PS2 - BMB 100A Problem Set#2 Fall 2011 Name 1 Using RasMol...

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BMB 100A Problem Set #2 Fall, 2011 Name_________________ 1. Using RasMol or PyMol, bring up the Dickerson DNA dodecamer (dickerson.12mer.pdb). The two complementary chains are called A and B, each of which are 12 nucleotides long. NOTES: (1) In looking at individual nucleotides or atoms in a complicated structure with it helps to use the "slab" mode to display thinner slabs or slices of the structure, for clarity. (2) Another helpful trick is to place the center of rotation of the molecule at an atom that you are focusing on. a. Zoom in on the middle of the dodecamer, and find the N3 position of T7 on the A chain. Then find the N1 atom of A6 on the B chain. Now measure the distance between the N3 of T7 and the N1 of A6. What kind of weak interaction does this distance correspond to? b. Find the phosphorus atoms belonging to T7 and T8, and measure their interatomic distance. This value is near the maximum possible P-P distance for adjacent nucleotides in an RNA or DNA chain. 2.
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This note was uploaded on 04/09/2012 for the course BIOCHEMIST 100a taught by Professor Harrynoller during the Fall '11 term at UCSC.

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PS2 - BMB 100A Problem Set#2 Fall 2011 Name 1 Using RasMol...

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