We show that the problem of describing conformations a semiflexible polymer confined to channel can be mapped onto an exactly solvable model in so-called extended de Gennes regime. This regime (where is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means computer simulations. The exact solution predicts precisely how conformational fluctuations depend upon width microscopic parameters characterising physical properties polymer.

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due the importance molecules in vivo. We here observe unfolding linear configuration as light-induced double-strand break occurs, characterize dynamics, compare equilibrium conformational statistics configurations. This is important because it allows us determine what extent existing statistical theories describe extension DNA. find that ratio extensions...

Semiflexible polymers in channels with a rectangular cross section are studied as models for DNA molecules confined to nanochannels. The authors find that the average extension of is approximately independent rectangle aspect ratio, whereas variance depends strongly on both dimensions rectangle.

Experiments measuring DNA extension in nanochannels are at odds with even the most basic predictions of current scaling arguments for conformations confined semiflexible polymers such as DNA. We show that a theory based on weakly self-avoiding, one-dimensional "telegraph" process collapses experimental data and simulation results onto single master curve throughout experimentally relevant region parameter space explains mechanisms play.

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments model calculations are difficult because most theoretical predictions involve undetermined prefactors, the parameters (contour length, Kuhn effective width) compute reliably, leading substantial uncertainties. Here we use a recent asymptotically exact theory for ``extended de Gennes regime'' that allows us compare experimental results with theory....

We study how the orientational correlations of DNA confined to nanochannels depend on channel diameter $D$ by means Monte Carlo simulations and a mean-field theory. This theory describes conformations in experimentally relevant regime where Flory--de Gennes does not apply. show local determine dependence end-to-end distance molecule upon $D$. Tapered provide necessary resolution extension molecules depends Our experimental theoretical results are qualitative agreement.

The final step in the biosynthesis of nicotinamide‐adenine dinucleotide, a major coenzyme cellular redox reactions and involved intracellular signaling, is catalyzed by enzyme nicotinamide mononucleotide adenylyltransferase (NMNAT). X‐ray structure human NMNAT complex with was solved single‐wavelength anomalous dispersion method at resolution 2.9 Å. Human symmetric hexamer whose subunit formed large six‐stranded parallel β‐sheet helices on both sides. displays different oligomerization...

The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. protein splicing domain I catalyzes the excision mature (intein) a precursor and religation flanking amino acid sequences (exteins) to functional protein. Furthermore, is involved in binding recognition specific DNA substrate. Domain II PI-SceI, domain, which structurally homologous other endonucleases LAGLIDADG family, harbors endonucleolytic center vivo initiates process by introducing double-strand cut...

We study the conformations of a self-avoiding polymer confined to channel by computing cross-sectional distributions positions its monomers. By means Monte-Carlo simulations for self-avoiding, freely-jointed chain we determine how distribution given monomer depends on location in polymer, and strongly this is affected self avoidance. To end analyze frequency intra-chain collisions between monomers their spatial position within polymer. show that most occur closely neighboring As consequence...

RAD51 is the key component of homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate physical properties formed DNA using nanofluidic channels fluorescence microscopy. Contrary to bacterial ortholog RecA, forms inhomogeneous long vitro, consisting several protein patches. We demonstrate that a permanent "kink" filament where two patches meet if stretch naked between short. The kinks are readily seen present...

Binding of cAMP receptor protein (CRP) and CytR mediates both positive negative control transcription from Escherichia coli deoP2. Transcription is activated by CRP repressed a multi-protein CRP·CytR·CRP complex. The latter stabilized cooperative interactions between CytR. Similar at the other transcriptional units regulon coordinate expression transport proteins enzymes required for nucleoside catabolism. A fundamental question in prokaryotic eukaryotic gene regulation how combinatorial...

Theoretical results for the extension of a polymer confined to channel are usually derived in limit infinite contour length. But experimental studies and simulations DNA molecules nanochannels not necessarily this asymptotic limit. We calculate statistics span end-to-end distance semiflexible finite length extended de Gennes regime, exploiting fact that problem can be mapped one-dimensional weakly self-avoiding random walk. The thus obtained compare favourably with pruned-enriched Rosenbluth...

If a semiflexible polymer confined to narrow channel bends around by 180°, the is said exhibit hairpin. The equilibrium extension statistics of are well understood when hairpins vanishingly rare or they plentiful. Here, we analyze in intermediate situation via experiments with DNA coated protein RecA, which enhances stiffness molecule approximately one order magnitude. We find that distribution highly non-Gaussian, good agreement Monte-Carlo simulations discrete wormlike chains. develop...

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along channel axis provide large-scale genomic information. It is difficult, however, make channels enough molecule fully stretched. practice, its conformations may form hairpins change spacings between internal segments molecule, and thus label axis. Here, we describe a theory for distribution explains heavy tails observed...

When DNA molecules are heated they denature. This occurs locally so that loops of molten single strands form, connected by intact double-stranded pieces. The properties this ``melting'' transition have been intensively investigated. Recently there has a surge interest in question, part caused experiments determining the partially bound confined to nanochannels. But how does such confinement affect melting transition? To answer question we introduce and solve model predicting affects for...

When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands separated. The statistical physics of this process has a long history and is commonly described in terms Poland-Scheraga (PS) model. Crucial model configurational entropy for melted region (compared an intact same size), quantified by loop factor. In study, we investigate how confinement affects melting transition, using factor ideal Gaussian chain. By subsequent numerical solutions PS model,...

Nanochannels provide means for detailed experiments on the effect of confinement biomacromolecules, such as DNA. We here introduce a model complete unfolding DNA from circular to linear configuration. Two main ingredients are entropic force well friction coefficient process, and we describe associated dynamics by non-linear Langevin equation. By analyzing experimental data where molecules photo-cut unfolded inside nanochannel, our allows us extract values first time. In order numerical these...

Nicotinamide mononucleotide adenylyltransferase catalyses the final step in synthesis of nicotinamide-adenine dinucleotide (NAD+) by transferring adenylyl moiety ATP to nicotinamide (NMN) with release pyrophosphate. The human enzyme was crystallized presence NAD+. Crystals grew orthorhombic space group C2221, unit-cell parameters a = 140.3, b 235.5, c 89.3 Å, and diffract maximum resolution 3.0 Å. Packing considerations suggest trimer or higher multimer be present asymmetric unit crystal....