THE EFFECT OF CROSS-LINKS ON THE CONFORMATIONAL DYNAMICS OF DUPLEX DNA

The base pair lifetimes and apparent dissociation constants of a 21 ba se DNA hairpin and an analog possessing a disulfide cross-link bridgin g the 3'- and 5'-terminal bases were determined by measuring imino pro ton exchange rates as a function of exchange catalyst concentration an d 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 involve d in fraying nor alters the lifetime, dissociation constant, or the op ened structure from which exchange occurs for the base pairs that are not frayed. The cross-link does, however, stabilize the frayed penulti mate base pair of the stem duplex. Significantly, it appears that the disulfide cross-link is more effective at preventing fraying of the pe nultimate base pair than is the 5 base hairpin loop, Because this disu lfide cross-link can be incorporated site specifically, and does not a dversely affect static or dynamic properties of DNA, it should prove v ery useful in studies of nucleic acid structure and function.