BMB170a_2011_PS3_key

BMB170a_2011_PS3_key - Problem Set 3: Nucleic Acids Due...

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Problem Set 3: Nucleic Acids Due November 11, 2010 (Please turn in hard copies) 1. Basic Nucleic Chemical and Structural Properties 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) . O O O P O O O P O - O O N N H O N H H N N N N O N H H 5 ' O P O - O - O O 3' O P O - O O O N N O H O O N N N H H N N O O P O O - O O N N O N H H P O - O O O N N N N O H N H H O P O O - O O O N N O O H N N N H H N N O O P O 5' - O O O P - O O P O - O O 3' b) Which structure is more stable, ssDNA or ssRNA, and why? Draw a mechanism to demonstrate your reasoning (5 pts) .
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ssDNA is more stable than ssRNA because the oxygen of the hydroxl-group on the 2’- carbon on the ribose in RNA that does not exist in DNA can attack the adjacent phosphate group, resulting in the cleavage of the phosphate backbone. O O O O O 5 ' 5 ' O P - O O O O OH 3 ' BASE BASE P - O O BASE OH 3 ' HO BASE H+ 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) ? To ensure stability at high temperatures, one could elevate Tm by designing a structure with long hairpin/double-stranded regions and by making sure those double stranded regions had high GC content. If one wished to avoid alternative structures that the sequence could adopt, it would be better to keep GC content at about 50% to ensure that the sequence was as random as possible to avoid alternative base pairing structures. 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) . 1) A “slippery” heptanucleotide repeat in the codoing portion of the mRNA allows the ribosome-bound tRNAs to slip into the -1 frame. 2) Immediately after this repeat, the mRNA forms some kind of secondary structure, usually a pseudoknot, which stalls helicase activity, facilitating the -1 shift. 2. Using NUPACK The following questions will involve the program NUPACK ( http://www.nupack.org/ ) a software suite put together by the Pierce lab.
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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). One can enter the structure using dot-parentheses notation by typing in the following:
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BMB170a_2011_PS3_key - Problem Set 3: Nucleic Acids Due...

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