Stability and structure of DNA oligonucleotides containing non-specific base analogues

The nature of DNA containing the deoxyribosyl derivative of 5-nitroindole has been investigated. 5-Nitroindole has been shown to give good stability when present in duplexes opposite natural bases, with only slightly reduced melting temperatures. However, enhanced stability occurs when it is incorporated as an additional bulged base in duplexes. It also markedly enhances the stability of duplexes when it is present as a pendant base at either the 5' or 3'-ends of the two strands. The stabilisation is presumed to be due to enhanced stacking interactions for the nitroindole base. Oligomers containing a number of consecutive 5-nitroindole residues form stable, stacked secondary structures. An oligomer containing 21 such substitutions is presumed to exist as a hairpin structure. This was further investigated by circular dichroism melting experiments, which demonstrated that the single-stranded oligomer contains significant secondary structure in the region of the 5-nitroindole tract, which appears to contain a double-stranded stem. X-ray analysis of 5-nitroindole deoxyriboside provides some indication of how the mode of stacking observed in crystals of the nucleoside may also be responsible for stabilising secondary structures of oligonucleotides.