Inverted repeat sequences derived from the ColE1 cruciform were invest
igated by nuclear magnetic resonance (NMR) and UV spectroscopy. It was
shown that 15 different sequences exist as stable hairpin structures
over a range of buffer conditions and DNA concentrations. Experiments
with six oligomers (1-6) containing the native stem sequence and five
base loops, found that the two hairpins with the wild-type loops (1-2)
served as upper and lower bounds for the thermodynamic stability of a
ll the other sequences. NMR experiments, including rotational correlat
ion time measurements and NOESY spectra, were then performed on 1, the
most stable hairpin sequence to begin to uncover a structural basis o
f its stability.