Melting of persistent double-stranded polymers

Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a bubble. There is also bending stiffness at the branch points between the two segment types. The transfer matrix technique for single persistent chains is generalized to describe the branching bubbles. Properties of spherical harmonics are then exploited in truncating and numerically solving the resulting transfer matrix. This allows efficient computation of phase diagrams and force-extension curves (isotherms). While the main focus is on exposition of the transfer matrix technique, we provide general arguments for a reentrant melting transition in stiff double strands. Our theoretical approach can also be extended to study polymers with bubbles of any number of strands, with potential applications to molecules such as collagen.Comment: 9 pages, 7 figure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

DNA stretching and compression: large-scale simulations of double helical structures

Computer-simulated elongation and compression of A-and B-DNA structures beyond the range of thermal¯uctuations provide new insights into high energy``activated'' forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG) Á poly(dC) and poly(dA) Á poly(dT) double helices, stretched from compressed states of 2.0 A Ê per base-pair step to highly extended forms of 7.0 A Ê per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of doublehelical DNA identi®ed in single crystals as well as non-canonical forms, such as the original``Watson-Crick'' duplex with trans conformations about the P Ð O5 H and C5 H ÐC4 H backbone bonds. The lowest energy minima correspond to canonical A and B-form duplexes. The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identi®ed by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual`v ertical'' duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition. Signi®cantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy pro®les show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy``activated'' forms calculated here are critical for DNA processing, e.g. nucleoprotein recognition, DNA/RNA synthesis, and strand exchange. E-mail addresses of the corresponding authors: [email protected]; [email protected]