Single linear DNA molecules were bound at multiple sites one extremity to a treated glass cover slip and the other magnetic bead. The was therefore torsionally constrained. A field used rotate beads thus coil pull DNA. stretching force determined by analysis of Brownian fluctuations Here elastic behavior individual lambda over- underwound up 500 turns studied. sharp transition discovered from low high extension state approximately 0.45 piconewtons for 3 overwound ones. These transitions,...

In a process called "molecular combing," DNA molecules attached at one end to solid surface were extended and aligned by receding air-water interface left dry on the surface. Molecular combing was observed extend length of bacteriophage λ molecule 21.5 ± 0.5 micrometers (unextended length, 16.2 micrometers). With process, it possible (i) chromosomal Escherichia coli fragment (10 6 base pairs) (ii) detect minute quantity 3 molecules). These results open way for faster physical mapping genome...

This review is an expository treatment of the displacement one fluid by another in a two-dimensional geometry (a Hele-Shaw cell). The Saffman-Taylor equations modeling this system are discussed. They simulated random-walk techniques and studied methods from complex analysis. stability generated patterns (fingers) WKB approximation analytic techniques. primary conclusions reached that (a) fingers linearly stable even at highest velocities, (b) they nonlinearly unstable against noise or...

A detailed experimental and theoretical analysis of the alignment grafted DNA molecules by a moving meniscus is presented. The existence extent stretching (up to $2.14$ times unstretched length) depends critically on properties surface. Molecules at both ends exhibit looplike shape which scale invariant. An elastic model this process, we have called molecular combing, introduced (a) yields extension force various surfaces, (b) value for tensile strength DNA,...

We investigate structural transitions within a single stretched and supercoiled DNA molecule. With negative supercoiling, for stretching force >0.3 pN, we observe the coexistence of B-DNA denatured from σ ≈ −0.015 down to = −1. Surprisingly, positively ( > +0.037) by 3 similar new, highly twisted structure. Experimental data molecular modeling suggest that this structure has ≈2.62 bases per turn an extension 75% larger than B-DNA. This tightly interwound phosphate backbones exposed in...

A new approach to the study of DNA/protein interactions has been opened through recent advances in manipulation single DNA molecules. These allow behavior individual molecular motors be studied under load and compared with bulk measurements. One example such a motor is polymerase, which replicates DNA. We measured replication rate by enzyme stretched strand The marked difference between elasticity single- double-stranded allows for monitoring real time. have found that depends strongly on...

In this paper we review the biophysics revealed by stretching single biopolymers. During last decade various techniques have emerged allowing micromanipulation of molecules and simultaneous measurements their elasticity. Using such techniques, it has been possible to investigate some interactions playing a role in biology. We shall first simplest case non-interacting polymer then present structural transitions DNA, RNA proteins that studied single-molecule techniques. explain how these...

We report experimental observations of traveling-wave convection in a binary fluid mixture an annular container---a flow which approximates large, one-dimensional dynamical system. In this geometry, the convective rolls align themselves radially and propagate azimuthally. observe competition between several non- equilibrium states. This leads to rich variety behavior, including coexisting regions conduction convection, sources sinks rolls, more complex spatiotemporal defects.

The Schr\"odinger equation is solved on a variety of fractal lattices using recursive technique. In this method, the energy levels and wave functions lattice with ${N}_{n}$ sites calculated in terms corresponding quantities smaller ${N}_{n\ensuremath{-}1}$ sites, via kind decimation process. As $n\ensuremath{\rightarrow}\ensuremath{\infty}$ resulting are discrete, very closely spaced, highly degenerate. Smoothed densities states have wide singularities.

The elastic properties of single stranded (ss)DNA, studied by pulling on an isolated molecule, are shown to agree with a recent model ssDNA that takes into account base pairings and screened electrostatic repulsion the phosphodiester backbone. By appropriate physicochemical treatment, pairing interactions were suppressed used as experimental for generic polyelectrolyte. behavior such altered deviates strongly from ideal polymer. This deviation is result elasticity chain its self-avoiding...

We deduced the torque applied on a single stretched and twisted DNA by integrating change in molecule's extension with respect to force as it is coiled. While consistent previous direct measurements of at high forces (F>1 pN), this method, which simple does not require sophisticated setup, allows for lower estimates. used approach deduce effective torsional modulus DNA, decreases force, estimate buckling function various salt conditions.

An effective interface dynamics is derived for a Stefan-type moving-boundary-value problem corresponding to electrostatic aggregation in two dimensions. With the help of conformal-mapping techniques may be reduced many-body-type described by system ordinary differential equations. The method allows one show that Mullins-Sekerka instability this case leads generation cusp singularities finite time.

DNA helicases are enzymes capable of unwinding double-stranded (dsDNA) to provide the single-stranded template required in many biological processes. Among these, UvrD, an essential repair enzyme, has been shown unwind dsDNA while moving 3′-5′ on one strand. Here, we use a single-molecule manipulation technique monitor real-time changes extension single, stretched, nicked substrate as it is unwound by single enzyme. This offers means for measuring rate, lifetime, and processivity enzymatic...

The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one the signatures this chirality, coupling between stretch and twist deformations. We show that extension stretched molecule increases linearly by 0.42 nm per excess turn applied double helix. This result contradicts intuition should lengthen as it is unwound get shorter with overwinding. then present numerical results energy minimizations torsionally restrained display behavior...

The maintenance of cooperation in populations where public goods are equally accessible to all but inflict a fitness cost on individual producers is long-standing puzzle evolutionary biology. An example such scenario the secretion siderophores by bacteria into their environment fetch soluble iron. In planktonic culture, these molecules diffuse rapidly, that same concentration experienced bacteria. However, solid substrates, form dense and packed colonies may alter diffusion dynamics through...

In this work, we discuss the active or passive character of helicases. past years, several studies have used theoretical framework proposed by Betterton and Julicher [Betterton, M.D. Julicher, F. (2005) Opening nucleic-acid double strands helicases: versus opening. Phys. Rev. E, 71, 11904-11911.] to analyse unwinding data assess mechanism helicase under study (active passive). However, procedure has given rise apparently contradictory interpretations: helicases exhibiting similar behaviour...

The small and synthetically easily accessible 7-diethylamino-4-thiocoumarinylmethyl photolabile protecting group has been validated for uncaging with blue light. It exhibits a significant action cross-section in the 470–500 nm wavelength range low light absorption between 350 400 nm. These attractive features have implemented living zebrafish embryos to perform chromatic orthogonal photoactivation of two biologically active species controlling biological development UV blue-cyan sources,...

Abstract Surface colonization underpins microbial ecology on terrestrial environments. Although factors that mediate bacteria–substrate adhesion have been extensively studied, their spatiotemporal dynamics during the establishment of microcolonies remains largely unexplored. Here, we use laser ablation and force microscopy to monitor single-cell course microcolony formation. We find forces rod-shaped bacteria Escherichia coli Pseudomonas aeruginosa are polar. This asymmetry induces...

Nancy J. Crisona1, Terence R. Strick2, David Bensimon2, Vincent Croquette2, and Nicholas Cozzarelli1,3 Department of Molecular Cell Biology, University California, Berkeley, California 94720, USA; 2Laboratoire de Physique Statistique l'ENS, associé aux universités Paris VI et VII, 75231 Cedex 05, France