Conformational Change of DNA in Specific Recognition Complexes between DNA and Protein
Specific recognition between protein and DNA is one of the most fundamental interactions in the cell. Many experiments suggest that in such recognition systems, a protein binds to DNA “non-specifically” first, then searches for the cognate DNA sequence by sliding, short hopping and/or inter-strand jumping. When it finds the target site, it may “passively” stop, or “interactively” binds to DNA, resulting in conformational changes of DNA and/or protein in forming the complex. Our study with two “specific recognition” systems shows that DNA in the specific complexes is bent and/or unwound, but no measurable DNA distortion is revealed in non-specific interaction.
The small magnitude of the DNA distortion suggests a mechanism of the active recognition, whereby a population of thermally fluctuating DNA structures (compatible to formation of a specific recognition complex) is “captured”, thus freezing the distorted DNA structure in the complex, rather than the protein twisting DNA into a structure normally absent in a free state. This mechanism also provides an explanation for the effect of the flanking sequence around the recognition site on DNA because the flexibility of DNA is likely to be a function of the DNA sequence on and around the recognized sequence.
KeywordsActive Recognition Specific Recognition EcoRI Site EcoRI Restriction EcoRI Restriction Enzyme
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