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By R F Bruinsma

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Extra resources for Physics of protein-DNA interaction

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Dependence of the on-rate on salt concentration. 1 M (which happens to be the physiological salt concentration). There are also functional objections against Eigen’s idea. DNA does not really provide a nice one-dimensional “track” for a rondom walh. Under realistic conditions, the repressor will encounter many obstacles such as other repressor proteins bound to their respective operator sites or structural proteins that keep the DNA properly folded. These obstacles would quickly terminate a one-dimensional search.

Assume that the DNA of the 10 nm fiber is wrapped around the nucleosomes like a belt around a cylinder. In that case, we can simply adopt the preceding formulae. 75 times the number of nucleosomes N . 0 times N . This is known as the “Linking Number Paradox”. It is not really a paradox: it only shows that that DNA is not wrapped around the nucleosome the way a belt is wrapped around a cylinder. 75 per nucleosome. A mathematical theorem is providing us with detailed, microscopic information on the association of DNA with histones!

Instead chemical ✐ ✐ ✐ ✐ ✐ ✐ ✐ 36 “bruinsma” 2002/8/8 page 36 ✐ Physics of Bio-Molecules and Cells Fig. 15. Electron micrographs of the 30 nm fiber (first panel) and the 10 nm fiber (second panel). From reference [20]. modification of the histones, in particular acetylation, changes the binding affinity of DNA. Certain proteins (such as DNaseI) cut DNA strands that are not complexed with proteins. Such “digestion” experiments on chromatin produced DNA strands with lengths quantized in units of the order of about 200 bp, depending on the species.

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