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The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein-DNA recognition in the kB family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-base pair DNA encompassing a cognate kB site recognized by the proto-oncogenic c-Rel subfamily of NF-kB transcription factors. Simulations of the kB DNA in explicit water were extended to microsecond duration, providing a broad, atomically-detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation -- including a peculiar state arising at ~ 0.7 us and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally-sheared base pair, followed (at ~ 1 us) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the us-scale simulation include implications for a dynamical NF-kB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp contrast wi
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical reaction net
The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used in the se
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other biological mole