The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
Thermodynamic Analysis of Interacting Nucleic Acid Strands
Abstract
Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single‐stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base‐pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.
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Cites
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“Although pseudoknots exist in nature [43] and have been incorporated in synthetic DNA systems [46, 42], many natural and synthetic structures of interest do not include pseudoknots [23, 32, 38], and we will not consider them here.”
BackgroundSelf-citationA unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
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Convex Analysis and Minimization Algorithms I
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Improved Estimation of Secondary Structure in Ribonucleic Acids
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THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
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Cited by
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844
Dynamic DNA nanotechnology using strand-displacement reactions
Zhang, D. Y., & Seelig, G. (2011) · Nature Chemistry · doi:10.1038/nchem.957 · Cited by 1,785
NUPACK: Analysis and design of nucleic acid systems
Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., & Pierce, N. A. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21596 · Cited by 1,670
Self-citationProgramming biomolecular self-assembly pathways
Yin, P., Choi, H. M. T., Calvert, C. R., & Pierce, N. A. (2008) · Nature · doi:10.1038/nature06451 · Cited by 1,600
Self-citationControl of DNA Strand Displacement Kinetics Using Toehold Exchange
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Metadata
- Authors
- Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E., & Pierce, N. A.
- Venue
- SIAM Review
- Published
- 2007-01
- Volume
- 49
- Issue
- 1
- Pages
- 65-88
- ISSN
- 0036-1445 (ISSN-L)
- 1095-7200
- OpenAlex
- W2053783019
- Cited by
- 356
- References
- 49
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Open access
- closed
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- Dirks, R. M., Bois, J. S., Schaeffer, J. M., Winfree, E., & Pierce, N. A. (2007). Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM Review. https://doi.org/10.1137/060651100
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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