Minor groove hybrid duplex

An RNA-HNA (hexitol) hybrid duplex structure has been studied by NMR. " The P-P distances across the minor groove are a determinant for cleavage by RNase H. In the structure, the duplex is in an A-form, and the P-P bond distance similar to that for an RNA-RNA duplex, which may explain the resistance of HNA duplexes to RNase H. A self-complementary HNA duplex h(GCGCTTTTGCGC) containing a central T-tract has been studied by NMR. " The duplex exists in the A-form in the stem regions, with minor distortions in the T-tract causing a 9 A displacement of the helical axes. The T-tract is stabilised by wobble pairs enhancing the overall stability of the duplex. 

DNA-RNA hybrid duplexes are substrates for RNase H and reverse transcriptase. The crystal structure of a hybrid deoxy-polypyrimidine with polypurine RNA has been solved. The structure showed an A-form duplex, and the terminal base pair abuts the minor groove of another duplex creating a bend. RNase H is believed to interact through the minor groove but of an intermediate width between an A- and B-form duplex. The present structure did not exhibit an intermediate width of minor groove. A crystal structure of the chimeric ODN d(CCACTAGTG)rG shows that the presence of the 3 -ribonucleotide induces a... 

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