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.
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