CONFORMATION OF SHORT DNA FRAGMENTS BY MODULATED FLUORESCENCE POLARIZATION ANISOTROPY

The technique of fluorescence polarization anisotropy (FPA) decay of i ntercalated ethidium has been used to study DNA conformation and dynam ics, which are being recognized as primary determinants in transcripti on control and other cellular processes. Frequency modulated FPA when applied to two DNA molecules, a ''straight'' 50 base-pairs duplex frag ment, and a bent fragment of similar length, has yielded different rot ational diffusion coefficients for the two fragments. The data have be en processed with an analytical model and with Brownian dynamics simul ations, obtaining a good fit and a quantitative agreement between the two models. Both analyses have confirmed that one fragment can be desc ribed as a straight cylinder, while the other fragment is bent, with a n angle estimated to be 45 degrees +/- 3 degrees. FPA has proved to be very powerful in determining simple conformations of short DNA duplex es and also particularly apt to probe the dynamical features of DNA fr agments where conventional methods are either too cumbersome or fail t o give quantitative results. (C) 1995 John Wiley & Sons, Inc.