While the Watson–Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occ

We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two-particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial partic

We study diffusion of (fluorescently) tagged hard-core interacting particles of finite size in a finite one-dimensional system. We find an exact analytical expression for the tagged particle probability density function using a Bethe ansatz, from which the mean square displacement is calculated. The analysis shows the existence of three regimes of drastically different behavior for short, intermed

While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiatio

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few kBT. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We inve

Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quant

We study the search process of a target on a rapidly folding polymer (“DNA”) by an ensemble of particles (“proteins”), whose search combines 1D diffusion along the chain, Lévy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.

We use a master equation approach based on the Poland–Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore–quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins that se

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We investigate the translocation of a stiff polymer consisting of M monomersthrough a nanopore in a membrane, in the presence of binding particles(chaperones) that bind onto the polymer, and partially prevent backsliding ofthe polymer through the pore. The process is characterized by the rates: kfor the polymer to make a diffusive jump through the pore, q for unbinding ofa chaperone, and the rate

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in de

Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out