Local Conformational Changes of DNA

The structural variations can affect the width of the major groove, the extent of base stacking, as well as the tilt of the basepairs to each other. The local conformational changes are sequence dependent and can be intrinsic properties and thus permanent occurrences they can, however, also be induced by protein binding. The DNA sequence can thus serve a double purpose for the recognition between DNA and protein. 

Direct recognition The order of bases can determine the pattern of weak interaction and the specificity of the complex formation. In this case there is a direct recognition of the sequence by the protein. 

Indirect recognition The DNA sequence can predetermine a particular conformation, which is a prerequisite for specific protein binding. Alternative DNA conformations will not be boimd and recognized. We speak here of an indirect recognition of a sequence  

The detailed analysis of DNA structure in the region of contact with the binding protein often displays distinct divergence from the parameters of classical B-DNA structure. The specific sequence-determined conformation of the DNA is often a prerequisite for a specific recognition. This recognition mechanism is, for example, realized with the Trp-repressor, where the sequence determines a certain spatial arrangement of the 

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