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1
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Lewis FD. Distance-Dependent Electronic Interactions Across DNA Base Pairs: Charge Transport, Exciton Coupling, and Energy Transfer. Isr J Chem 2013. [DOI: 10.1002/ijch.201300035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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2
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McLeod D, McNulty J. Mild Chemical and Biological Synthesis of Donor-Acceptor Flanked Reporter Stilbenes: Demonstration of a Physiological Wittig Olefination Reaction. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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3
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Nakamura S, Ogasawara S, Matuda S, Saito I, Fujimoto K. Template directed reversible photochemical ligation of oligodeoxynucleotides. Molecules 2011; 17:163-78. [PMID: 22202805 PMCID: PMC6268978 DOI: 10.3390/molecules17010163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 12/12/2022] Open
Abstract
We demonstrated that 5-vinyldeoxyuridine ((V)U) and 5-carboxyvinyldeoxyuridine ((CV)U) can be used to photoligate a longer oligonucleotide (ODN) from smaller ODNs on a template. By performing irradiation at 366 nm, these artificial nucleotides make photoligated ODNs with high efficiency without any side reactions. Moreover, by performing irradiation at 312 nm, these photoligated ODNs were reversed to the original ODN. (V)U needs to be irradiated 366 nm for 6 h, but (CV)U needs to be irradiated at 366 nm for 15 min. Finally, we made a self-assembled structure with an ODN containing (CV)U and observed the photoligated ODN by photoirradiation.
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Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Shinzi Ogasawara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | - Shigeo Matuda
- Department of Synthetic Chemistry and Biological Chemistry, Factly of Enginnering, Kyoto University, Kyoto 606-8501, Japan
| | - Isao Saito
- Department of Synthetic Chemistry and Biological Chemistry, Factly of Enginnering, Kyoto University, Kyoto 606-8501, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
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Yoshimura Y, Okada H, Fujimoto K. Photoreversible DNA end capping for the formation of hairpin structures. Org Biomol Chem 2010; 8:1523-6. [PMID: 20237661 DOI: 10.1039/b924989c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.
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Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Bang EK, Kim BH. Synthesis of hairpin siRNA using 18β-glycyrrhetinic acid derivative as a loop motif. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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6
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Kilin DS, Tsemekhman KL, Kilina SV, Balatsky AV, Prezhdo OV. Photoinduced Conductivity of a Porphyrin−Gold Composite Nanowire. J Phys Chem A 2009; 113:4549-56. [DOI: 10.1021/jp811169c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dmitri S. Kilin
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville Florida 32611-8435, Department of Chemistry, University of Washington, Seattle Washington 98195-1700, and T-Division and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Kiril L. Tsemekhman
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville Florida 32611-8435, Department of Chemistry, University of Washington, Seattle Washington 98195-1700, and T-Division and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Svetlana V. Kilina
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville Florida 32611-8435, Department of Chemistry, University of Washington, Seattle Washington 98195-1700, and T-Division and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Alexander V. Balatsky
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville Florida 32611-8435, Department of Chemistry, University of Washington, Seattle Washington 98195-1700, and T-Division and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Oleg V. Prezhdo
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville Florida 32611-8435, Department of Chemistry, University of Washington, Seattle Washington 98195-1700, and T-Division and Center for Integrated Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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El-Sagheer AH, Brown T. Synthesis of alkyne- and azide-modified oligonucleotides and their cyclization by the CuAAC (click) reaction. ACTA ACUST UNITED AC 2009; Chapter 4:Unit 4.33. [PMID: 19085984 DOI: 10.1002/0471142700.nc0433s35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction has been used to synthesize cyclic mini-DNA duplexes. The reaction is carried out on 5'-alkyne-3'-azide-labeled hairpin loop oligonucleotides and proceeds in high yield under mild conditions in as little as 5 min. The resultant duplexes have very high thermal stability and their CD spectra are characteristic of normal B-DNA.
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Affiliation(s)
- Afaf H El-Sagheer
- School of Chemistry, University of Southampton, Highfield Southampton, UK
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McCullagh M, Zhang L, Karaba AH, Zhu H, Schatz GC, Lewis FD. Effect of Loop Distortion on the Stability and Structural Dynamics of DNA Hairpin and Dumbbell Conjugates. J Phys Chem B 2008; 112:11415-21. [DOI: 10.1021/jp802378a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Ligang Zhang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Andrew H. Karaba
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Huihe Zhu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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McCullagh M, Prytkova T, Tonzani S, Winter ND, Schatz GC. Modeling Self-Assembly Processes Driven by Nonbonded Interactions in Soft Materials. J Phys Chem B 2008; 112:10388-98. [DOI: 10.1021/jp803192u] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Tatiana Prytkova
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Stefano Tonzani
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Nicolas D. Winter
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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10
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El-Sagheer AH, Kumar R, Findlow S, Werner JM, Lane AN, Brown T. A very stable cyclic DNA miniduplex with just two base pairs. Chembiochem 2008; 9:50-2. [PMID: 18058775 DOI: 10.1002/cbic.200700538] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Afaf H El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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