Local cooperativity mechanism in the DNA melting transition.

We propose a statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsically accounts for the cooperativity related to the free energy penalty of bubble nucleation. The model describes both the unpairing and unstacking parts of the spectroscopically determined experimental melting curves. Furthermore, the model explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. We compute the partition function for the model through the transfer matrix formalism, which we also generalize to include nonlocal chain entropy terms.

• Publication year

  2005

• Venue

  Physical review. E, Statistical, nonlinear, and soft matter physics

• Publication date

  2005-04-20

• Fields of study

  Biology, Medicine, Physics, Chemistry

• Identifiers
  DOI 10.1103/PhysRevE.71.041909arXiv cond-mat/0506067PMID 15903703
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Bubble nucleation and cooperativity in DNA melting.

  2004cited by this paper
• Statistical mechanics of base stacking and pairing in DNA melting.

  2004influential reference
• Length and statistical weight of bubbles in DNA melting.

  2003cited by this paper
• DNA unzipped under a constant force exhibits multiple metastable intermediates

  2003cited by this paper
• Physical chemistry of nucleic acids.

  2002cited by this paper
• Phase diagram of force-induced DNA unzipping in exactly solvable models.

  2001cited by this paper
• Dynamical scaling of the DNA unzipping transition.

  2001cited by this paper
• Roles of stiffness and excluded volume in DNA denaturation.

  2001cited by this paper
• Melting and unzipping of DNA

  2001cited by this paper
• Nucleic Acids: Structures, Properties and Functions

  2001cited by this paper
• I and i

  2001cited by this paper
• Why is the DNA denaturation transition first order?

  2000cited by this paper
• Pulling pinned polymers and unzipping DNA.

  2000cited by this paper
• Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects.

  1999cited by this paper
• Heat capacity effects on the melting of DNA. 1. General aspects.

  1999cited by this paper
• A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

  1998cited by this paper
• Dynamics and thermodynamics of a nonlinear model for DNA denaturation.

  1993cited by this paper
• An optimal formulation of the matrix method in statistical mechanics of one‐dimensional interacting units: Efficient iterative algorithmic procedures

  1990cited by this paper
• Statistical mechanics of a nonlinear model for DNA denaturation.

  1989cited by this paper
• Allowance for heterogeneous stacking in the DNA helix-coil transition theory.

  1984cited by this paper
• Biopolymers

  1984cited by this paper
• Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp.

  1983cited by this paper
• Exactly solved models in statistical mechanics

  1982cited by this paper
• Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid).

  1981cited by this paper
• Biophysical chemistry

  1979cited by this paper
• Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations

  1974cited by this paper
• Occurrence of a phase transition in nucleic acid models.

  1966cited by this paper
• Phase transitions in one dimension and the helix-coil transition in polyamino acids.

  1966cited by this paper
• Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

  1959cited by this paper

• Non-enzymatic error correction in self-replicators without extraneous energy supply

  2025cites this paper
• On the comparison of models and experiments in the study of DNA open states: the problem of degrees of freedom

  2025cites this paper
• Cooperative Rheological State‐Switching of Enzymatically‐Driven Composites of Circular DNA And Dextran

  2023cites this paper
• On the retraction of an adhesive cylindrical indenter from a viscoelastic substrate

  2021cites this paper
• Left-handed compact multi-band circular metamaterial for S-, C- and Ku-band applications

  2021cites this paper
• Direct numerical simulation of permeation of particles through a realistic fibrous filter obtained from X-ray computed tomography images utilizing signed distance function

  2021cites this paper
• The impact of pore-throat shape evolution during dissolution on carbonate rock permeability: pore network modelling and experiments

  2021cites this paper
• A dual-band polarization-independent left-handed symmetrical metamaterial for communication system application

  2021cites this paper
• Influence of slip length on filtration performance of fine particles

  2021cites this paper
• Joint optimization of replication potential and information storage set the letter size of primordial genetic alphabet

  2021cites this paper
• Comprehensive kinetic model for acetylene pretreated mesoporous silica supported bimetallic Co-Ni catalyst during Fischer-Trospch synthesis

  2021cites this paper
• A study on street network resilience in urban areas by urban network analysis: comparative study of old, new and middle fabrics in shiraz

  2021cites this paper
• Analysis of fatigue in the biceps brachii by using rapid refined composite multiscale sample entropy

  2021cites this paper
• In situ X-ray analysis of montmorillonite suspensions in polydimethylsiloxane: Orientation in shear and electric field

  2021cites this paper
• Metamaterial inspired pin wheel fractal shaped antenna using parasitic split ring resonator for modern wireless applications

  2021cites this paper
• Effect of sintering temperature and soaking time on the magnetic properties and transmission behavior of nano crystalline Mg0.8Mn0.2Al0.1Fe1.9O4

  2021cites this paper
• Can high-frequency ECG fluctuations differentiate between healthy and myocardial infarction cases?

  2021cites this paper
• Symmetric square shaped metamaterial structure with quintuple resonance frequencies for S, C, X and Ku band applications

  2021cites this paper
• All-optical tunable slow-light based on an analogue of electromagnetically induced transparency in a hybrid metamaterial

  2021cites this paper
• On the dynamic behaviour of discrete metamaterials: From attenuation to energy localization

  2021cites this paper
• Pore scale modelling of moisture transfer in building materials with the phase field method

  2020cites this paper
• Principles of organelle membrane bridging established using cytosolic tether mimics

  2020cites this paper
• Performance improvement of microstrip patch antenna using a novel double‐layer concentric rings metaplate for 5G millimeter wave applications

  2020cites this paper
• On the signless Laplacian Estrada index of uniform hypergraphs

  2020cites this paper
• Analytical model for drag reduction on liquid-infused structured non-wetting surfaces.

  2020cites this paper
• Signatures of the autonomic nervous system and the heart’s pacemaker cells in canine electrocardiograms and their applications to humans

  2020cites this paper
• Evaporation-driven colloidal cluster assembly using droplets on superhydrophobic fractal-like structures.

  2020cites this paper
• Identification of jamming transition: a critical appraisal

  2020cites this paper
• RADDOSE-XFEL: femtosecond time-resolved dose estimates for macromolecular X-ray free-electron laser experiments

  2020cites this paper
• Temporal dynamics of functional networks in long-term infant scalp EEG

  2020cites this paper
• Composite Thin Films Formed via the Mobile Meniscus Method from Nanodispersed Silver Particles. Structure and Conductivity

  2020cites this paper
• Evaporation Dynamics of a Sessile Droplet on a Hydrophobic Surface

  2020cites this paper
• Scale-free vertical tracking microscopy

  2020cites this paper
• 4D synchrotron microtomography and pore-network modelling for direct in situ capillary flow visualization in 3D printed microfluidic channels.

  2020cites this paper
• Diffuse neural coupling mediates complex network dynamics through the formation of quasi-critical brain states

  2020cites this paper
• Size Polydispersity Tunes Slip Avalanches of Granular Gouge

  2020cites this paper
• Surficial fractures in the Navajo sandstone, south‐western USA: the roles of thermal cycles, rainstorms, granular disintegration, and iterative cracking

  2020cites this paper
• Can artificial neural replicators be useful for studying RNA replicators?

  2020cites this paper
• The dynamics of the aggressive order during a crisis

  2020cites this paper
• A heavy intruder in a locally-shaken granular solid.

  2020cites this paper
• Stability of a directional Marangoni flow.

  2020cites this paper
• A method combining refined composite multiscale fuzzy entropy with PSO-SVM for roller bearing fault diagnosis

  2019cites this paper
• Evaluation of monofractal and multifractal properties of inter-beat (R-R) intervals in cardiac signals for differentiation between the normal and pathology classes

  2019cites this paper
• Experimental evidence of symmetry breaking of transition-path times

  2019cites this paper
• Particle diffusion in extracellular hydrogels.

  2019cites this paper
• Far-field Raman color superlensing based on disordered plasmonics.

  2019cites this paper
• Design of compact dual-band patch antenna loaded with D-shaped complementary split ring resonator

  2019cites this paper
• Experimental investigation on the grain-scale compression behavior of loose wet granular material

  2019cites this paper
• Quantification of Contractile Dynamic Complexities Exhibited by Human Stem Cell-Derived Cardiomyocytes Using Nonlinear Dimensional Analysis

  2019cites this paper
• Performance, complexity and dynamics of force maintenance and modulation in young and older adults

  2019cites this paper
• Generative Model: Intertexture of Firm and Inventor

  2019cites this paper
• Smoothed particle hydrodynamics simulation: a tool for accurate characterization of microfluidic devices

  2019cites this paper
• Optoacoustic mesoscopy analysis and quantitative estimation of specific imaging metrics in Fitzpatrick skin phototypes II to V

  2019cites this paper
• Solid-state polymer electrolytes for high-performance lithium metal batteries

  2019cites this paper
• Photoacoustic assessment of hemodynamic changes in foot vessels

  2019cites this paper
• Vulnerability of public transportation networks against directed attacks and cascading failures

  2019cites this paper
• Directed Transport in Symmetrically Periodic Potentials Induced by Cross-Correlation among Colored Gaussian Noises

  2019cites this paper
• Scalable approximations to k-cycle transversal problems on dynamic networks

  2019cites this paper
• Examining Intensive Groups in YouTube Commenter Networks

  2019cites this paper
• The worm-LBM, an algorithm for a high number of propagation directions on a lattice Boltzmann grid: The case of phonon transport

  2019cites this paper
• Improved Performance of Railroad Ballast Using Geogrids

  2019cites this paper
• A Tunable Optimized Low-Temperature Sensor Based on the Hybrid Photonic Crystals (F4/Bg5/F4) and (Bg5/F4/Bg5)

  2019cites this paper
• Beyond early development: observing zebrafish over 6 weeks with hybrid optical and optoacoustic imaging

  2019cites this paper
• Partial Discharge Fault Diagnosis Based on Multi-Scale Dispersion Entropy and a Hypersphere Multiclass Support Vector Machine

  2019cites this paper
• Underpinning transport phenomena for the patterning of biomolecules.

  2019cites this paper
• An Insight of Machine Learning in Web Network Analysis

  2019cites this paper
• Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment

  2019cites this paper
• Synthesis of Colloidal SU‐8 Polymer Rods Using Sonication

  2019cites this paper
• Structure and Electrical Conductivity of Ring Deposits Resulting from Evaporation of Droplets of Dispersions Containing Gold Nanoparticles with Different Degrees of Anisotropy

  2018cites this paper
• Environmental and sound divergence effects on the performance of rectangular sonic crystals with Helmholtz resonators

  2018cites this paper
• Characterizing information propagation patterns in emergencies: A case study with Yiliang Earthquake

  2018cites this paper
• Entropy-Assisted Emotion Recognition of Valence and Arousal Using XGBoost Classifier

  2018cites this paper
• Mathematical interpretation of Brownian motor model: Limit cycles and directed transport phenomena

  2018cites this paper
• Numerical simulation of a three-layer porous heat exchanger considering lattice Boltzmann method simulation of fluid flow

  2018cites this paper
• Realization of software based imaging energy analyzer on GPU

  2018cites this paper
• A numerical study of droplet dynamic behaviors on a micro-structured surface using a three dimensional color-gradient lattice Boltzmann model.

  2018cites this paper
• On the existence of non-polarized azimuthal-symmetric electromagnetic waves in circular dielectric waveguide filled with nonlinear isotropic homogeneous medium

  2018cites this paper
• Physical vapor deposition of multiphase materials with phase nucleation via a coupled phase-field approach

  2018cites this paper
• Effects of sodium β-sitosteryl sulfate on the phase behavior of dipalmitoylphosphatidylcholine.

  2018cites this paper
• Improved Neural Control of Movements Manifests in Expertise-Related Differences in Force Output and Brain Network Dynamics

  2018cites this paper
• A Review of Models for Bubble Clusters in Cavitating Flows

  2018cites this paper
• A Methodology to Prioritize Security Vulnerabilities in Ports

  2018cites this paper
• Neuroimaging Studies of Primary Dysmenorrhea.

  2018cites this paper
• From classical periodic orbits in integrable $ \pi$π-rational billiards to quantum energy spectrum

  2018cites this paper
• Synthesis of corrugated C-based nanostructures by Br-corannulene oligomerization.

  2018cites this paper
• Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population

  2018cites this paper
• Module-Based Knowledge Discovery for Multiple-Cytosine-Variant Methylation Profile

  2018cites this paper
• Multiphase-field model of small strain elasto-plasticity according to the mechanical jump conditions

  2018cites this paper
• Measuring Brain Complexity During Neural Motor Resonance

  2018cites this paper
• Adapting principles of developmental biology and agent-based modelling for automated urban residential layout design

  2018cites this paper
• The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation

  2018cites this paper
• Modification of capillary pressure by considering pore throat geometry with the effects of particle shape and packing features on water retention curves for uniformly graded sands

  2018cites this paper
• Scale-free networks are rare

  2018cites this paper
• Control of Pyragas Applied to a Coupled System with Unstable Periodic Orbits

  2018cites this paper
• Nanoparticle forming reactive plasmas: a multidiagnostic approach

  2018cites this paper
• Compound Pressure Signal Acquisition

  2018cites this paper
• Cardinal B-Spline Wavelet Based Numerical Method for the Solution of Generalized Burgers–Huxley Equation

  2018cites this paper
• A Triangular Complementary Split Ring Resonator Based Compact Metamaterial Antenna for Multiband Operation

  2018cites this paper
• Assessing prefrontal cortex oxygenation after sport concussion with near‐infrared spectroscopy

  2018cites this paper
• Influence of the long-range ordering of gold-coated Si nanowires on SERS

  2018cites this paper