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Clint's Project Page - RISE Summer 2008 |
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Intern: Clint Perlaki, Bioengineering, Oregan State University
Mentor: Omar Saleh
Faculty Supervisor: Omar Saleh
Department: Materials |
ELECTROSTATIC PARING BETWEEN HOMOLOGOUS dsDNA STRANDS
DNA recombination, a vital function for all living organisms, highly depends on recognition between two identical
strands of double stranded DNA (dsDNA). A recent theory posits recognition is due to dipole attractions between
basepairs; these attractions are only significant for identical sequences because of correlated deformations between
the helices. If this theory is correct, we expect to observe characteristic changes in the elasticity of single dsDNA
dimers upon self-binding. We measured the elasticity of experimental and control strands of dsDNA using magnetic
tweezers and using solutions where the electrostatic repulsion between strands is minimized (i.e. in condensing
conditions). Experimental strands consisted of two identical sequences connected together, while control strands had
a random sequence. We were unable to find conditions where the experimental strand exhibited self-binding (i.e.
condensation) and the control strand did not, so we instead studied the kinetics of self-binding. We measured both
the time to condensation, and the time to decondensation, and found that while both strands condensed at the same
rate, the experimental strand decondensed much more slowly than the control strand. These results are consistent
with the following picture: the time to condensation depends on the first non-specific binding event between
segments, and thus does not vary between the strands. However, once condensed, the strands are free to rearrange,
allowing identical segments to bind; this strong binding leads to slow decondensation for only the experimental
strand. These results support the hypothesis; however, we will continue testing this hypothesis by varying the time
allowed for strand rearrangement.
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