bmb428_problemset18

bmb428_problemset18 - BMB428 Physical Chemistry with...

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BMB428 Dr. Song Tan Physical Chemistry with Biological Applications Fall 2007 1 Problem Set 18: Physical Chemistry in the Laboratory Due Nov 1, 2007 PCR (Polymerase Chain Reaction) 1. DNA is usually found in its double-stranded form. Draw a graph for the percentage of double- stranded DNA as a function of temperature. Answer the following questions to help you draw this graph. (a) At very high temperatures, do you expect more double-stranded or single-stranded DNA? (b) At very low temperatures, do you expect more double-stranded or single-stranded DNA? (c) How do you expect the graph to look like at intermediate temperatures? (d) The melting temperature (T m ) of DNA provides us a measure of the thermal stability of DNA, i.e. at what temperature double-stranded DNA will melt into two individual strands. Mark the Tm on the graph. 2. The polymerase chain reaction PCR has revolutionized modern biology since its invention in 1983 (the basic concept was actually described in a publication in 1971). There are three basic steps in PCR: denaturation to separate the double-strands of DNA, annealing to allow the PCR primers to bind to the denatured template, and elongation to extend the primer-template typically using a thermophilic DNA polymerase. In PCR experiments, you usually want to maximize the yield of the specific PCR product you want and therefore to minimize non-specific products that might result from the PCR primers annealing to nonideal (i.e. imperfect matches of) DNA sequences. If you are not familiar with PCR, please consult your biochemistry textbooks or the internet for more background (Wikipedia has a decent write-up, including a detailed diagram). A typical PCR experiment might involve the following thermal cycles:
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This note was uploaded on 07/23/2008 for the course BMB 428 taught by Professor Tan during the Fall '07 term at Penn State.

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bmb428_problemset18 - BMB428 Physical Chemistry with...

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