SOLUTION STRUCTURE OF A DNA HAIRPIN AND ITS DISULFIDE CROSS-LINKED ANALOG

The solution structures of a 21 base long DNA hairpin derived from the ColE1 cruciform, and an analog possessing a disulfide cross-link brid ging the terminal bases, have been determined by NMR spectroscopy. The 8 bp long stem of these sequences adopts a B-form helix whereas the f ive base long single-stranded loop appears to be flexible and cannot b e represented by a unique static conformation. NOESY cross-peak volume s, proton and phosphorus chemical shifts, and both homo- and heteronuc lear coupling constants for the cross-linked hairpin are virtually ide ntical to those measured for the unmodified sequence, even for the res idues that are proximal to the cross-link. These results indicate that both hairpins are structurally isomorphous. Because this cross-link c an be incorporated site specifically in a sequence independent manner, and does not appear to alter native conformation, it should prove bro adly applicable in studies of DNA structure and function.