RESUMO
The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water. They become weaker still and the DNA less stable as the ethanol concentration increases but, conversely, the fibers become more compact and the distances between base pairs become more regular. The results show that the melting transition is relatively insensitive to local confinement and depends more on the interaction between the DNA and its aqueous environment.
Assuntos
DNA/química , Etanol/química , Calorimetria , DNA/metabolismo , Modelos Moleculares , Difração de Nêutrons , Conformação de Ácido Nucleico , Desnaturação de Ácido Nucleico , Transição de Fase , Espalhamento a Baixo Ângulo , Soluções/química , Termodinâmica , Temperatura de Transição , Água/químicaRESUMO
Biological organisms exist over a broad temperature range of -15°C to +120°C, where many molecular processes involving DNA depend on the nanoscale properties of the double helix. Here, we present results of extensive molecular dynamics simulations of DNA oligomers at different temperatures. We show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of the DNA melting pathway. The basepair step elasticity contains a weaker, but detectable, entropic contribution in the roll, tilt, and rise degrees of freedom. To extend the validity of our results to the temperature interval beyond the standard melting transition relevant to extremophiles, we estimate the effects of superhelical stress on the stability of the basepair steps, as computed from the Benham model. We predict that although the average twist decreases with temperature in vitro, the stabilizing external torque in vivo results in an increase of â¼1°/bp (or a superhelical density of Δσ ≃ +0.03) in the interval 0-100°C. In the final step, we show that the experimentally observed apparent bending persistence length of torsionally unconstrained DNA can be calculated from a hybrid model that accounts for the softening of the double helix and the presence of transient denaturation bubbles. Although the latter dominate the behavior close to the melting transition, the inclusion of helix softening is important around standard physiological temperatures.
Assuntos
DNA/química , Elasticidade , Nanoestruturas/química , Conformação de Ácido Nucleico , Temperatura , Pareamento de Bases , Sequência de Bases , Entropia , Timina/químicaRESUMO
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.
Assuntos
Pareamento de Bases , DNA/química , Modelos Teóricos , Temperatura , Simulação por ComputadorRESUMO
The melting transition of DNA, whereby the strands of the double-helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fiber DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.
Assuntos
DNA/química , Difração de Nêutrons , Temperatura de Transição , Desnaturação de Ácido NucleicoRESUMO
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced melting have been correctly described by Rouzina and Bloomfield [Biophys. J. 80, 882 (2001)BIOJAU0006-349510.1016/S0006-3495(01)76067-5], neither force threshold has been exactly calculated by theory. In this work, a detailed analysis of the force-extension curve is presented, based on a description of single-stranded (ss) DNA in terms of the discrete Kratky-Porod model, consistent with (i) the contour length expected from the crystallographically determined monomer distance and (ii) a high value of the elastic stretch modulus arising from covalent bonding. The value estimated for the ss-DNA persistence length, λ=1.0 nm, is at the low end of currently known estimates and reflects the intrinsic stiffness of the partially, or fully stretched state, where electrostatic repulsion effects are expected to be minimal. A detailed analysis of single- and double-stranded DNA free energies provides estimates of the overstretching force thresholds. In the unconstrained geometry, the predicted threshold is 64 pN. In the constrained geometry, after allowing for the entropic penalty of the plectonemic topology of the molten state, the predicted threshold is 111 pN.
Assuntos
DNA de Forma B , DNA de Cadeia Simples , Modelos Químicos , Modelos Moleculares , Algoritmos , Fenômenos Biofísicos , Simulação por Computador , DNA de Forma B/química , DNA de Cadeia Simples/química , Módulo de Elasticidade , Modelos Genéticos , Desnaturação de Ácido Nucleico , TermodinâmicaRESUMO
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over fewer than ten base pairs are associated with much larger free energies of formation per site than larger bubbles. As the critical temperature is approached, the free energy associated with further bubble growth becomes vanishingly small. An analysis of average displacement profiles of bubbles of varying sizes at different temperatures reveals almost identical scaled shapes in the absence of nonlinear stacking; nonlinear stacking leads to distinct scaled shapes of large and small bubbles.
Assuntos
Biofísica/métodos , DNA/química , Pareamento de Bases , Simulação por Computador , Modelos Químicos , Modelos Moleculares , Modelos Estatísticos , Conformação de Ácido Nucleico , Desnaturação de Ácido Nucleico , Temperatura , TermodinâmicaRESUMO
The influence of molecular confinement on the melting transition of oriented Na-DNA fibers submerged in poly(ethylene glycol) (PEG) solutions has been studied. The PEG solution exerts an osmotic pressure on the fibers which, in turn, is related to the DNA intermolecular distance. Calorimetry measurements show that the melting temperature increases and the width of the transition decreases with decreasing intermolecular distance. Neutron scattering was used to monitor the integrated intensity and width of a Bragg peak from the B-form of DNA as a function of temperature. The data were quantitatively analyzed using the Peyrard-Bishop-Dauxois model. The experiments and analysis showed that long segments of double-stranded DNA persist until the last stages of melting and that there appears to be a substantial increase of the DNA dynamics as the melting temperature of the DNA is approached.
Assuntos
DNA/química , Temperatura de Transição , Animais , Varredura Diferencial de Calorimetria , Nêutrons , Polietilenoglicóis , Salmão , Espalhamento de Radiação , SoluçõesRESUMO
One-dimensional thermodynamic instabilities are phase transitions, not prohibited by Landau's argument because the energy of the domain wall which separates the two phases is infinite. Whether they actually occur in a given system of particles must be demonstrated on a case-by-case basis by examining the properties of the corresponding singular transfer integral (TI) equation. The present work deals with the generic Peyrard-Bishop model of DNA denaturation. In the absence of exact statements about the spectrum of the singular TI equation, I use Gauss-Hermite quadratures to achieve a single-parameter-controlled approach to rounding effects; this allows me to employ finite-size scaling concepts in order to demonstrate that a phase transition occurs and to derive the critical exponents.
RESUMO
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.
Assuntos
Biofísica , DNA/química , Fenômenos Biofísicos , Modelos Estatísticos , Modelos Teóricos , Conformação de Ácido Nucleico , Temperatura , TermodinâmicaRESUMO
Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured. These results, complemented by a differential calorimetry study of the melting of B-DNA fibers as well as electrophoresis and optical observation data, are analyzed in terms of a one-dimensional mesoscopic model of DNA.
Assuntos
DNA de Forma B/química , Temperatura de Transição , Animais , Modelos Moleculares , Difração de Nêutrons , Desnaturação de Ácido NucleicoRESUMO
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the ÏX174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.
Assuntos
DNA Viral/química , DNA Viral/ultraestrutura , Genoma Viral , Modelos Químicos , Modelos Moleculares , Simulação por Computador , Dinâmica não Linear , Conformação de Ácido NucleicoRESUMO
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, interpolating between bound and unbound segments of the chain. Their free energy 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 domain wall formation.