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A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
Open accessAbstract
A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented. DNA NN ΔG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made. The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used different methods of data analysis; used different salt concentrations; and presented the NN thermodynamics in different formats. As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA polymers and oligomers. Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain. Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics. Empirical salt dependencies are also derived for oligonucleotides and polymers.
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Programmable materials and the nature of the DNA bond
Jones, M. R., Seeman, N. C., & Mirkin, C. A. (2015) · Science · doi:10.1126/science.1260901 · Cited by 1,347
The Thermodynamics of DNA Structural Motifs
SantaLucia, J., & Hicks, D. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.141800 · Cited by 1,314
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Self-citation
Metadata
- Authors
- SantaLucia, J.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 1998-02-17
- Volume
- 95
- Issue
- 4
- Pages
- 1460-1465
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2135995702
- Cited by
- 2,793
- References
- 3
- FWCI
- 14.07
- Type
- journal article
- Language
- en
- Open access
- green
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