BMB170a_2011_PS3

BMB170a_2011_PS3 - BMB 170a 2010 Problem Set 3: Nucleic...

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1 BMB 170a 2010 Problem Set 3: Nucleic Acids – 100 pts total (Please turn in hard copies) 1. Basic Nucleic Chemical and Structural Properties (25 pts) a) Hand-draw out the DNA sequence AGTC and its complement including sugars and phosphate backbone. Show the hydrogen-bonding between the base pairs and label the directionality of each strand. (5 pts) b) Which structure is more stable, ssDNA or ssRNA, and why? Draw a mechanism to demonstrate your reasoning. (5 pts) c) If you wanted to design an RNA sequence to adopt a desired structure, what are two characteristics of your sequence you could use to ensure that it was stable at high temperatures? Would this design strategy be the same if you wanted to ensure that the structure encoded by that sequence was favored above all other alternate structures that sequence could adopt (5 pts) ? d) Viruses of many varieties have the tricky problem of producing a set amount of proteins from a genome of limited size. In order to do this, many viruses rely on -1 frame-shifts during translation without the aid of protein regulators. Describe the two mechanisms (both essential) by which the mRNA of these viruses causes the frame- shifting events. (10 pts) 2. Using NUPACK (25 pts) The following questions will involve the program NUPACK ( http://www.nupack.org/ ) a software suite put together by the Pierce lab. a) Propose a sequence of RNA that would give you the following structure. In addition, show the resulting structure that your sequence adopts with (1) probability base shading in the (2) tick base style with (3) drawn letter annotation (5 pts) (Hint: Use Design first and then export your result to Utilities).
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2 b) What is the ensemble defect for this structure and what does that mean? What are the
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This note was uploaded on 01/03/2012 for the course BI 170a taught by Professor List during the Fall '09 term at Caltech.

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BMB170a_2011_PS3 - BMB 170a 2010 Problem Set 3: Nucleic...

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