alpha-homo-DNA and RNA form a parallel oriented non-A, non-B-type double helical structure

Cross-talking between nucleic acids is a prerequisite for information trans fer. The absence of observed base pairing interactions between pyranose and furanose nucleic acids has excluded considering the former type as a (pote ntial) direct precursor of contemporary RNA and DNA. We observed that alpha -pyranose oligonucleotides (alpha -homo-DNA) are able to hybridize with RN A and that both nucleic acid strands are parallel oriented. Hybrids between alpha -homo-DNA and DNA are less stable. During the synthesis of alpha -ho mo-DNA we observed extensive conversion of N-6 benzoyl-5-methylcytosine int o thymine under the usual deprotection conditions of oligonucleotide synthe sis. alpha -Homo-DNA:RNA represents the first hybridization system between pyranose and furanose nucleic acids. The duplex formed between a-homo-DNA a nd RNA was investigated using CD, NMR spectroscopy, and molecular modeling. The general rule that orthogonal orientation of base pairs prevents hybrid ization is infringed. NMR experiments demonstrate that the base moieties of a-homo-DNA in its complex with RNA, are equatorially oriented and that the base moieties of the parallel RNA strand are pseudoaxially oriented. Model ing experiments demonstrate that the duplex formed is different from the cl assical A- or B-type double stranded DNA. We observed 15 base pairs in a fu ll helical turn. The average interphosphate distance in the RNA strand is 6 .2 Angstrom and in the alpha -homo-DNA strand is 6.9 Angstrom. The interstr and P-P distance is much larger than found in the typical Aand B-DNA. Most helical parameters are different from those of natural duplexes.