Abstract
Base stacking is centrally involved in controlling the structure of ‘Watson-Crick’ double-stranded (ds) DNA. However, the local conformations adopted by nucleic acid bases as a consequence of DNA breathing, and their roles in protein-DNA binding, are not well understood. Here we employ the fluorescent base analogue 6-methyl isoxanthopterin (6-MI), which displays a chemical structure and base-pairing interactions similar to guanine, to probe the local conformations of nucleic acid bases at site-specific positions at and near single-stranded (ss)-dsDNA junctions.
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