Stretches of the parallel-stranded (ps) DNA can arise within the antiparallel-stranded (aps) Watson-Crick DNA by formation of loops or from mismatched sequnces (1). Groove-binding ligands were shown to facilitate folding of a 5-bp ps region from an imperfect aps mismatch (1). On the other hand, the ligands may induce interconversion of ps DNA to an imperfect aps duplex provided the aps duplex comprises specific ligand-binding sites (2). The formation of ps DNA regions upon binding of protein or other ligands may participate in the regulation of gene function. The introduction of a fluorescent probe at the end (2) and within the nucleotide sequence provides the means for monitoring the mutual orientation of the strands in a duplex. In this work, we checked whether the 2-aminopurine (2AP) can be used as a structural fluorescent probe able to distinguish between the ps and aps DNA duplexes.

Two DNA duplexes, ps-2AP and aps-2AP (having 2AP in a single position in one of the strands) as well as the control duplexes ps-N1 and aps-N1, were studied by various spectroscopic techniques:

where a stands for 2-aminopurine.

2AP can form cis 2A