institute of Science Rehovot 76100 Israel; Departments of Organic Chemistry Weizmann Institute of Science Rehovot 76100 Israel
| | - Israel Pecht
- Departments of Immunology Weizmann Institute of Science Rehovot 76100 Israel
| | - Mordechai Sheves
- Departments of Organic Chemistry Weizmann Institute of Science Rehovot 76100 Israel
| | - David Cahen
- Departments of Materials and Interfaces Weizmann Institute of Science Rehovot 76100 Israel
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14
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Intermediate tunnelling–hopping regime in DNA charge transport. Nat Chem 2015; 7:221-6. [DOI: 10.1038/nchem.2183] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/14/2015] [Indexed: 12/22/2022]
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15
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Yin X, Kong J, De Leon A, Li Y, Ma Z, Wierzbinski E, Achim C, Waldeck DH. Luminescence quenching by photoinduced charge transfer between metal complexes in peptide nucleic acids. J Phys Chem B 2014; 118:9037-45. [PMID: 24975518 DOI: 10.1021/jp5027042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.
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Affiliation(s)
- Xing Yin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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16
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Abstract
Biological electron-transfer (ET) reactions are typically described in the framework of coherent two-state electron tunneling or multistep hopping. However, these ET reactions may involve multiple redox cofactors in van der Waals contact with each other and with vibronic broadenings on the same scale as the energy gaps among the species. In this regime, fluctuations of the molecular structures and of the medium can produce transient energy level matching among multiple electronic states. This transient degeneracy, or flickering electronic resonance among states, is found to support coherent (ballistic) charge transfer. Importantly, ET rates arising from a flickering resonance (FR) mechanism will decay exponentially with distance because the probability of energy matching multiple states is multiplicative. The distance dependence of FR transport thus mimics the exponential decay that is usually associated with electron tunneling, although FR transport involves real carrier population on the bridge and is not a tunneling phenomenon. Likely candidates for FR transport are macromolecules with ET groups in van der Waals contact: DNA, bacterial nanowires, multiheme proteins, strongly coupled porphyrin arrays, and proteins with closely packed redox-active residues. The theory developed here is used to analyze DNA charge-transfer kinetics, and we find that charge-transfer distances up to three to four bases may be accounted for with this mechanism. Thus, the observed rapid (exponential) distance dependence of DNA ET rates over distances of ≲ 15 Å does not necessarily prove a tunneling mechanism.
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17
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Yin X, Wierzbinski E, Lu H, Bezer S, de Leon AR, Davis KL, Achim C, Waldeck DH. A three-step kinetic model for electrochemical charge transfer in the hopping regime. J Phys Chem A 2014; 118:7579-89. [PMID: 24813905 DOI: 10.1021/jp502826e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-step nonadiabatic electron tunneling models are widely used to analyze electrochemical rates through self-assembled monolayer films (SAMs). For some systems, such as nucleic acids, long-range charge transfer can occur in a "hopping" regime that involves multiple charge transfer events and intermediate states. This report describes a three-step kinetic scheme to model charge transfer in this regime. Some of the features of the three-step model are probed experimentally by changing the chemical composition of the SAM. This work uses the three-step model and a temperature dependence of the charge transfer rate to extract the charge injection barrier for a SAM composed of a 10-mer peptide nucleic acid that operates in the hopping regime.
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Affiliation(s)
- Xing Yin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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18
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Venkatramani R, Wierzbinski E, Waldeck DH, Beratan DN. Breaking the simple proportionality between molecular conductances and charge transfer rates. Faraday Discuss 2014; 174:57-78. [DOI: 10.1039/c4fd00106k] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A theoretical framework is presented to describe and to understand the observed relationship between molecular conductances and charge transfer rates across molecular bridges as a function of length, structure, and charge transfer mechanism. The approach uses a reduced density matrix formulation with a phenomenological treatment of system–bath couplings to describe charge transfer kinetics and a Green's function based Landauer–Buttiker method to describe steady-state currents. Application of the framework is independent of the transport regime and includes bath-induced decoherence effects. This model shows that the relationship between molecular conductances and charge transfer rates follows a power-law. The nonlinear rate–conductance relationship is shown to arise from differences in the charge transport barrier heights and from differences in environmental decoherence rates for the two experiments. This model explains otherwise puzzling correlations between molecular conductances and electrochemical kinetics.
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Affiliation(s)
- Ravindra Venkatramani
- Department of Chemical Sciences
- Tata Institute of Fundamental Research
- Mumbai 400 005, India
- Department of Chemistry
- Duke University
| | | | | | - David N. Beratan
- Department of Chemistry
- Duke University
- Durham, USA
- Departments of Biochemistry and Physics
- Duke University
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19
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Abstract
Not long after the discovery of the double-helical structure of DNA in 1952, researchers proposed that charge transfer along a one-dimensional π-array of nucleobases might be possible. At the end of the 1990s researchers discovered that a positive charge (a hole) generated in DNA migrates more than 200 Å along the structure, a discovery that ignited interest in the charge-transfer process in DNA. As a result, DNA became an interesting potential bottom-up material for constructing nanoelectronic sensors and devices because DNA can form various complex two-dimensional and three-dimensional structures, such as smiley faces and cubes. From the fundamental aspects of the hole transfer process, DNA is one of the most well-studied organic molecules with many reports on the synthesis of artificial nucleobase analogues. Thus, DNA offers a unique system to study how factors such as the HOMO energy and molecular flexibility affect hole transfer kinetics. Understanding the hole transfer mechanism requires a discussion of the hole transfer rate constants (kHT). This Account reviews the kHT values determined by our group and by Lewis and Wasielewski's group, obtained by a combination of the synthesis of modified DNA and time-resolved spectroscopy. DNA consists of G/C and A/T base pairs; the HOMO localizes on the purine bases G and A, and G has a lower oxidation potential and a higher energy HOMO. Typically, long-range hole transfer proceeded via sequential hole transfer between G/C's. The kinetics of this process in DNA sequences, including those with mismatches, is reproducible via kinetic modeling using the determined kHT for each hole transfer step between G/C's. We also determined the distance dependence parameter (β), which describes the steepness of the exponential decrease of kHT. Because of this value, >0.6 Å(-1) for hole transfer in DNA, DNA itself does not serve as a molecular wire. Interestingly, hole transfer proceeded exceptionally fast for some sequences in which G/C's are located close to each other, an observation that we cannot explain by a simple sequential hole transfer between G/C's but rather through hole delocalization over the nucleobases. To further investigate and refine the factors that affect kHT, we examined various artificial nucleobases. We clearly demonstrated that kHT depends strongly on the HOMO energy gap between the bases (ΔHOMO), and that kHT can be increased with decreasing ΔHOMO. We reduced ΔHOMO between the two type of base pairs by replacing adenines (A's) with deazaadenines ((z)A's) or diaminopurines (D's) and showed that the hole transfer rate through the G/C and A/T mix sequence increased by more than 3 orders of magnitude. We also investigated how DNA flexibility affects kHT. Locked nucleic acid (LNA) modification, which makes DNA more rigid, lowered kHT by more than 2 orders of magnitude. On the other hand, 5-Me-2'-deoxyzebularine (B) modification, which increases DNA flexibility, increased kHT by more than 1 order of magnitude. These new insights in hole transfer kinetics obtained from modified DNAs may aid in the design of new molecular-scale conducting materials.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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20
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Wierzbinski E, Venkatramani R, Davis KL, Bezer S, Kong J, Xing Y, Borguet E, Achim C, Beratan DN, Waldeck DH. The single-molecule conductance and electrochemical electron-transfer rate are related by a power law. ACS NANO 2013; 7:5391-401. [PMID: 23692478 DOI: 10.1021/nn401321k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes and peptide nucleic acid (PNA) oligomers as a function of the length, structure, and charge transport mechanism. The experimental data show a power-law relationship between conductances and charge transfer rates within a given class of molecules with the same bridge chemistry, and a lack of correlation when a more diverse group of molecules is compared, in contrast with some theoretical predictions. Surprisingly, the PNA duplexes exhibit the lowest charge-transfer rates and the highest molecular conductances. The nonlinear rate-conductance relationships for structures with the same bridging chemistries are attributed to differences in the charge-mediation characteristics of the molecular bridge, energy barrier shifts and electronic dephasing, in the two different experimental settings.
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Affiliation(s)
- Emil Wierzbinski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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21
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Sek S. Review peptides and proteins wired into the electrical circuits: An SPM-based approach. Biopolymers 2013; 100:71-81. [DOI: 10.1002/bip.22148] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/26/2012] [Accepted: 08/08/2012] [Indexed: 12/30/2022]
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22
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Skourtis SS. Reviewprobing protein electron transfer mechanisms from the molecular to the cellular length scales. Biopolymers 2013; 100:82-92. [DOI: 10.1002/bip.22169] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/14/2012] [Accepted: 09/23/2012] [Indexed: 11/10/2022]
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23
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Osakada Y, Kawai K, Majima T. Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Yasuko Osakada
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University
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24
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Wierzbinski E, Yin X, Werling K, Waldeck DH. The Effect of Oxygen Heteroatoms on the Single Molecule Conductance of Saturated Chains. J Phys Chem B 2012; 117:4431-41. [DOI: 10.1021/jp307902v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Emil Wierzbinski
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xing Yin
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Keith Werling
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David H. Waldeck
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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25
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Amdursky N, Pecht I, Sheves M, Cahen D. Doping Human Serum Albumin with Retinoate Markedly Enhances Electron Transport across the Protein. J Am Chem Soc 2012; 134:18221-4. [DOI: 10.1021/ja308953q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nadav Amdursky
- Departments of †Materials and Interfaces, ‡Organic Chemistry, and §Immunology, Weizmann Institute of Science, Rehovot
76100, Israel
| | - Israel Pecht
- Departments of †Materials and Interfaces, ‡Organic Chemistry, and §Immunology, Weizmann Institute of Science, Rehovot
76100, Israel
| | - Mordechai Sheves
- Departments of †Materials and Interfaces, ‡Organic Chemistry, and §Immunology, Weizmann Institute of Science, Rehovot
76100, Israel
| | - David Cahen
- Departments of †Materials and Interfaces, ‡Organic Chemistry, and §Immunology, Weizmann Institute of Science, Rehovot
76100, Israel
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26
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Breuer R, Schmittel M. Redox-Stable SAMs in Water (pH 0–12) from 1,1′-Biferrocenylene-Terminated Thiols on Gold. Organometallics 2012. [DOI: 10.1021/om300718k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rochus Breuer
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Straße
2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering, Organische Chemie I, Universität Siegen, Adolf-Reichwein-Straße
2, D-57068 Siegen, Germany
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27
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Thuo MM, Reus WF, Simeone FC, Kim C, Schulz MD, Yoon HJ, Whitesides GM. Replacing −CH2CH2– with −CONH– Does Not Significantly Change Rates of Charge Transport through AgTS-SAM//Ga2O3/EGaIn Junctions. J Am Chem Soc 2012; 134:10876-84. [DOI: 10.1021/ja301778s] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Martin M. Thuo
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - William F. Reus
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Felice C. Simeone
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Choongik Kim
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Michael D. Schulz
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Hyo Jae Yoon
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department
of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
- Kavli Institute for Bionano Science & Technology, School of Engineering and Applied Sciences, Harvard University, Pierce Hall, 29 Oxford Street, Cambridge, Massachusetts 02138, United States
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28
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Kawai K, Hayashi M, Majima T. Hole transfer in LNA and 5-Me-2'-deoxyzebularine-modified DNA. J Am Chem Soc 2012; 134:9406-9. [PMID: 22591000 DOI: 10.1021/ja302641e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the measurement of hole-transfer rate constants (k(ht)) in locked nucleic acid (LNA) and 5-Me-2'-deoxyzebularine (B)-modified DNA. LNA modification, which makes DNA more rigid, caused a decrease of more than 2 orders of magnitude in k(ht), whereas B modification, which increases DNA flexibility, increased k(ht) by more than 20-fold. The present results clearly showed that hole-transfer efficiency in DNA can be increased by increasing DNA flexibility.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan.
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29
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Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Reppireddy S, Venkatramani R, Keinan S, Ly DH, Madrid M, Beratan DN, Achim C, Waldeck DH. Effect of Backbone Flexibility on Charge Transfer Rates in Peptide Nucleic Acid Duplexes. J Am Chem Soc 2012; 134:9335-42. [DOI: 10.1021/ja301677z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emil Wierzbinski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Arnie de Leon
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Xing Yin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Alexander Balaeff
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Kathryn L. Davis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Srinivas Reppireddy
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Ravindra Venkatramani
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Shahar Keinan
- Department
of Chemistry, Duke University, Durham,
North Carolina 27708, United
States
| | - Danith H. Ly
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - Marcela Madrid
- Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania 15213, United States
| | - David N. Beratan
- Departments of Chemistry, Biochemistry,
and Physics, Duke University, Durham, North
Carolina 27708, United States
| | - Catalina Achim
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
15213, United States
| | - David H. Waldeck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
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30
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Siriwong K, Voityuk AA. Electron transfer in DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1102] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Kawai K, Hayashi M, Majima T. HOMO energy gap dependence of hole-transfer kinetics in DNA. J Am Chem Soc 2012; 134:4806-11. [PMID: 22335550 DOI: 10.1021/ja2109213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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32
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Wierzbinski E, de Leon A, Davis KL, Bezer S, Wolak MA, Kofke MJ, Schlaf R, Achim C, Waldeck DH. Charge transfer through modified peptide nucleic acids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1971-1981. [PMID: 22217076 DOI: 10.1021/la204445u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We studied the charge transfer properties of bipyridine-modified peptide nucleic acid (PNA) in the absence and presence of Zn(II). Characterization of the PNA in solution showed that Zn(II) interacts with the bipyridine ligands, but the stability of the duplexes was not affected significantly by the binding of Zn(II). The charge transfer properties of these molecules were examined by electrochemistry for self-assembled monolayers of ferrocene-terminated PNAs and by conductive probe atomic force microscopy for cysteine-terminated PNAs. Both electrochemical and single molecular studies showed that the bipyridine modification and Zn(II) binding do not affect significantly the charge transfer of the PNA duplexes.
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Affiliation(s)
- Emil Wierzbinski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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33
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Han Y, Noguchi H, Sakaguchi K, Uosaki K. Formation process and solvent-dependent structure of a polyproline self-assembled monolayer on a gold surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:11951-11957. [PMID: 21902210 DOI: 10.1021/la2020995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The formation process and structure of a self-assembled monolayer (SAM) of lipoic-acid-terminated polyproline on a gold surface in aqueous solution were investigated by several techniques. The amount of polyproline molecules on the gold surface was determined from the area of the reductive desorption peak, and orientation and thickness of the polyproline SAM were determined in situ by attenuated total reflection infrared (ATR-IR) spectroscopy and ellipsometry. The kinetics of the polyproline SAM formation process were discussed on the basis of these results. The in situ IR study confirmed that the conformation of the polyproline SAM was changed by changing the solvent from water to methanol and methanol to water, as is the case for polyproline dissolved in solution.
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Affiliation(s)
- Ying Han
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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