Molecular motion of DNA as measured by triplet anisotropy decay.

Abstract

Triplet anisotropy decay techniques were used to measure the internal flexibility and overall rotational motion of [calf thymus] DNA, covering a time range from 15 ns to 200 .mu.s. Nearly monodisperse DNA fragments 65-600 base pairs long were studied by using the intercalating dye methylene blue as a triplet probe. The slow end-over-end tumbling of short DNA fragments (.ltoreq. 165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motion of its helix axis. At the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when bound, methylene blue monitors fast internal motion of the helix. Since the rod-like end-over-end tumbling of short fragments rules out fast bending motions, the fast components of DNA anisotropy decay are probably due to twisting motion of the helix, occurring with a time constant near 50 ns.