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Force-induced unzipping of DNA with long-range correlated sequence  [PDF]
A. E. Allahverdyan,Zh. S. Gevorkian
Quantitative Biology , 2002,
Abstract: We consider force-induced unzipping transition for a heterogeneous DNA model with a long-range correlated base-sequence. It is shown that as compared to the uncorrelated situation, long-range correlations smear the unzipping phase-transition, change its universality class and lead to non-self-averaging: the averaged behavior strongly differs from the typical ones. Several basic scenarios for this typical behavior are revealed and explained. The results can be relevant for explaining the biological purpose of long-range correlations in DNA.
Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case  [PDF]
Valentina Baldazzi,Serena Bradde,Simona Cocco,Enzo Marinari,Remi Monasson
Quantitative Biology , 2007, DOI: 10.1103/PhysRevE.75.011904
Abstract: The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands.
Unzipping of DNA with correlated base-sequence  [PDF]
A. E. Allahverdyan,Zh. S. Gevorkian,Chin-Kun Hu,Ming-Chya Wu
Physics , 2004, DOI: 10.1103/PhysRevE.69.061908
Abstract: We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase stability of DNA with respect to the external unzipping force. Due to long-range correlations the number of unzipped base-pairs displays two widely different scenarios depending on the details of the base-sequence: either there is no unzipping phase-transition at all, or the transition is realized via a sequence of jumps with magnitude comparable to the size of the system. Both scenarios are different from the behavior of the average number of unzipped base-pairs (non-self-averaging). The results can be relevant for explaining the biological purpose of correlated structures in DNA.
Force and kinetic barriers in unzipping of DNA  [PDF]
S. Cocco,R. Monasson,J. Marko
Quantitative Biology , 2002, DOI: 10.1073/pnas.151257598
Abstract: A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss) simply determine the sequence dependent =12 pN force threshold for DNA strand separation. Using a semi-microscopic model of the binding between nucleotide strands, we show that the greater rigidity of the strands when formed into dsDNA, relative to that of isolated strands, gives rise to a potential barrier to unzipping. The effects of this barrier are derived analytically. The force to keep the extremities of the molecule at a fixed distance, the kinetic rates for strand unpairing at fixed applied force, and the rupture force as a function of loading rate are calculated. The dependence of the kinetics and of the rupture force on molecule length is also analyzed.
Unzipping DNA - towards the first step of replication  [PDF]
Somendra M. Bhattacharjee
Quantitative Biology , 1999, DOI: 10.1088/0305-4470/33/48/501
Abstract: The opening of the Y-fork - the first step of DNA replication - is shown to be a critical phenomenon under an external force at one of its ends. From the results of an equivalent delocalization in a non-hermitian quantum-mechanics problem we show the different scaling behavior of unzipping and melting. The resultant long-range critical features within the unzipped part of Y might play a role in the highly correlated biochemical functions during replication.
Unzipping dsDNA with a force: scaling theory  [PDF]
Jeff Z. Y. Chen
Quantitative Biology , 2001,
Abstract: A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for relationships amongst basic length scales is presented that takes into account the heterogeneity of the sequence. The result agrees with our numerical simulation data, which provides a critical test of the power laws in the unzipping transition region.
Unzipping DNA by force: thermodynamics and finite size behaviour  [PDF]
Rajeev Kapri,Somendra M. Bhattacharjee
Physics , 2005, DOI: 10.1088/0953-8984/18/14/S06
Abstract: We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.
Probing the mechanical unzipping of DNA  [PDF]
N. K. Voulgarakis,A. Redondo,A. R. Bishop,K. O. Rasmussen
Physics , 2005, DOI: 10.1103/PhysRevLett.96.248101
Abstract: A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for $\lambda$-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between {\em in vivo} and {\em in vitro} DNA unzipping.
Unzipping Dynamics of Long DNAs  [PDF]
S. Cocco,R. Monasson,J. F. Marko
Quantitative Biology , 2002, DOI: 10.1103/PhysRevE.66.051914
Abstract: The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For unzipping of 50 kilobase DNAs at less than about 1000 bases per second, thermal equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above kBT in the dsDNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during respectively unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.
Phase diagram of force-induced DNA unzipping in exactly solvable models  [PDF]
D. Marenduzzo,A. Trovato,A. Maritan
Quantitative Biology , 2001, DOI: 10.1103/PhysRevE.64.031901
Abstract: The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of interacting pairs of directed walks in the (1,1,...,1) direction on the hypercubic lattice, and the phase diagram in the force-temperature plane is studied for a variety of cases. The scaling behaviour is determined at both the unzipping and the melting transition. We confirm the existence of a cold denaturation transition recently observed in numerical simulations: for a finite range of forces the system gets unzipped by {\it decreasing} the temperature. The existence of this transition is rigorously established for generic lattice and continuum space models.
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