Conformation of short DNA fragments by modulated fluorescence polarization anisotropy.

The technique of fluorescence polarization anisotropy (FPA) decay of intercalated ethidium has been used to study DNA conformation and dynamics, which are being recognized as primary determinants in transcription control and other cellular processes. Frequency modulated FPA when applied to two DNA molecules, a "straight" 50 base-pairs duplex fragment, and a bent fragment of similar length, has yielded different rotational diffusion coefficients for the two fragments. The data have been processed with an analytical model and with Brownian dynamics simulations, obtaining a good fit and a quantitative agreement between the two models. Both analyses have confirmed that one fragment can be described as a straight cylinder, while the other fragment is bent, with an angle estimated to be 45 degrees +/- 3 degrees. FPA has proved to be very powerful in determining simple conformations of short DNA duplexes and also particularly apt to probe the dynamical features of DNA fragments where conventional methods are either too cumbersome or fail to give quantitative results. In addition, the ligand no longer behaves ideally due to its complex structure and charge distribution. Thus for the protein the slope is no longer related simply to the net ligand charge, and the PB model gives a much larger slope than the LL model.(ABSTRACT TRUNCATED AT 400 WORDS)