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The sequence-dependent structural variability and conformational dynamics ofDNA play pivotal roles in many biological milieus, such as in the site-specificbinding of transcription factors to target regulatory elements. To betterunderstand DNA structure, function, and dynamics in general, and protein-DNArecognition in the 'kB' family of genetic regulatory elements in particular, weperformed molecular dynamics simulations of a 20-base pair DNA encompassing acognate kB site recognized by the proto-oncogenic 'c-Rel' subfamily of NF-kBtranscription factors. Simulations of the kB DNA in explicit water wereextended to microsecond duration, providing a broad, atomically-detailedglimpse into the structural and dynamical behavior of double helical DNA overmany timescales. Of particular note, novel (and structurally plausible)conformations of DNA developed only at the long times sampled in thissimulation -- including a peculiar state arising at ~ 0.7 us and characterizedby cross-strand intercalative stacking of nucleotides within alongitudinally-sheared base pair, followed (at ~ 1 us) by spontaneous baseflipping of a neighboring thymine within the A-rich duplex. Results andpredictions from the us-scale simulation include implications for a dynamicalNF-kB recognition motif, and are amenable to testing and further explorationvia specific experimental approaches that are suggested herein.

Molecular Dynamics of a kB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation