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Origins of high sequence selectivity: a stopped-flow kinetics study of DNA/RNA hybridization by duplex- and triplex-forming oligonucleotides

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dc.contributor.author Wang, Shaohui en_US
dc.contributor.author Friedman, Alan en_US
dc.contributor.author Kool, Eric en_US
dc.date.accessioned 2006-08-18T15:00:47Z en_US
dc.date.available 2006-08-18T15:00:47Z en_US
dc.date.issued 1995-08-01 en_US
dc.identifier.citation Biochemistry 34N30 (1995) 9774-9784 en_US
dc.identifier.issn 1520-4995 en_US
dc.identifier.uri http://hdl.handle.net/1850/2299 en_US
dc.description.abstract Stopped-flow UV kinetics and thermal denaturation experiments are used to examine the origins of high sequence selectivity and binding affinity of circular triplex-forming oligonucleotides with single-stranded DNA/RNA targets. These 34-nt probes are hybridized to a series of 12-nt target sequences which are fully complementary or which contain a single mismatch. Also studied for comparison are standard 12-nt Watson-Crick DNA or RNA complements. Several novel findings are described: (1) Circular triplex-forming oligomers bind targets with very high thermodynamic selectivity (up to 8- 10 kcal/mol against a single-nucleotide mismatch), while linear strands show only 2- 3 kcal/mol selectivity. (2) Rates for triplex formation by circular ligands are much greater than other reported triplex formation modes and are nearly the same as for Watson-Crick duplex formation. (3) DNA-DNA and RNARNA hybridization rates are similar for both duplex and triplex formation. (4) For both modes of binding, hybridization rates do not vary when a mismatch is introduced into the target, and, therefore, binding selectivity is reflected in large variations in dissociation, rather than association rates. Finally, (5) binding selectivity of circular ligands becomes significantly greater as pH is lowered; results indicate that the high sequence selectivity of the circular DNA ligand is due in large part to the special stability of the protonated CfG-C triad relative to unprotonated mismatched triads. The results are useful in the understanding of properties of nucleic acid complexes in general and give insight into optimum design for synthetic DNA-binding ligands. en_US
dc.description.sponsorship This work was supported by the National Institutes of Health (GM46625). E.T.K. also acknowledges awards from the Office of Naval Research, the Army Research Office, and an American Cyanamid Faculty Award. en_US
dc.format.extent 31371 bytes en_US
dc.format.mimetype application/pdf en_US
dc.language.iso en_US en_US
dc.publisher The American Chemical Society: Biochemistry en_US
dc.subject Hybridization en_US
dc.subject Kinetics en_US
dc.subject Nucleic acid complexes en_US
dc.title Origins of high sequence selectivity: a stopped-flow kinetics study of DNA/RNA hybridization by duplex- and triplex-forming oligonucleotides en_US
dc.type Abstract en_US
dc.identifier.url http://dx.doi.org/10.1021/bi00030a015

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