DNA Curvature in Solution Measured by Fluorescence Resonance Energy Transfer

Abstract

The sequence-induced curvature of DNA fragments free in solution was characterized by measurements of the end-to-end distance using fluorescence resonance energy transfer (FRET). The 31 bp oligonucleotides were labeled at their 5‘ ends with fluorescein as the donor and rhodamine X as the acceptor. We compared a curved oligonucleotide with three phased A₆ blocks and a control containing (AT)₃ instead of the A₆ blocks. The increased efficiency of energy transfer of the A₆-containing DNA indicates the existence of a permanent sequence-induced curvature, the magnitude of which is in good agreement with estimates from theoretical curvature predictions. Energy transfer efficiency and correspondingly curvature increases with NaCl concentration.