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Nardi AN, Olivieri A, D'Abramo M. Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations. J Phys Chem B 2022; 126:5017-5023. [PMID: 35671051 PMCID: PMC9289878 DOI: 10.1021/acs.jpcb.2c02391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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The effect of the
environment on the guanine redox potential is
studied by means of a theoretical–computational approach. Our
data, in agreement with previous experimental findings, clearly show
that the presence of consecutive guanine bases in both single- and
double-stranded DNA oligomers lowers their reduction potential. Such
an effect is even more marked when a G-rich quadruplex is considered,
where the oxidized form of guanine is particularly stabilized. To
the best of our knowledge, this is the first computational study reporting
on a quantitative estimate of the dependence of the guanine redox
potential on sequence and conformational effects in complex DNA molecules,
ranging from single-stranded DNA to G-quadruplex.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy 00185
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy 00185
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2
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:molecules27031077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
- Correspondence:
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3
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Valdiviezo J, Zhang P, Beratan DN. Electron ratcheting in self-assembled soft matter. J Chem Phys 2021; 155:055102. [PMID: 34364335 DOI: 10.1063/5.0044420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 109 V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source-drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.
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Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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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] [MESH Headings] [Track Full Text] [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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