Microscopic implications of S-DNA Stephen Whitelam ∗ $^{1}$, Phillip L. Geissler2 and Sander Pronk 3 $^{1}$The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA $^{2}$Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA $^{3}$Center for Biomembrane Research, Department of Biochemistry & Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden Recent experiments [J. van Mameren et al. PNAS 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed that this observation rules out the existence of an elongated, hybridized form of DNA (S-DNA). Here we argue that the S-DNA picture is consistent with the observation of unpeeling during overstretching. We demonstrate that assuming the existence of S-DNA does not imply DNA overstretching to consist of the complete or near-complete conversion of the molecule from B- to S- form. Instead, this assumption implies in general a more complex dynamic coexistence of hybridized and unhybridized forms of DNA. We argue that such coexistence can rationalize several recent experimental observations. ∗ swhitelam@lbl.gov 1 arXiv:1002.2169v2 [cond-mat.soft] 3 Jun 2010 Abstract