1- What features of the major groove make it especially useful for sequence-spec
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Question
1- What features of the major groove make it especially useful for sequence-specific recognition by proteins? Give at least two examples of DNA-binding motifs that bind primarily to the major groove. Provide an example of a protein that does NOT use the major groove to recognize its target. How does it accomplish its specific binding?
2- Address the contribution made by nonspecific contacts with the DNA backbone to the binding affinity of typical DNA-binding proteins. What constraints are imposed on a protein by relying on such contacts for sequence-specific DNA binding? What advantages are provided?
3- Describe the role of water in protein structure formation.
4-DNA repair proteins, such as DNA glycosylase, recognize and remove damaged nucleotides. Based on what you know about protein-DNA interactions, suggest how these repair enzymes recognize mismatches or damaged bases in double-helix DNA, and suggest what specific contacts are made between the DNA repair protein and the mismatched (or damaged) base.
Explanation / Answer
1)
DNA contains major grooves and minor grooves, most of the proteins like transcription factors would bind on the major grove of DNA. The interaction of DNA and proteins plays a major role in various central metabolic and biological processes.
The feature that would responsible for protein binding is that DNA major groove is wider (12
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