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homework4 - Biophysical Chemistry I Fall 2010 Homework...

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Biophysical Chemistry I, Fall 2010 Homework Assignment #4, due Oct. 21 1. Go to http://w3dna.rutgers.edu . Ask to analyze PDB code 1BNA, which is the crystal structure of the “Drew-Dickerson dodecamer”, which was the first atomic level resolution crystal structure of DNA to be re- ported. What is the nucleic acid sequence of this short piece of DNA? Compare the sequences of the two strands; why do think this relation was important? (Save the files here, or bookmark this page, since you will need to return to it below.) 2. At the same web site, go back to the home page and click on “re- construction”. This provides a facility to build a structure (given its sequence) from a fiber-diffraction model. (X-ray analysis of fibers of DNA was the principal method used from the 1950’s to the 1970’s to explore the structure of DNA; it is an averaged process, which does not provide structures that are sequence-specific.) Choose a “B-DNA generic” fiber model and reconstruct the model using the sequence from part 1 above. Download the resulting PDB file, go back to the
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