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Register a new userSecondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization
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Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low temperature / low force compact (folded) structure and a high temperature / high force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c < 2.479 a melting transition is possible; for c <= 2 the chain is always in the folded phase and for 2.479 < c always in the unfolded phase. A force induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ~ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent c^, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.
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We present a new method for calculating internal forces in DNA structures using coarse-grained models and demonstrate its utility with the oxDNA model. The instantaneous forces on individual nucleotides are explored and related to model potentials, and using our framework, internal forces are calculated for two simple DNA systems and for a recently-published nanoscopic force clamp. Our results highlight some pitfalls associated with conventional methods for estimating internal forces, which are based on elastic polymer models, and emphasise the importance of carefully considering secondary structure and ionic conditions when modelling the elastic behaviour of single-stranded DNA. Beyond its relevance to the DNA nanotechnological community, we expect our approach to be broadly applicable to calculations of internal force in a variety of structures -- from DNA to protein -- and across other coarse-grained simulation models.
We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono peaked behavior, depending on the interconversion rates between the conformations, the applied electric field, and the initial conditions. The cumulative probability function of the FPT, in a field-free environment, is shown to have two regimes, characterized by fast and slow timescales. An analytical expression for the mean first passage time of the translocation process is derived, and provides, in addition to the interconversion rates, an extensive characterization of the translocation process. Relationships to experimental observations are discussed.
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized, allowing them to be characterized and the statistics of individual trajectories studied to provide insight into biomolecular folding and function. Because the observed quantity (force or extension) is not necessarily an ideal reaction coordinate, individual observations cannot be uniquely associated with kinetically distinct conformations. While maximum-likelihood schemes such as hidden Markov models have solved this problem for other classes of single-molecule experiments by using temporal information to aid in the inference of a sequence of distinct conformational states, these methods do not give a clear picture of how precisely the model parameters are determined by the data due to instrument noise and finite-sample statistics, both significant problems in force spectroscopy. We solve this problem through a Bayesian extension that allows the experimental uncertainties to be directly quantified, and build in detailed balance to further reduce uncertainty through physical constraints. We illustrate the utility of this approach in characterizing the three-state kinetic behavior of an RNA hairpin in a stationary optical trap.
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.
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