MCB124_PROBLEM_SET4

MCB124_PROBLEM_SET4 - DNA-protein interactions A) Protein X...

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DNA-protein interactions A) Protein X (RepX) of bacteria Undergraduo miserablis is a helix-turn-helix protein that binds the sequences below, which were obtained from PCR oligonucleotide selection experiments and aligned to give the best agreement. 1. CGTTCTACATTGAACA 2. CGTCCGACGTGGAACT 3. GGTTCTATGTTGAACC 4. AATAGGGCGCACGGTG 5. CGTTCCATATGGAACA 6. TGTTCAACATAGAACA 7. AGCTCCATGTCGAACT 8. TGTTCTATGTTGAACC 9. AATTCAATCTAGAACG 10. AGTTCGAGGTCGAACT 11. GGTTCAATTTGGAACG 1) CONSENSUS _________________ (USE X FOR SITES WITH NO OBVIOUS PREFERENCE) 1) What is the consensus binding sequence? ( call it sytA, put it above ). 2) Which selected site(s) likely is bound by RepX most tightly ( circle it (them ))? 3) What is a notable about the sytA sequence? 4) How many individual RepX molecules contact one sytA site? _____________ 5) One sequence is an obvious deviant. Which one? What is deviant about it? Briefly, provide an explanation for why was it recovered? B) Sequence surfing the
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MCB124_PROBLEM_SET4 - DNA-protein interactions A) Protein X...

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