Nonlinearity in DNA and its relation to specific functions

Abstract

In memory of Alwyn Scott, we discuss the connection between the nonlinear dynamics of double-stranded DNA, experimental findings, and specific DNA functions. We begin by discussing how thermally induced localized openings (bubbles) of the DNA double-strand are important for interpreting dynamic force spectroscopy data. Then, we demonstrate a correlation between the sequence-dependent propensity for bubble formation and transcription initiation and other regulatory effects in viral DNA. Finally, we discuss the possibility of a connection between DNA dynamics and the ability of repair proteins to recognize ultraviolet-radiation damage. © 2009 Springer Science+Business Media B.V.