Spectroscopic probe for the detection of local DNA bending at an AAA triplet

Abstract

Spectroscopic evidence of a DNA bend in solution is presented by analyzing model 15-mer duplexes spin-labeled with the five-atom-tethered nitroxide DUAP located in the major groove. Three 15-mers containing AATT with DUAP enzymatically incorporated into three different positions yielded nearly identical line shapes while a fourth 15-mer containing AAATT produced an EPR spectrum with significant additional line broadening. These results are interpreted according to the dynamic cylinder model where the DNA dynamics are decoupled into overall and internal contributions. It is shown that the AAATT sequence induces a change in the internal dynamics characterized by local ordering of DUAP. The increase in ordering evident in 15-mers containing AAATT rather than AATT suggests that the former sequence gives rise to a bend toward the major groove resulting in spatial restriction of the probe.