An investigation into the solution structure of the single-stranded DNA undecamer 5'd AAGTGTGATAT by means of nuclear Overhauser enhancement measurements.

Abstract

A 500-MHz 1H-NMR study on the single-stranded DNA undecamer (11-mer) 5'd AAGTGTGATAT is presented. Using a combination of one-dimensional pre-steady-state nuclear Overhauser enhancement (NOE) measurements and two-dimensional homonuclear J-correlated spectroscopy, virtually complete resonance assignments are obtained. The relative magnitudes of the intra- and internucleotide NOEs indicate that the overall structure of the single-stranded 11-mer is a right-handed B-type helix with extensive base stacking. Within this overall structure there is quite a large degree of variability, as exemplified by variations in glycosidic bond and sugar pucker conformations, most likely determined by base sequence.