Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insight

The genomic materials from some Bacillus subtilis bacteriophages are found to contain 5-(hydroxymethyl)-2'-deoxyuridine in glace of thymine. Phage-enc oded proteins such as transcription factor I specifically and preferentiall y bind ro the minor grooves of these hmU-containing DNA but not to thymine- containing DNA. Data from electrophoretic mobility shift assays suggest tha t the inherent, localized flexibility of hmU-DNA, which is sequence-specifi c, is responsible Sor its discriminative binding. We discuss here, from the NMR-derived structural point of view, how differential DNA flexibility can contribute to specific binding of TF1 to hmU-DNA. (C) 2000 John Wiley & So ns, Inc.