MCB124_PROBLEM_SET2

MCB124_PROBLEM_SET2 - MCB 124 Enoch Baldwin PROBLEM SET II...

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MCB 124 Nucleic Acid Structure Enoch Baldwin PROBLEM SET II page 1 I. Nucleic Acids A. Structures 1) Building blocks. Sketch the following, label the 5’ and 3’ ends; • 5’-uridine monophosphate • pA • dGp • cytosine deoxyribonucleoside 2) Oligonucleotides, show all bonds • pApTpGp • (dC)p(dG)pU 3) Sketch, using lines to represent the phosphodiester backbone, the following structures • a duplex • a step loop • a four-way junction • a D-loop B. Structure-to-sequence relationships Create RNA sequences that will fold into the following structures (use U,C,G,A like “ACUUGA”, etc). Write ALL sequences in the 5’->3’ direction. In the line diagrams (below), the arrows point from 5’ to 3’. 1) a duplex with 8 basepairs in 3 bp single-strand extension at each 5’-end (2 sequences required) 2) a 4-way junction that can migrate with 6 basepairs on each arm and no unpaired bases (4 sequences required) 3) as in 2) except design the sequence so that the junction cannot migrate (4 sequences) 4) A single sequence that folds into a 3-way junction and contains two stem-loop structures containing 3 bp loops (1 sequence)
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This note was uploaded on 04/06/2011 for the course MCB 124 taught by Professor Baldwin during the Summer '09 term at UC Davis.

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MCB124_PROBLEM_SET2 - MCB 124 Enoch Baldwin PROBLEM SET II...

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