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Nucleic Acids Research, Vol 25, Issue 4 836-842, Copyright © 1997 by Oxford University Press

ARTICLES

The effect of cross-links on the conformational dynamics of duplex DNA [published erratum appears in Nucleic Acids Res 1997 Apr 15;25(8):164]

RJ Cain and GD Glick
University of Michigan, Department of Chemistry, Ann Arbor 48109-1055, USA.

The base pair lifetimes and apparent dissociation constants of a 21 base DNA hairpin and an analog possessing a disulfide cross-link bridging the 3'- and 5'-terminal bases were determined by measuring imino proton exchange rates as a function of exchange catalyst concentration and temperature. A comparison of the lifetimes and apparent dissociation constants for corresponding base pairs of the two hairpins indicates that the cross-link neither increases the number of base pairs involved in fraying nor alters the lifetime, dissociation constant, or the opened structure from which exchange occurs for the base pairs that are not frayed. The cross-link does, however, stabilize the frayed penultimate base pair of the stem duplex. Significantly, it appears that the disulfide cross-link is more effective at preventing fraying of the penultimate base pair than is the 5 base hairpin loop. Because this disulfide cross-link can be incorporated site specifically, and does not adversely affect static or dynamic properties of DNA, it should prove very useful in studies of nucleic acid structure and function.
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