DNA's Self-Regard

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Science  15 Feb 2008:
Vol. 319, Issue 5865, pp. 879
DOI: 10.1126/science.319.5865.879c

Recognition of double-stranded (ds) DNA sequences is usually thought to require some unwinding of the double helix to expose the bases for interactions with single-stranded nucleic acid sequences or with proteins. Thus, it would be reasonable to assume that recognition between dsDNA sequences in solution would require processes involving single-stranded DNA, such as triple-helix formation. Baldwin et al. examined a binary mixture of two different dsDNA sequences of identical length (294 base pairs) and GC base proportion (50%) in electrolytic solution under minor osmotic stress. Under conditions of low fluorescent labeling to avoid quenching, liquid- crystalline spherulites form, and the two DNAs within these structures prefer to self-associate rather than mix. The authors suggest, based on their recent theoretical work, that association between identical DNAs is favored as this arrangement maintains registry of the phosphate backbone and surrounding counterions; different sequences result in small changes in pitch that can disrupt these interactions and extract an energetic penalty. Other mechanisms may also operate, but dsDNA recognition occurs in the presence of intervening solution. — PDS

J. Phys. Chem. B 112, 1060 (2008).

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