Single-molecule derivation of salt dependent base-pair free energies in DNA

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 unique 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.DNA thermodynamics | DNA unzipping | nearest-neighbor model | optical tweezers T he nearest-neighbor (NN) model (1-4) for DNA thermodynamics has been successfully applied to predict the free energy of formation of secondary structures in nucleic acids. The model estimates the free-energy change to form a double helix from independent strands as a sum over all of resulting bp and adjacent-bp stacks, depending on the constituent four bases of the stack, by using 10 nearest-neighbor base-pair (NNBP) energies. These energies themselves contain contributions from stacking, hydrogen-bonding, and electrostatic interactions as well as configurational entropy loss. Accurately predicting free energies has many applications in biological science: to predict self-assembled structures in DNA origami (5, 6); achievement of high selectivity in the hybridization of synthetic DNAs (7); antigene targeting and siRNA design (8); characterization of translocating motion of enzymes that mechanically disrupt nucleic acids (9); prediction of nonnative states (e.g., RNA misfolding) (10); and DNA guided crystallization of colloids (11).Some of the most reliable estimates of the NNBP energies to date have been obtained from thermal denaturation studies of DNA oligos and polymers (2). Although early studies showed large discrepancies in the NNBP values, nowadays they are remarkably consistent among several groups. In these studies it is assumed that duplexes melt in a two-state fashion. However this assumption is not often the case and a discrepancy between the values obtained using oligomers vs. polymers remains a persistent problem that has been attributed to many factors such as the slow dissociation kinetics induced by a population of transient nondenatured intermediates that develop during thermal denaturation experiments (12). Single-molecule techniques (13) circ...

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