ArticleBiochemistry2006
Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- DNA calorimetric force spectroscopy at single base pair resolution.Nature communications · 2025Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters.Chemical physics · 2019Article
- Linking Temperature, Cation Concentration and Water Activity for the B to Z Conformational Transition in DNA.Molecules (Basel, Switzerland) · 2018Article
- The Role of Structural Enthalpy in Spherical Nucleic Acid Hybridization.Journal of the American Chemical Society · 2018Article
- Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site.PloS one · 2018Article
- LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature.Journal of the American Chemical Society · 2017Article
- Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization.Nucleic acids research · 2015Article
- Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.Journal of the American Chemical Society · 2014Article
- Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex.Biophysical journal · 2012Article
- Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer.Biochemistry · 2012Article
- DNA duplex stability: the role of preorganized electrostatics.The journal of physical chemistry. B · 2010Article
- Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- A mesoscale model of DNA and its renaturation.Biophysical journal · 2009Article
- Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry.Biophysical journal · 2009Article
- Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry.Methods in enzymology · 2009Article
- Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.Journal of molecular biology · 2008Article
- RNA helix stability in mixed Na+/Mg2+ solution.Biophysical journal · 2007Article
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2 authors.
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Abstract
Duplexes are the most fundamental elements of nucleic acid folding. Although it has become increasingly clear that duplex formation can be associated with a significant change in heat capacity (deltaC(p)), this parameter is typically overlooked in thermodynamic studies of nucleic acid folding. Analogy to protein folding suggests that base stacking events coupled to duplex formation should give rise to a deltaC(p) due to the release of waters solvating aromatic surfaces of nucleotide bases. In previous work, we showed that the deltaC(p) observed by isothermal titration calorimetry (ITC) for RNA duplex formation depended on salt and sequence [Takach, J. C., Mikulecky, P. J., and Feig, A. L. (2004) J. Am. Chem. Soc. 126, 6530-6531]. In the present work, we apply calorimetric and spectroscopic techniques to a series of designed DNA duplexes to demonstrate that both the salt dependence and sequence dependence of deltaC(p)s observed by ITC reflect perturbations to the same fundamental phenomenon: stacking in the single-stranded state. By measuring the thermodynamics of single strand melting, one can accurately predict the deltaC(p)s observed for duplex formation by ITC at high and low ionic strength. We discuss our results in light of the larger issue of contributions to deltaC(p) from coupled equilibria and conclude that observed deltaC(p)s can be useful indicators of intermediate states in nucleic acid folding phenomena.
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