Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites.
The variations in several double helical DNA angular parameters have been calculated along about 60 bacterial and phage sequences, each several hundreds nucleotides long. Regions of large geometric irregularities are found at, or in the vicinity of, regulatory protein recognition sites. Based on these extensive computations I suggest that these structurally "wrinkled" regions facilitate the first stage of the recognition process.
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Nussinov
D010582:Bacteriophage lambda / Q000235:genetics; D001483:Base Sequence; D003201:Computers; D004269:DNA, Bacterial; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D007763:Lac Operon; D009690:Nucleic Acid Conformation; D009876:Operon; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D014158:Transcription, Genetic
D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012335:RNA, Ribosomal