Abstract
DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
Keywords
DNABase pairChemistryComputational biologyBiological systemBiology
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Publication Info
- Year
- 2004
- Type
- review
- Volume
- 33
- Issue
- 1
- Pages
- 415-440
- Citations
- 1320
- Access
- Closed
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Cite This
John SantaLucia,
Donald A. Hicks
(2004).
The Thermodynamics of DNA Structural Motifs.
Annual Review of Biophysics and Biomolecular Structure
, 33
(1)
, 415-440.
https://doi.org/10.1146/annurev.biophys.32.110601.141800
Identifiers
- DOI
- 10.1146/annurev.biophys.32.110601.141800