NMR structure of the chimeric hybrid duplex r(gcaguggc)center dot r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

A high-quality NMR solution structure of the chimeric hybrid duplex r(gcagu ggc).r(gcca)d(CTGC) was determined using the program DYANA with its recentl y implemented new module FOUND, which performs exhaustive conformational gr id searches for dinucleotides. To ensure conservative data interpretation, the use of H-1-H-1 lower distance limit constraints was avoided. The duplex comprises the tRNA-DNA junction formed during the initiation of HIV-1 reve rse transcription. It forms an A-type double helix that exhibits distinct s tructural deviations from a standard A-conformation. In particular, the min or groove is remarkably narrow, and its width decreases from about 7.5 Angs trom in the RNA/RNA stem to about 4.5 Angstrom in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid dupl exes of similar to 11 Angstrom and similar to 8.5 Angstrom, respectively, w ere previously reported. The present, new structure supports that reverse t ranscriptase-associated RNaseH specificity is related primarily to conforma tional adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex.