D. Loakes et al., STABILITY AND STRUCTURE OF DNA OLIGONUCLEOTIDES CONTAINING NONSPECIFIC BASE ANALOGS, Journal of Molecular Biology, 270(3), 1997, pp. 426-435
The nature of DNA containing the deoxyribosyl derivative of 5-nitroind
ole has been investigated. 5-Nitroindole has been shown to give good s
tability when present in duplexes opposite natural bases, with only sl
ightly reduced melting temperatures. However, enhanced stability occur
s when it is incorporated as an additional bulged base in duplexes. It
also markedly enhances the stability of duplexes when it is present a
s a pendant base at either the 5' or 3'-ends of the two strands. The s
tabilisation is presumed to be due to enhanced stacking interactions f
or the nitroindole base. Oligomers containing a number of consecutive
5-nitroindole residues form stable, stacked secondary structures. An o
ligomer containing 21 such substitutions is presumed to exist as a hai
rpin structure. This was further investigated by circular dichroism me
lting experiments, which demonstrated that the single-stranded oligome
r contains significant secondary structure in the region of the 5-nitr
oindole tract, which appears to contain a double-stranded stem. X-ray
analysis of 5-nitroindole deoxyriboside provides some indication of ho
w the mode of stacking observed in crystals of the nucleoside may also
be responsible for stabilising secondary structures of oligonucleotid
es. (C) 1997 Academic Press Limited.