Physics of Life Reviews 7 (2010) 346–347 www.elsevier.com/locate/plrev Comment DNA–ligand binding and the force-extension experiments Comment on “Biophysical characterization of DNA binding from single molecule force measurements” by Chaurasiya et al. Alexander Vologodskii * Department of Chemistry, New York University, New York, NY 10003, United States Received 23 June 2010; accepted 30 June 2010 Communicated by M. Frank-Kamenetskii The review by Chaurasiya et al. [1] gives a comprehensive, although rather compressed, picture of the force- extension studies of interaction between DNA molecules and various ligands. This beautiful and powerful method remains a hottest field of molecular biophysics, and appearance of such review with very extensive list of references is very useful. The authors show that a lot of information on ligands binding with DNA can be obtained from the force-extension experiments. I would like to make some comments on specific issues touched in the review. There is a very short description of the determination of the bend angle induced in DNA by the protein binding. This is a difficult and very important problem for proteins that bind DNA with low sequence specificity. Although the effect of the binding on the DNA extension can be very large, it strongly depends on the applied force [2]. Therefore, it is not clear how the number of bound proteins and, correspondingly, the bend angles were determined in a cited unpublished study. In addition, the measurements in the cited study were performed under the force of tens of pN that may change the protein binding mode. This and many other problems touched in the review are related to properties of the wormlike chain (WLC) which is a base for a quantitative interpretation of the force-extension experiments. Sometime the properties of WLC are misrepresented in the review. I was surprised to read in Section 3.2.1 that WLC model does not work for DNA segments shorter than 100 bp. Even in its simplest isotropic version the model works for segments as short as 20 bp, if the segments are not bent too much. The conventional WLC model assumes that the chain is intrinsically straight. If proteins bind the double helix with low sequence specificity, they efficiently convert DNA to a chain with randomly distributed intrinsic bends. It has been shown, however, that the equation for the force-extension dependence for WLC holds in this case as well, although the value of DNA persistence length should be replaced by an effective value [3,4]. This effective persistence length is shorter than the original one, but it does not mean that DNA becomes more flexible, as is concluded in [1] for DNA bound with HMG and HU proteins. Actually, the opposite is possible since DNA segments bound with proteins may become more rigid than the naked segments. I would also like to comment on the overstretching transition in DNA that occurs at the stretching force of 65 pN. Indeed, discussion on the nature of this conformational transition has lasted for nearly a decade. One side supports the DOI of original article: 10.1016/j.plrev.2010.06.001. * Tel.: +1 212 998 3599. E-mail address: alex.vologodskii@nyu.edu. 1571-0645/$ – see front matter  2010 Elsevier B.V. All rights reserved. doi:10.1016/j.plrev.2010.06.008