MCB124_ANSWERS_SET2

MCB124_ANSWERS_SET2 - MCB 124 Nucleic Acid Structure Enoch...

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Unformatted text preview: MCB 124 Nucleic Acid Structure Enoch Baldwin PROBLEM SET II page 1 I. Nucleic Acid Structures A. Structures ( LOOK EM UP. ) 1) Building blocks. Sketch the following, label the 5 and 3 ends; 5-uridine monophosphate: uracil + ribose + 5 phosphate pA : adenine + ribose + 5 phosphate dGp guanine + 2deoxyribose + 3 phosphate cytosine deoxyribonucleoside: cytosine + deoxyribose 2) Oligonucleotides, show all bonds ( LOOK EM UP ) pApUpGp : 5-phosphate-riboadenine-3-P-5-ribothymine-3-P-5-riboguanine-3- phosphate (dC)p(dG)pU 5-OH-deoxyribocytosine-3-P-5-deoxyriboguanine-3-P-5- ribouridine-3-OH (mixed DNA-RNA, like in replication priming (although the directionality of this oligo is reversed from that expected) 3) Sketch, using lines to represent the phosphodiester backbone, the following structures a duplex a step loop a four-way junction a D-loop MCB 124 Nucleic Acid Structure Enoch Baldwin PROBLEM SET II page 2 B. Structure-to-sequence relationships Create DNA sequences that will fold into the following structures (use T,C,G,A like ACTTGA, etc). Write ALL sequences in the 5->3 direction. In the line aadiagrams (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) The key here is 8 bp of complimentary regions with 5 extensions of non-complimentary regions. Since I am lazy, my answer will involve a palindrome so I only have to write one strand! (This is just an EXAMPLE-any sequence that fits the criteria is fine) Sequence 5-CCAATTGCAAT-3 (self complimentary region is underlined) which will form the following duplex 5-CCAATTGCAAT |||||||| TAACGTTAACC-5 2) Using four 18 nt oligonucleotides, a 4-way junction in which branch-migration is limited to the central 12 basepair s, but not beyond, without forming mismatches. The key here for a migrating junction is that the two pairs of strands must be the same at the 6 bp junction region to allow migration, but the outer bases must be different to assure junction formation. 35 A-T A-T A-T T-A C-G G-C C-G G-C A-T 5-GGG ATAGGT ACCTAT TGT-3 ||| |||||| |||||| ||| 3-CCC TATCCA TGGATA ACT-5 T-A C-G G-C C-G G-C T-A C-G C-G C-G 53 and the linear sequences 5-3 are 5-GGGATAGGTAGCGCT AAA 5-TTTAGCGCTACCTAT TGT 5-TCAATAGGTAGCGCG AGG 5-CCTCGCGCTACCTAT CCC Note that the underlined parts are the same for two sets of oligos- that is a signature for mobile junctions MCB 124 Nucleic Acid Structure Enoch Baldwin PROBLEM SET II page 3 3) as in 2) except design the sequence so that the junction cannot migrate (4 sequences) In this case only half (6 bp) of each adjacent oligo are complimentary- such a junction cannot migrate....
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MCB124_ANSWERS_SET2 - MCB 124 Nucleic Acid Structure Enoch...

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