Association of short DNA fragments: Steady state fluorescence polarization study

We have studied aggregation/association of monodisperse DNA fragments (ranging from 30–90 base pairs) by steady-state fluorescence polarization of intercalculated ethidium. The method of excitation at different wavelengths in the ethidium absorption spectrum provides information about anisotropic twisting and tumbling mobility of the fragments. We find that end-over-end tumbling rather than axial spinning and internal twisting motions are affected by aggregation/association. The critical concentration for observing the effects of intermolecular interactions is approximately 5 mg DNA/mL at room temperature, independent of fragment length. Association is favored by low temperature and high (> 10 mM) concentration of Mg²⁺. From temperature-and salt-dependence experiments we infer that the “aggregates” are similar to those observed in a recently discovered DNA sol–gel transition M. G. Fried and V. A. Bloomfield (1984) Biopolymers 23 , 2141–2155]. We also discuss possible arrangements of the fragments within the aggregates and their possible relation to formation of DNA liquid crystals.