Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p: reinterpretation of recent single molecule experiments

Biophysical Chemistry
Dirk Stigter

Abstract

Brewer et al. (Biophys. J. 85 (2003) 2519-2524) have studied the compaction of dsDNA in a double flow cell by observing the extension of stained DNA tethered in buffer solutions with or without Abf2p. They use a Langmuir adsorption model in which one Abf2p molecule adsorbs on one site on the DNA, and the binding constant, K, is given as the ratio of the experimental rates of adsorption and desorption. This paper presents an improved interpretation. Instead of Langmuir adsorption we use the more appropriate McGhee-von Hippel (J. Mol. Biol. 86 (1974) 469-489) theory for the adsorption of large ligands to a one-dimensional lattice. We assume that each adsorbed molecule shortens the effective contour length of DNA by the foot print of Abf2p of 27 base pairs. When Abf2p adsorbs to DNA stretched in the flowing buffer solution, we account for a tension effect that decreases the adsorption rate and the binding constant by a factor of 2 to 4. The data suggest that the accessibility to Abf2p decreases significantly with increasing compaction of DNA, resulting in a lower adsorption rate and a lower binding constant. The kinetics reported by Brewer et al. (Biophys. J. 85 (2003) 2519-2524) lead to a binding constant K=3.6 x 10(6) M(-1) at t...Continue Reading

References

Apr 7, 1995·Science·T T PerkinsS Chu
Sep 3, 1998·Biophysical Journal·D Stigter, C Bustamante

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Citations

Sep 6, 2007·The Journal of Clinical Investigation·Jana S EatonGerald S Shadel
Apr 12, 2008·PLoS Genetics·Heidi M BlankMichael Polymenis
Dec 4, 2009·PloS One·Heidi M BlankMichael Polymenis
Feb 3, 2005·Yeast
Aug 23, 2020·Biomolecules·Veronika VozárikováĽubomír Tomáška

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