Probing the mechanical unzipping of DNA

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 lamda-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between in vivo and in vitro DNA unzipping.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

Envisaging quantum transport phenomenon in a muddled base pair of DNA

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au–AT base pair–Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T(E) and HOMO–LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.     

Pulling pinned polymers and unzipping DNA

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA. When the pulling force is increased to a critical value, an "unzipping" transition occurs. For random DNA sequences with short-ranged correlations, we obtain exact results for the number of monomers liberated and the specific heat, including the critical behavior at the transition. Related systems include a random heteropolymer pulled away from an adsorbing surface and a vortex line in a type II superconductor tilted away from a fragmented columnar defect.     

Statistical theory of force-induced unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force F_c(T) for unzipping calculated in the constant force ensemble is found to depend on the potential parameter k which measures the stiffness associated with a single strand of DNA and on D, the well depth of the on-site potential representing the strength of hydrogen bonds in a base pair. The dependence on temperature of F_c(T) is found to be (T_D - T)^1/2 (T_D being the thermal denaturation temperature) with F_c(T_D) = 0 and F_c(0) = . We used the constant extension ensemble to calculate the average force F(y) required to stretch a base pair a y distance apart. The value of F(y) needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance for y 1.0 . The force F(y) in both cases is found to have a very large value for y 0.2 compared to the critical force found from the constant force ensemble to which F(y) approaches for large values of y. It is shown that the value of F(y) at the peak depends on the value of k which measures the energy barrier associated with the reduction in DNA strand rigidity as one passes from dsDNA to ssDNA and on the value of the depth of the on-site potential. The effect of defects on the position and height of the peak in the F(y) curve is investigated by replacing some of the base pairs including the one being stretched by defect base pairs. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of an eye when a base pair far from ends is stretched are investigated.     

Measurement of the phase diagram of DNA unzipping in the temperature-force plane

We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15 to 50 degrees C, and measure the minimum force required to separate the two strands. The measurements also offer information on the free energy of double stranded DNA (dsDNA) at temperatures where dsDNA does not thermally denature in the absence of force. While parts of the phase diagram can be explained using existing models and free energy parameters, others deviate significantly. Possible reasons for the deviations between theory and experiment are considered.     

碱基序列对DNA分子电子结构的影响

将DNA分子看成一维二元随机序列，利用负本征值理论计算其态密度，针对碱基对分布和相对含量等参量，讨论了DNA分子的电子结构.结果表明碱基对分布和相对含量都对电子能态结构影响较大，说明碱基序列对DNA分子的电子结构影响很大. 关键词： DNA分子 电子态密度 碱基对     

DNA unzipping and the unbinding of directed polymers in a random media

We consider the unbinding of a directed polymer in a random media from a wall in d=1+1 dimensions and a simple one-dimensional model for DNA unzipping. Using the replica trick we show that the restricted partition functions of these problems are identical up to an overall normalization factor. Our finding gives an example of a generalization of the stochastic matrix form decomposition to disordered systems, a method which allows us to reduce the dimensionality of the problem. The equivalence between the two problems, for example, allows us to derive the probability distribution for finding the directed polymer a distance z from the wall. We discuss implications of these results for the related Kardar-Parisi-Zhang equation and the asymmetric exclusion process.     

Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA

We demonstrate the first site-specific single-molecule characterization of the prominent activation barrier for the disruption of a protein-DNA binding complex. We achieved this new capability by combining dynamic force spectroscopy with unzipping force analysis of protein association and used the combination to investigate restriction enzyme binding to specific DNA sites. Analysis revealed lifetimes and interaction distances for three protein-DNA interactions. This new method is able to distinguish protein-DNA binding complexes on a site-specific, single-molecule basis.     

Effect of genome sequence on the force-induced unzipping of a DNA molecule

We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force F(y) vs. extension y is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in F(y) curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of F(y).     

Inference of DNA sequences from mechanical unzipping: an ideal-case study

The performances of Bayesian inference to predict the sequence of DNA molecules from fixed-force unzipping experiments are investigated. We show that the probability of misprediction decreases exponentially with the amount of collected data. The decay rate is calculated as a function of biochemical parameters (binding free energies), the sequence content, the applied force, the elastic properties of a DNA single strand, and time resolution.     

Kinetic barriers in RNA unzipping

We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting two-barrier energy landscape accounts for the dependence of the unfolding kinetics on the pulling rate. Furthermore at intermediate force, the two barriers cannot be distinguished by the analysis of the opening kinetic, which turns out to be dominated by a single macro-barrier, whose properties depend non-trivially on the two single barriers. Our results suggest that in pulling experiments on RNA molecule containing tertiary structures, the details of the single kinetic barriers can only be obtained using a low pulling rate value, or in the high force regime.Received: 19 January 2004, Published online: 12 July 2004PACS: 87.14.Gg DNA, RNA - 82.37.-j Single molecule kineticsL. Peliti: Associato INFN, Sezione di Napoli     

Coherence and stacking interaction in DNA duplex

It is shown that a chaotic (deterministic) order, rather than a stochastic randomness, controls the energy minima positions of the stacking interactions in the DNA sequences on large-scales. The chaotic order results in a long-range chaotic coherence between the two complimentary DNA-duplex?s strands. A competition between this broad-band chaotic coherence and the resonance coherence produced by genetic code has been briefly discussed.     

Orbital SCF energies in the double proton transfer of the adenine-thymine base pair

Summary The double-minimum potential generated by the proton motion involved in the two hydrogen bonds of the adenine-thymine base pair can be accounted for through the orbital-energy spectrum. The results show that the greatest interaction between the molecular orbitals is found when the interprotonic distance of the protons is optimum,i.e. at the top of the barrier of the double-minimum potential. This raises the question of charge transfer electronic transitions as a possibility of modelling the behaviour of the double proton transfer in the excited states of this base pair. To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences

In this work, we consider the critical force required to unzip two different naturally occurring sequences of double-stranded DNA (dsDNA) at temperatures ranging from 20 ^°C to 50 ^°C, where one of the sequences has a 53% average guanine-cytosine (GC) content and the other has a 40% GC content. We demonstrate that the force required to separate the dsDNA of the 53% GC sequence into single-stranded DNA (ssDNA) is approximately 0.5 pN, or approximately 5% greater than the critical force required to unzip the 40% GC sequence at the same temperature. In the temperature range between 20 and 40 ^°C the measured critical forces correspond reasonably well to predictions based on a simple theoretical homopolymeric model, but at temperatures above 40 ^°C the measured critical forces are much smaller than the predicted forces. The correspondence between theory and experiment is not improved by using Monte Carlo simulations that consider the heteropolymeric nature of the sequences.     

Micromechanics of polymers

Polymers possess a very large inherent capacity for property modifications. The bridge between structure or morphology and mechanical properties is created by the micromechanical processes of deformation and fracture, the “micromechanics.” Developments mainly in electron microscopy (EM) (scanning, transmission, and high-voltage electron microscopy) and scanning force microscopy (SFM) opened up a wide range of experiments previously impossible, including the in situ study of micromechanical processes. These new techniques are reviewed and used to study micromechanical properties of amorphous and semi-crystalline polymers and several toughened polymers. On the basis of the detailed knowledge of micromechanical mechanisms, a new method of polymer modification becomes a realistic possibility, a method of micromechanical construction of new polymeric systems.     

Oxygen-driven unzipping of graphitic materials

Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.     

Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma

Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.(Communicated by Takao SEKIYA, M.J.A.).     

Complete phase diagram of DNA unzipping: eye, Y fork, and triple point

We study the unzipping of double stranded DNA by applying a pulling force at a fraction s (0< or =s < or =1) from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase diagram shows a strong ensemble dependence for various values of s. In addition, we show the existence of an eye phase and a triple point.