The interaction of β-cyclodextrin with dinucleoside phosphates

Circular dichroism studies of the interaction of β-cyclodextrin with a series of eight dinucleoside phosphates, and with 3′-AMP are reported. From results with ApU and ApA, it is shown that β-cyclodextrin binding is sensitive to dinucleoside stacking in approximately the same way as optical measures of stacking. Some qualitative uses of β-cyclodextrin binding are suggested, based on the fact that the change in the CD spectrum caused by cyclodextrin binding is unique to each of the dinucleosides studied. Hoffman and Bock have previously suggested the use of β-cyclodextrin as a probe of nucleic acid structure. Their work indicated that only binding to adenosine and inosine would have to be considered. The present paper shows that binding to other bases cannot be neglected, and will impose serious restrictions on the use of β-cyclodextrin as a structural probe.