Single-molecule derivation of salt dependent base-pair free energies in DNA
arXiv:1010.1188 · doi:10.1073/pnas.1001454107
Abstract
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our new energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies and entropies in conditions not accessible by bulk methodologies.
arXiv commentMain text: 27 pages, 4 figures, 2 tables. Supporting Information: 51 pages, 19 figures, 4 tables
References in corpus (4)
Cited by in corpus (53)
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- Coarse-graining DNA for simulations of DNA nanotechnology
- Large work extraction and the Landauer limit in a continuous Maxwell demon
- Experimental free energy measurements of kinetic molecular states using fluctuation theorems
- Force-induced rupture of a DNA duplex
- Non-specific binding of Na and Mg to RNA determined by force spectroscopy methods
- Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles
- A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
- Coarse-grained simulations of DNA overstretching
- Improving free-energy estimates from unidirectional work measurements: theory and experiment
- Effect of salt concentration on the stability of heterogeneous DNA
- Experimental measurement of binding energy, selectivity and allostery using fluctuation theorems
- Theory and Monte Carlo simulations for the stretching of flexible and semi-flexible single polymer chains under external fields
- Stem-loop formation drives RNA folding in mechanical unzipping experiments
- Theory of force-extension curve for modular proteins and DNA hairpins
- Single molecule study of the DNA denaturation phase transition in the force-torsion space
- Sawtooth patterns in biomolecules force-extension curves: an equilibrium-statistical-mechanics theory
- Single-molecule stochastic resonance
- Electrostatic Binding and Hydrophobic Collapse of Peptide-Nucleic Acid Aggregates Quantified Using Force Spectroscopy
- Recent progress in fluctuation theorems and free energy recovery
- Theory for RNA folding, stretching, and melting including loops and salt
- Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization
- Counter-propagating dual-trap optical tweezers based on linear momentum conservation
- Entropy involved in fidelity of DNA replication
- First passage time study of DNA strand displacement
- Phase diagram of mechanically stretched DNA: The salt effect
- Force Spectroscopy with Dual-Trap Optical Tweezers: Molecular Stiffness Measurements and Coupled Fluctuations Analysis
- Cooperativity-Dependent Folding of Single-Stranded DNA
- The role of non-conservative scattering forces and damping on Brownian particles in optical traps
- Force Feedback Effects on Single Molecule Hopping and Pulling Experiments
- Pulling short DNA molecules having defects on different locations
- Folding and unfolding of a triple-branch DNA molecule with four conformational states
- Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways
- Calculating potential of mean force between like-charged nanoparticles: a comprehensive study on salt effects
- Efficient methods for determining folding free energies in single-molecule pulling experiments
- Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
- Dissipation reduction and information-to-measurement conversion in DNA pulling experiments with feedback protocols
- Thermodynamic relations for DNA phase transitions
- Unzipping of DNA under the influence of external fields
- Single-molecule pulling: phenomenology and interpretation
- Experimental test of Sinai's model in DNA unzipping
- Stacking correlation length in single-stranded DNA
- Nonequilibrium thermodynamics of DNA nanopore unzipping
- Sugar-Pucker Force-Induced Transition in Single-Stranded~DNA
- Force Dependence of Proteins' Transition State Position and the Bell-Evans Model
- The possibility of blocking the process of DNA base pairs opening by hydrogen peroxide
- A polymer model of bacterial supercoiled DNA including structural transitions of the double helix
- Universal Axial Fluctuations in Optical Tweezers
- Information-to-work conversion in single molecule experiments: from discrete to continuous feedback
- Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
- Detecting molecular folding from noise measurements
- Possible scenarios of DNA double helix unzipping process
- Steady state of overdamped particles in the non-conservative force field of a simple non-linear model of optical trap