DNA is subject to large deformations in a wide range of biological processes.
Two key examples illustrate how such deformations influence the readout of the
genetic information: the sequestering of eukaryotic genes by nucleosomes, and
DNA looping in transcriptional regulation in both prokaryotes and eukaryotes.
These kinds of regulatory problems are now becoming amenable to systematic
quantitative dissection with a powerful dialogue between theory and experiment.
Here we use a single-molecule experiment in conjunction with a statistical
mechanical model to test quantitative predictions for the behavior of DNA
looping at short length scales, and to determine how DNA sequence affects
looping at these lengths. We calculate and measure how such looping depends
upon four key biological parameters: the strength of the transcription factor
binding sites, the concentration of the transcription factor, and the length
and sequence of the DNA loop. Our studies lead to the surprising insight that
sequences that are thought to be especially favorable for nucleosome formation
because of high flexibility lead to no systematically detectable effect of
sequence on looping, and begin to provide a picture of the distinctions between
the short length scale mechanics of nucleosome formation and looping.Comment: Nucleic Acids Research (2012); Published version available at
http://nar.oxfordjournals.org/cgi/content/abstract/gks473?
ijkey=6m5pPVJgsmNmbof&keytype=re
