Title
Single-molecule derivation of salt dependent base-pair free energies in DNA
Date Issued
31 August 2010
Access level
open access
Resource Type
journal article
Author(s)
University of California
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/TTand 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.
Start page
15431
End page
15436
Volume
107
Issue
35
Language
English
OCDE Knowledge area
Biofísica
Bioquímica, Biología molecular
Scopus EID
2-s2.0-77957269559
PubMed ID
Source
Proceedings of the National Academy of Sciences of the United States of America
ISSN of the container
00278424
Sources of information:
Directorio de Producción Científica
Scopus