Abstract:In this study the effect of sequence context on the binding affinity and conformation of DNA dodecamers are explored. The Cre binding site (ACGT) was studied with a number of different flanking sequences. 31P-NMR was used to determine the conformational state (BI/BII ratio) of each step in the phosphate backbone. Importantly, the conformation of the binding site, the center tetrad which was not changed, varied significantly based on the sequence context. Fluorescence titration with the DNA intercalator 7-Amino… Show more
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