Template directed reversible photochemical ligation of oligodeoxynucleotides

Molecules

Volumn 17, Issue 1, 2012, Pages 163-178

  Nakamura, Shigetaka ^a   Ogasawara, Shinzi ^a   Matuda, Shigeo ^b   Saito, Isao ^b   Fujimoto, Kenzo ^a  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

5 carboxyvinyldeoxyuridine; 5 vinyldeoxyuridine; DNA nanotechnology; Photochemical ligation

Indexed keywords

OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; CHEMISTRY; DNA TEMPLATE; NUCLEOTIDE SEQUENCE; PHOTOCHEMISTRY;

BASE SEQUENCE; OLIGODEOXYRIBONUCLEOTIDES; PHOTOCHEMICAL PROCESSES; TEMPLATES, GENETIC;

EID: 84856204440     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules17010163     Document Type: Article

References (25)

1. Lohman, G.J.; Chen, L.; Evans, T.C. Kinetic characterization of single strand break ligation in duplex DNA by T4 DNA Ligase. J. Biol. Chem. 2011, 286,44187-44196.
2. Liu, J.; Taylor, J.S. Template-directed photoligation of oligodeoxyribonucleotides via 4-thiothymidine. Nucleic. Acids. Res. 1998, 26, 3300-3304. (Pubitemid 28288933)
3. He, Y.; Liu, D.R. A sequential strand-displacement strategy enables efficient six-step DNA-templated synthesis. J. Am. Chem. Soc. 2011, 133, 9972-9975.
4. Gothelf, K.V.; Thomsen, A.; Nielsen, M.; Cló, E.; Brown, R.S. Modular DNA programmed assembly of linear and branched conjugated nanostructures. J. Am. Chem. Soc. 2004, 126, 1044-1046. (Pubitemid 38140733)
5. Kleiner, R.E.; Dumelin, C.E.; Tiu, G.C.; Sakurai, K.; Liu, D.R. In vitro selection of a DNA-templated small-molecule library reveals a class of macrocyclic kinase inhibitors. J. Am. Chem. Soc. 2010, 132, 11779-11791.
6. Zhou, Q.; Rokita, S.E. A general strategy for target-promoted alkylation in biological systems. Proc. Natl. Acad. Sci. USA 2003, 100, 15452-15457. (Pubitemid 38021010)
7. Yoshinaga, Y.; Daisuke, O.; Masayuki, O.; Kenzo, F. Highly selective and sensitive templatedirected photoligation of DNA via 5-carbamoylvinyl-2- deoxyuridine. Org. Lett. 2006, 8, 5049.
8. Leubke, K.J.; Dervan, P.B. Nonenzymatic ligation of oligodeoxyribonucleotides on a duplex DNA template by triple-helix formation. J. Am. Chem. Soc. 1987, 111, 8733-8735. (Pubitemid 20021827)
9. El-Sagheer, A.H.; Cheong, V.V.; Brown, T. Rapid chemical ligation of oligonucleotides by the Diels-Alder reaction. Org. Biomol. Chem. 2011, 9, 232-235.
10. Lewis, R.J.; Hanawalt, P.S. Nick sealing T4 DNA ligase on a modified DNA template: Tethering a functional molecules on D-threoninol. Nature 1982, 298, 393.
11. Ligang, Z.; Hai, L.; George, C.S.; Frederick, D.L. Synthesis and properties of nicked dumbbell and bumbbell DNA conjugates having stilbenedicarboxamide linkers. Org. Biomol. Chem. 2007, 5, 450-456.
12. Ihara, T.; Fuji, T.; Mukae, M.; Kitamura, Y.; Jyo, A. Photochemical ligation of DNA conjugates through anthracene cyclodimer formation and its fidelity to the template sequences. J. Am. Chem. Soc. 2004, 126, 8880-8881. (Pubitemid 38971046)
13. Fujimoto, K.; Matuda, S.; Takahashi, N.; Saito, Isao. Template-directed photoreversible ligation of deoxyoligonucleotides via 5-vinydeoxyuridine. J. Am. Chem. Soc. 2000, 122, 5646-5647. (Pubitemid 30431088)
14. You, Y.H.; Lee, D.H.; Yoon, J.H.; Nakajima, S.; Yasui, A.; Pfeifer, G.P. Cyclobutane pyrimidine dimers are responsible for the vast majority of mutations induced by UVB irradiation in mammalian cells. J. Biol. Chem. 2001, 276, 44688-44694.
15. Ogasawara, S.; Fujimoto, K. A novel method to synthesize versatile multiple-branched DNA (MB-DNA) by reversible photochemical ligation. Chem. Biol. Chem. 2005, 10, 1756.
16. Fujimoto, K.; Matuda, S.; Ogawa, N; Hayashi, M.; Saito, I. Template-directed reversible photocircularization of DNA via 5-vinyldeoxycytidine. Tetrahedron Lett. 2000, 41, 6451-6454. (Pubitemid 30646388)
17. Nakamura, F.; Ito, E.; Sakao, Y.; Ueno, N.; Gatuna, I.N.; Ohuchi, F.S.; Hara, M. Preparation of a branched DNA self-assembled monolayer toward sensitive dna biosensors. Nano. Lett. 2003, 3, 1083-1086 (Pubitemid 37289300)
18. Becerril, H.A.; Stoltenberg, R.M.; Wheeler, D.R.; Davis, R.C.; Harb, J.N.; Woolley, A.T. DNA-templated three-branched nanostructures for nanoelectronic devices. J. Am. Chem. Soc. 2005, 127, 2828-2829. (Pubitemid 40349841)
19. Ogasawara, S.; Ami, T.; Fujimoto, K. Autonomous DNA computing machine based on photochemical gate transition. J. Am. Chem. Soc. 2008, 130, 10050-10051.
20. Seeman, N.C. Nucleic acid junction and lattices. J. Theor. Biol. 1982, 99, 237-247.
21. Pothemund, P.W. Folding DNA to create nanoscale shaped and patterns. Nature 2006, 16, 297-302.
22. Lehman, I.R. DNA ligase: Structure, mechanism, and function. Science 1974, 29, 790-797.
23. Rinker, S.; Ke, Y.; Liu, Y.; Chhabra, R.; Yan, H. Self-assembled DNA nanostructures for distance dependent multivalent ligand-protein binding. Nat. Nanotechnol. 2008, 3, 418-422.
24. Maniatis, T.; Fritsch, E.F.; Sambrool, J. Molecular Cloning; Cold Spring Harbor Laboratory Press: Plainview, New York, NY, USA, 1982.
25. Sambrook, J.; Fritsch, E.F.; Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd ed.; Cold Spring Harbor Laboratory Press: New York, NY, USA, 1989.