DNA stretching as a probe for nucleic acid interactions

Abstract

We would like to thank the authors of the thoughtful commentaries on various aspects of our review. These commentaries represent a diverse set of opinions on the field of single molecule force spectroscopy. We are unable to address all of the detailed issues brought up in the commentaries due to space constraints. Therefore what follows is a more general view of the most commonly addressed issues.An isolated DNA molecule yields a lattice of binding sites, representing a microlab for the study of DNA-ligand interactions. Increasing tension along the double-stranded DNA (dsDNA) molecule disrupts tertiary DNA-ligand structures, then dislocates base pairing and stacking and ultimately separates the opposite strands to form single-stranded DNA (ssDNA). Varying the applied force alters the free energy to favor ligands that bind preferentially to DNA in one of these forms. These biophysical experiments not only discern the mode of DNA binding, but may also quantify the biochemistry of protein-DNA interactions [1,2]. These types of experiments offer particular advantages over bulk solution measurements, though important caveats remain. Specific issues surrounding DNA characterization and modeling, protein-DNA interactions under force and the ongoing discussion about overstretching highlight important questions that merit further comment and will hopefully propel additional study [2][3][4][5][6][7][8].In any review, some subjects may only be dealt with briefly, while others must regrettably be omitted altogether. The section on DNA models treats well known descriptions of polymer elasticity; the Worm-Like Chain and Freely-Jointed Chain models. These models are used specifically to quantify DNA-protein interactions in the stretching experiments described further in the review [1], but not as a review of the much larger and interesting field of molecular dynamics simulations. The sophistication of computational techniques has increased rapidly in the last few years, enabling fruitful comparisons between theory and experiment [4,9,10]. Further advances in theoretical treatments of DNA have shed light upon even finer structures

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

“…In their comments they provided supportive arguments in favor of S-DNA and exhibit some weakness of force induced melting picture. As a result McCauley et al [43] in their 'reply to comment' added both the model pictures associated with the overstretching transition of DNA without a concrete conclusion.…”

Molecular dynamics study of DNA oligomers under angled pulling

“…This is consistent with experimental results for long dsDNA. 55,56 It is also noteworthy that for all pulling angles, the yield forces obtained at v ¼ 0.3 m s À1 are much closer to the yield forces at v ¼ 0.03 m s À1 than to those obtained at v ¼ 3 m s À1 : This was not observed for the ultimate forces.…”