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Volumn 8, Issue 20, 2002, Pages 4796-4802

Stable oligonucleotide-directed triplex formation at target sites with CG interruptions: Strong sequence-specific recognition by 2′,4′-bridged nucleic-acid-containing 2-pyridones under physiological conditions

Author keywords

Molecular recognition; Nucleic acids; Nucleobases; Oligonucleotides

Indexed keywords

DNA; MONOMERS; PHYSIOLOGY; SODIUM COMPOUNDS;

EID: 0037131487     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/1521-3765(20021018)8:20<4796::AID-CHEM4796>3.0.CO;2-O     Document Type: Article
Times cited : (39)

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    • We defined BNA as a novel class of nucleic acid analogues containing 2′-O,4′-C or 3′-O,4′-C-methylene bridged structure (2′,4′-BNA or 3′,4′-BNA, respectively). The 2′,4′-BNA has been also called "LNA": a) S. K. Singh, P. Nielsen, A. A. Koshkin, J. Wengel, Chem. Commun. 1998, 455-456; b) S. K. Singh, J. Wengel, Chem. Commun. 1998, 1247-1248; c) A. A. Koshkin, S. K. Singh, P. Nielsen, V. K. Rajwanshi, R. Kumar, M. Meldgaard, C. E. Olsen, J. Wengel, Tetrahedron 1998, 54, 3607-3630; d) J. Wengel, Acc. Chem. Res. 1999, 32, 301-310; e) L. Kværnø, J. Wengel, Chem. Commun. 1999, 657-658; f) K. Bondensgaard, M. Petersen, S. K. Singh, V. K. Rajwanshi, R. Kumar, J. Wengel, J. P. Jacobsen, Chem. Eur. J. 2000, 6, 2687-2695; g) C. Wahlestedt, P. Salmi, L. Good, J. Kela, T. Johnsson, T. Hökfelt C. Broberger, F. Porreca, J. Lai, K. Ren, M. Ossipov, A. Koshkin, N. Jakobsen, J. Skouv, H. Oerum, M. H. Jacobsen, J. Wengel, Proc. Natl. Acad. Sci. USA 2000, 97, 5633-5638.
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    • A part of this work appeared in a preliminary communication: S. Obika, Y. Hari, M. Sekiguchi, T. Imanishi, Angew. Chem. 2001, 113, 2149-2151; Angew. Chem. Int. Ed. 2001, 40, 2079-2081.
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    • note
    • CCDC-152458 contains the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ (UK): fax: (+ 44) 1-223-336-033; or deposit@ccdc.cam.ac.uk).
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    • + · GC) triads lead to a marked decrease in the stability of the DNA triplex: a) L. L. Kiessling, L. C. Griffin, P. B. Dervan, Biochemistry 1992, 31, 2829-2834; b) D. Leitner, W. Schröder, K. Weisz, Biochemistry 2000, 39, 5886-5892.
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    • + · GC) triads lead to a marked decrease in the stability of the DNA triplex: a) L. L. Kiessling, L. C. Griffin, P. B. Dervan, Biochemistry 1992, 31, 2829-2834; b) D. Leitner, W. Schröder, K. Weisz, Biochemistry 2000, 39, 5886-5892.
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    • The UV-melting curves were a little broad, probably due to restriction of flexibility of TFOs by BNA units which were introduced in every other nucleotide, but the details are not clear. Triplex formation with target duplex 27 was also confirmed by UV-melting experiments at 284 nm as a second wavelength.
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    • A few attempts to form triplexes with dsDNA containing three CG interruptions by using T-CG triads were performed: a) D. M. Gowers, K. R. Fox, Nucleic Acids Res. 1997, 25, 3787-3794; b) D. M. Gowers, J. Bijapur, T. Brown, K. R. Fox, Biochemistry 1999, 38, 13747-13758.
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    • A few attempts to form triplexes with dsDNA containing three CG interruptions by using T-CG triads were performed: a) D. M. Gowers, K. R. Fox, Nucleic Acids Res. 1997, 25, 3787-3794; b) D. M. Gowers, J. Bijapur, T. Brown, K. R. Fox, Biochemistry 1999, 38, 13747-13758.
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