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Michael's Project Page |
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Intern: Michael Bjorndal
Mentor/Faculty Supervisor: Professor Deborah Fygenson
Department: Physics |
DNA
MELTING AND HAIRPIN FORMATION IN THE PRESENCE OF INTERCALATING DYES
The effect of intercalating dyes
on the melting transition of DNA was seen through the use of a new gel electrophoresis
assay. The technique studies the duplex to hairpin transition using perfect
palindromic oligomers. After raising the temperature of the annealed duplexes
and then quenching quickly in a cold water bath, percentages of duplexes and
folded hairpins can be seen. One interpretation states that the hairpins represent
oligomers that were completely melted at the temperature of interest and then
folded quickly during quenching. By comparison to UV-visual absorption melting
curves, it is possible to determine the order of the transition. Work is being
done to determine if the formation of hairpins has another interpretation: the
DNA is not completely melted but can stay in the hairpin state favorably at
certain temperatures. Various concentrations of the dyes YoYo and YoPro were
used to see their effect on the DNA. The dyes clearly raise the overall melting
temperature, with YoYo having about the same effect as twice the concentration
of YoPro. This has been of use for people using these dyes to watch DNA at
and around its melting temperature. One other chemical commonly used with DNA,
Betamercaptoethanol (BME), obscures the UV-visual absorption curves. It is
the hope that this new assay will also give a clear estimate of the effect BME
has on DNA melting.
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