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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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Figazzolo C, Ma Y, Tucker JHR, Hollenstein M. Ferrocene as a potential electrochemical reporting surrogate of abasic sites in DNA. Org Biomol Chem 2022; 20:8125-8135. [DOI: 10.1039/d2ob01540d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have evaluated the possibility of replacing abasic sites with ferrocene for enzymatic synthesis of canonical and modified DNA.
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Affiliation(s)
- Chiara Figazzolo
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Learning Planet Institute, 8, rue Charles V, 75004 Paris, France
| | - Yifeng Ma
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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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: 18] [Impact Index Per Article: 6.0] [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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Nguyen HV, Zhao ZY, Sallustrau A, Horswell SL, Male L, Mulas A, Tucker JHR. A ferrocene nucleic acid oligomer as an organometallic structural mimic of DNA. Chem Commun (Camb) 2013; 48:12165-7. [PMID: 23090440 DOI: 10.1039/c2cc36428j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and electrochemical behaviour of an oligomer consisting of linked thymine-functionalised ferrocene units are reported, which, as a so-called form of ferrocene nucleic acid (FcNA), acts as a structural mimic of DNA.
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Affiliation(s)
- Huy V Nguyen
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Ihara T, Wasano T, Nakatake R, Arslan P, Futamura A, Jyo A. Electrochemical signal modulation in homogeneous solutions using the formation of an inclusion complex between ferrocene and β-cyclodextrin on a DNA scaffold. Chem Commun (Camb) 2011; 47:12388-90. [PMID: 22012412 DOI: 10.1039/c1cc15365j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Two DNA conjugates modified with ferrocene and β-cyclodextrin were prepared as a pair of probes that work cooperatively for DNA sensing, in which the electrochemical signal of ferrocene on one probe was significantly "quenched" by the formation of an inclusion complex with β-cyclodextrin of the other probe on the DNA templates.
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Affiliation(s)
- Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Kumamoto University, Kumamoto 860-8555, Japan.
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O’Donohue P, McAdam CJ, Courtney D, Ortin Y, Müller-Bunz H, Manning AR, McGlinchey MJ, Simpson J. Stilbene analogues incorporating the Co(η4-C4Ph4)(η5-C5H4-) end group. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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