Fluorescence dynamics of double- and single-stranded DNA bound to histone and micellar surfaces

Abstract

The study of structure and dynamics of bound DNA has special implications in the context of its biological as well as material functions. It is of fundamental importance to understand how a binding surface affects different positions of DNA with respect to its open ends. Because double-stranded (ds) and single-stranded (ss) DNA are the predominant functional forms, we studied the site-specific dynamics of these DNA forms, bound to the oppositely charged surface of histones, and compared the effects with that of DNA bound to cetyltrimethyl ammonium bromide micelles. We utilized a time-resolved fluorescence technique using fluorescent base analogue 2-aminopurine located at specific positions of synthetic poly-A DNA strands to obtain fluorescence lifetime and anisotropy information. It is observed that the binding leads to overall rigidification of the DNA backbone, and the highly flexible ends show drastic dampening of their internal dynamics as well as the fraying motions. In the case of ds-DNA, we find that the binding not only decreases the flexibility but also leads to significant weakening of base-stacking interactions. An important revelation that strong binding between DNA and the binding agents (histones as well as micelles) does not dampen the internal dynamics of the bases completely suggests that the DNA in its bound form stays in some semiactive state, retaining its full biological activity. Considering that the two binding agents (histones and micelles) are chemically very different, an interesting comparison is made between DNA−histones and DNA−micelle interactions.