The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
Abstract
In this paper, we derive the general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. Significantly, since the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. We briefly review how the reduced forms of the general equations have been used by many investigators to evaluate mono‐ and bimolecular transitions, and then explain how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecularities. We emphasize the strengths and weaknesses of each method of data analysis so that investigators can select the approach most appropriate for their experimental circumstances. We also describe how to analyze calorimetric heat capacity curves and noncalorimetric differentiated melting curves so as to extract both model‐independent and model‐dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described in this paper should be of particular interest to laboratories that currently are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than two.
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Cites
Nucleic acid junctions and lattices
Seeman, N. C. (1982) · Journal of Theoretical Biology · doi:10.1016/0022-5193(82)90002-9 · Cited by 2,497
Improved Estimation of Secondary Structure in Ribonucleic Acids
TINOCO, I., BORER, P. N., DENGLER, B., LEVINE, M. D., UHLENBECK, O. C., CROTHERS, D. M., & GRALLA, J. (1973) · Nature New Biology · doi:10.1038/newbio246040a0 · Cited by 2,268
Predicting DNA duplex stability from the base sequence
Breslauer, K. J., Frank, R., Blöcker, H., & Marky, L. A. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.11.3746 · Cited by 1,837
Self-citationImproved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
Tinoco, I. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082001.144341 · Cited by 789
Stability of ribonucleic acid double-stranded helices
Borer, P. N., Dengler, B., Tinoco, I., & Uhlenbeck, O. C. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90357-x · Cited by 762
Theory of helix-coil transitions in biopolymers
Poland, D. C. (1970) · Cited by 723
Estimation of Secondary Structure in Ribonucleic Acids
TINOCO, I., UHLENBECK, O. C., & LEVINE, M. D. (1971) · Nature · doi:10.1038/230362a0 · Cited by 680
An immobile nucleic acid junction constructed from oligonucleotides
Kallenbach, N. R., Ma, R.-I., & Seeman, N. C. (1983) · Nature · doi:10.1038/305829a0 · Cited by 646
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Cited by
Self-assembled π-stacks of functional dyes in solution: structural and thermodynamic features
Chen, Z., Lohr, A., Saha-Möller, C. R., & Würthner, F. (2009) · Chem. Soc. Rev. · doi:10.1039/b809359h · Cited by 1,051
Engineered riboregulators enable post-transcriptional control of gene expression
Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., & Collins, J. J. (2004) · Nature Biotechnology · doi:10.1038/nbt986 · Cited by 554
Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future
Ray, A., & Nordén, B. (2000) · The FASEB Journal · doi:10.1096/fasebj.14.9.1041 · Cited by 416
Fletcher, J. M., Boyle, A. L., Bruning, M., Bartlett, G. J., Vincent, T. L., Zaccai, N. R., Armstrong, C. T., Bromley, E. H. C., Booth, P. J., Brady, R. L., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb300028q · Cited by 262
Single-molecule derivation of salt dependent base-pair free energies in DNA
Huguet, J. M., Bizarro, C. V., Forns, N., Smith, S. B., Bustamante, C., & Ritort, F. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001454107 · Cited by 254
Metadata
- Authors
- Marky, L. A., & Breslauer, K. J.
- Venue
- Biopolymers
- Publisher
- Wiley
- Published
- 1987-09
- Volume
- 26
- Issue
- 9
- Pages
- 1601-1620
- ISSN
- 0006-3525 (ISSN-L)
- 1097-0282
- OpenAlex
- W2035485234
- Cited by
- 1,047
- References
- 39
- FWCI
- 4.62
- Type
- journal article
- Language
- en
- Open access
- closed
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