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5.8 years ago
PhdinDNA
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How much a single mutation/alteration of a nucleotide affects the presence of a transcription factor binding site.? I am from computer science background(Obviously). I want to make a general assumption about mutation of how many bases in a TFBS minimize the binding affinity to a very low score?
What have you tried and read yet?
Following on from ATpoint, your question is way too general such that anybody could give an accurate response. TFs bind to DNA wherever there is an electromagnetic attraction, as mediated through the bases of the target DNA and the conformation and amino acid composition of the TF. TFs can still bind if there is a base mismatch, but binding affinity (and therefore downstream transcription of target genes) may be less or more, depending on whether the affinity is decreased or increased.
Remember that TFs don't follow the rules that we study them by. They bind wherever there is an electromagnetic potential such that they can bind. Given a strong enough potential, transcription may thereafter occur if other conditions are met.
Thanks kevin. You have explained very clearly. The answer I will accept is (Tell me If I am wrong), No we cannot make any assumption.
No, well, there are studies that look at, for example, how different SNPs alter the expression of nearby genes. These SNPs are modulating enhancer protein binding and / or transcription factor binding. I would encourage you to read these, as good examples:
Thanks for asking ATpoint, I have read that there are factors unknown to us, because of which a TF will bind on a position in DNA sequence. I have been reading papers , read more than 20 research papers till now, mostly on TFBS, since you asked. I was thinking if it is even possible to say that after mutation, this sequence does not contain any TFBS now ?