By mutating a DNA binding site for a protein, I seem to have created a new binding site for some other protein. This speculation is based on a new phenotype being observed. Now I want to know if there is any software that can predict a protein binding to the mutated sequence.
Thank you !! Yes it is a transcription factor in enterobacterial system. I have done GC rich 4 base pairs substitution. The mutation is downstream of +1. When I cloned it into a plasmid that carries transcriptional terminator at the end of the sequence, the host bacteria (MG1655) shows very slow growth in culture. The colonies on the plates are very small too. The mutated site is very important for my work. By DNase I footprinting I have confirmed that sequence as the binding site for a transcription factor under my study. Yes you are right. It is possible that formed mRNA might be inhibiting something.
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