Academic literature on the topic 'DNA unzipping'

The paper deals with the analysis of a nonlinear Fokker–Planck equation modeling the mechanical unzipping of double-stranded DNA under the influence of an applied force. The dependent variable is the probability density of unzipping m base pairs. The nonlinear Fokker–Planck equation we propose here is obtained when we couple the model proposed in [D. K. Lubensky and D. R. Nelson, Pulling pinned polymers and unzipping DNA, Phys. Rev. Lett.85 (2000) 1572–1575] with a transcendental equation for the applied force. The resulting model incorporates nonlinear effects in a different way than the usual models in kinetic theory. We show the well-posedness of this model. For that we require a combination of techniques coming from second-order kinetic equations and compensated compactness arguments in conservation laws.

In this thesis we develop coarse grained models aiming at understanding physical problems arising from phase transitions which occur at the single molecule level. The thesis will consist of two parts, grossly related to and motivated by the two subjects dealt with above. In the first half, we will focus on critical phenomena in stretching experiments, namely in DNA unzipping and polymer stretching in a bad solvent. In the second part, we will develop a model of thick polymers, with the goal of understanding the origin of the protein folds and the physics underlying the folding ‘transition’, as well as with the hope of shedding some light on some of the fundamental questions highlighted in this Introduction. In the first part of the thesis we will introduce a simple model of self-avoiding walks for DNA unzipping. In this way we can map out the phase diagram in the force vs. temperature plane. This reveals the present of an interesting cold unzipping transition. We then go on to study the dynamics of this coarse grained model. The main result which we will discuss is that the unzipping dynamics below the melting temperature obeys different scaling laws with respect to the opening above thermal denaturation, which is governed by temperature induced fluctuating bubbles. Motivated by this and by recent results from other theoretical groups, we move on to study the relation to DNA unzipping of the stretching of a homopolymer below the theta point. Though also in this case a cold unzipping is present in the phase diagram, this situation is richer from the theoretical point of view because the physics depends crucially on dimension: the underlying phase transition indeed is second order in two dimensions and first order in three. This is shown to be intimately linked to the failure of mean field in this phenomena, unlike for DNA unzipping. In particular, the globule unfolds via a series (hierarchy) of minima. In two dimensions they survive in the thermodynamic limit whereas if the dimension, d, is greater than 2, there is a crossover and for very long polymers the intermediate minima disappear. We deem it intriguing that an intermediate step in this minima hierarchy for polymers of finite length in the three-dimensional case is a regular mathematical helix, followed by a zig-zag structure. This is found to be general and almost independent of the interaction potential details. It suggests that a helix, one of the well-known protein secondary structure, is a natural choice for the ground state of a hydrophobic protein which has to withstand an effective pulling force. In the second part, we will follow the inverse route and ask for a minimal model which is able to account for the basic aspects of folding. By this, we mean a model which contains a suitable potential which has as its ground state a protein-like structure and which can account for the known thermodynamical properties of the folding transition. The existing potential which are able to do that[32] are usually constructed ‘ad hoc’ from knowledge of the native state. We stress that our procedure here is completely different and the model which we propose should be built up starting from minimal assumptions. Our main result is the following. If we throw away the usual view of a polymer as a sequence of hard spheres tethered together by a chain (see also Chapter 1) and substitute it with the notion of a flexible tube with a given thickness, then upon compaction our ’thick polymer’ or ’tube’ will display a rich secondary structure with protein-like helices and sheets, in sharp contrast with the degenerate and messy crumpled collapsed phase which is found with a conventional bead-and-link or bead-and-spring homopolymer model. Sheets and helices show up as the polymer gets thinner and passes from the swollen to the compact phase. In this sense the most interesting regime is a ‘twilight’ zone which consists of tubes which are at the edge of the compact phase, and we thus identify them as ‘marginally compact strucures’. Note the analogy with the result on stretching, in which the helices were in the same way the ‘last compact’ structures or the ‘first extended’ ones when the polymer is being unwinded by a force. After this property of ground states is discussed, we proceed to characterize the thermodynamics of a flexible thick polymer with attraction. The resulting phase diagram is shown to have many of the properties which are usually required from protein effective models, namely for thin polymers there is a second order collapse transition (O collapse) followed, as the temperature is lowered, by a first order transition to a semicrystalline phase where the compact phase orders forming long strands all aligned preferentially along some direction. For thicker polymers the transition to this latter phase occurs directly from the swollen phase, upon lowering T, through a first order transition resembling the folding transition of short proteins.

La technologie des nanopores s'est imposée comme un outil puissant pour étudier le transport biomoléculaire, en particulier pour la translocation et le dézippage des molécules d'ADN. Les études expérimentales ont montré la capacité des nanopores de l'α-hémolysine (αHL) à distinguer différentes séquences et orientations d'ADN. Cependant, les résultats expérimentaux fournissent principalement des informations sur le courant bloqué et le temps de translocation, laissant les détails au niveau moléculaire du processus de dézippage inexplorés. Bien que les simulations de dynamique moléculaire tout-atome soient informatives, elles sont limitées par des échelles de temps réduites. En revanche, les simulations de dynamique moléculaire à gros-grains utilisant le champ de force MARTINI permettent l'étude du transport de l'ADN sur des échelles de temps plus longues, se rapprochant ainsi de celles observées expérimentalement.Cette thèse explore les dynamiques de translocation de l'ADN simple-brin et de dézippage de l'ADN double-brin à travers le nanopore αHL à l'aide d'approches expérimentales et de simulations de dynamique moléculaire dirigées (SMD) à gros-grains. Les différences de temps de translocation entre les extrémités 3' et 5' de l'ADN simple-brin et les temps de dézippage de l'ADN double-brin dans différentes conditions, telles que la structure du duplex d'ADN et la tension appliquée, ont été observées dans les études expérimentales. En particulier, nous avons mesuré des temps de dézippage distincts pour les molécules d'ADN double-brin utilisées, et il a été observé que la dépendance du temps de dézippage à la tension appliquée suivait une loi exponentielle. À mesure que la longueur du duplex augmente, les mécanismes semblent changer en fonction de la structure du duplex. Cependant, les raisons derrière les comportements de translocation et de dézippage restent inaccessibles expérimentalement.En utilisant des simulations de dynamique moléculaire gros-grains, l'influence de l'orientation de l'ADN simple-brin, de la composition en séquences et de la force appliquée sur les dynamiques de translocation a été examinée de manière computationnelle. Nos résultats de simulation ont reproduit les principales observations expérimentales, telles que la large distribution des temps de translocation, les comportements de translocation dépendants de l'orientation, le rôle crucial des interactions électrostatiques entre l'ADN et le nanopore, soulignant l'impact des charges des phosphates de l'ADN sur les taux de translocation, et les dynamiques de translocation dépendantes des séquences sous des forces appliquées variables. En particulier, le rapport entre les temps de translocation des bases puriques et pyrimidiques a également été en bon accord avec les résultats expérimentaux. À la suite des simulations gros-grains, une relation non linéaire entre la vitesse de translocation et la force appliquée a été observée. De plus, les différences de conformations de l'ADN à l'intérieur du nanopore ont apporté des explications supplémentaires aux comportements de translocation dépendants de la séquence et de l'orientation.Cette étude valide le modèle MARTINI à gros-grains comme un outil efficace pour l'étude du transport de l'ADN, montrant sa capacité à compléter les travaux expérimentaux. Nos résultats suggèrent que les simulations de MD gros-grains sont bien adaptées pour dévoiler les mécanismes moléculaires du dézippage de l'ADN, offrant des perspectives inaccessibles par les techniques expérimentales actuelles
Nanopore technology has emerged as a powerful tool for studying biomolecular transport, particularly for the translocation and unzipping of DNA molecules. Experimental studies have shown the ability of α-hemolysin (αHL) nanopores to distinguish between different DNA sequences and ori-entations. However, experimental results primarily provide blocked current and translocation time information, leaving molecular-level details of the unzipping process unexplored. All-atom molecular dynamics (MD) simulations, though informative, are limited by short time scales. Coarse-grained (CG) MD simulations using the MARTINI force field, on the other hand, enable the study of DNA transport over extended time scales, approaching those observed experimentally.This thesis investigates the dynamics of both ssDNA translocation and dsDNA unzipping through the αHL nanopore using a combination of experimental techniques and CG-steered MD (SMD) simulations. Experimental studies explored the translocation times of ssDNA at the 3' and 5' ends, as well as the unzipping times of dsDNA under various conditions, including different duplex structures and applied voltages. Our findings on ssDNA translocation aligned with previous experimental and theoretical results, confirming faster translocation of 3' oriented ssDNA. Additionally, distinct unzipping times were observed for the different duplex structures under identical experimental conditions, with an exponential relationship noted between unzipping time and applied voltage. As the duplex length increased, the unzipping mechanisms appeared to vary depending on the duplex structure. However, the underlying molecular mechanisms behind these translocation and unzipping behaviors remain experimentally inaccessible, highlighting the need for further theoretical studies.By employing CG MD simulations, the influence of ssDNA orientation, sequence composition, and pulling force on translocation dynamics were computationally examined. Our simulation results reproduced the key experimental findings, such as the wide distribution of the translocation times, the orientation-dependent translocation behaviors, the crucial role of electrostatic interactions be-tween DNA and the nanopore, highlighting the impact of DNA phosphate charges on translocation rates, and the sequence-dependent translocation dynamics under varying applied forces. Specifically, the ratio of translocation times of purine and pyrimidine bases was also found to be in good agreement with the experimental findings. As a result of the CG simulations, a non-linear relation-ship between translocation velocity and the applied force was observed. Additionally, differences in DNA conformations inside the nanopore provided additional explanation for the sequence- and orientation-dependent translocation behaviors.This study validates the MARTINI CG model as an effective tool for investigating DNA transport, demonstrating its ability to complement experimental data. Our findings suggest that CG MD simulations are well suited for uncovering the molecular mechanisms underlying DNA unzipping, offering insights that are otherwise inaccessible through current experimental techniques

This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.

In this chapter we discuss the various structural transitions observed on dsDNA upon twisting and stretching: the transition to denatured DNA at negative twist and to P-DNA at positive twist; the transition to S-DNA at large force and its relation with DNA melting. We discuss mechanical unzipping of DNA and show how DNA rehybridization under tension in the presence of complementary oligonucleotides can be used to sequence the molecule.