Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Dynamics of a bubble formed in double stranded DNA

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let

Modelling DNA at the mesoscale: a challenge for nonlinear science?

Invited paper, in the series "Open Problems" of NonlinearityInternational audienceWhen it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be used as a guide to improve them. There are nevertheless many open problems, particularly to describe DNA at the scale of a few tens of base pairs, which is relevant for many biological phenomena

Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls (DW), interpolating between bound and unbound segments of the chain. The free energy of the DWs is calculated to leading order beyond the Gaussian approximation. Thermodynamic instabilities (e.g. DNA unzipping and/or thermal denaturation) can be understood in terms of DW formation.Comment: 4 pages, 5 figures, to appear in Phys. Rev. Let

Anharmonic stacking in supercoiled DNA

Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.Comment: In pres

Effects of mechanical strain on thermal denaturation of DNA

As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the undenatured sections can, in principle, alter the nature of the thermal denaturation process. Assuming that the strains associated with this overwinding are not relieved, we find that a simple model of strain-altered melting leads to a suppression of the melting transition when the unaltered transition is continuous. When the melting transition is first order in the absence of strain associated with overwinding, the modification is to a third order phase transition.Comment: 4 pages, 5 figures, RevTe

Effects of distance dependence of exciton hopping on the Davydov soliton

The Davydov model of energy transfer in molecular chains is reconsidered assuming the distance dependence of the exciton hopping term. New equations of motion for phonons and excitons are derived within the coherent state approximation. Solving these nonlinear equations result in the existence of Davydov-like solitons. In the case of a dilatational soliton, the amplitude and width is decreased as a results of the mechanism introduced here and above a critical coupling strength our equations do not allow for localized solutions. For compressional solitons, stability is increased.Comment: RevTeX 13 pages, 3 Postscript figure

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

Experimental evidence of solitary wave interaction in Hertzian chains

We study experimentally the interaction between two solitary waves that approach one to another in a linear chain of spheres interacting via the Hertz potential. When these counter propagating waves collide, they cross each other and a phase shift respect to the noninteracting waves is introduced, as a result of the nonlinear interaction potential. This observation is well reproduced by our numerical simulations and it is shown to be independent of viscoelastic dissipation at the beads contact. In addition, when the collision of equal amplitude and synchronized counter propagating waves takes place, we observe that two secondary solitary waves emerge from the interacting region. The amplitude of secondary solitary waves is proportional to the amplitude of incident waves. However, secondary solitary waves are stronger when the collision occurs at the middle contact in chains with even number of beads. Although numerical simulations correctly predict the existence of these waves, experiments show that their respective amplitude are significantly larger than predicted. We attribute this discrepancy to the rolling friction at the beads contacts during solitary wave propagation