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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.

SynopsisFrom the study of circular dichroism (CI)) spect.ra and hypochroniism we conclude that t,he diriucleoside phosphates IpA, ApI, and IpI stack, while IpU stacks very little. St>rtdies wit,h various concentrations of IpI in low salt arid 1M NaCl indicate that the st,acking geometry of this compound is sensitive to the ionic strength of soliition. The CI) of poly I is presented and compared to the data for IpI. Little chaiige was found in the CI) of poly ((-;,I) (1: 1) with change of salt concentration, and we conclude that, inilike poly I, there is no major struct.ura1 change. From the CD of poly (G,I), IpI, and GpC, the CI) of Ip(: plus GpI is calculat,ed by using the nearest-neighbor approximation. From the calculated spectnim, we tentatively conchide that there is stacking in either IpG or(;pI or both.

The possible difference in conformation between aminoacylated and deacylated tRNA is examined using the optical and photochemical properties of the 4-thiouridine residue of E coli tRNAf(Met). No differences were seen between fMet-tRNAf(Met) and tRNAf(Met) observing the native fluorescence of 4-thiouridine, energy transfer from 4-thiouridine to the bound lanthanide ions, Tb3+ or Eu3+, or the rates of the photochemical cross-linking reaction of 4-thiourdine. While these results do not necessarily mean that there is no conformational difference between the aminoacylated and deacylated species, they do restrict the possible nature and magnitude of any conformational difference between the two species. In addition, preliminary thermal denaturation studies of tRNAf(Met), monitoring 4-thiouridine emission and energy transfer to Tb3+, indicate an unexplained melting phenomenon near 25 degrees C in the presence of Mg2+.