Thermodynamic Analysis of Interacting Nucleic Acid Strands

DOI10.1137/060651100MaRDI QIDQ3427770zbMATH OpenOpenAlexWikidataFDO

Authors Robert M. Dirks, Justin S. Bois, J. Schäeffer, Erik Winfree, Niles A. Pierce

Publication date 27 March 2007

Published in SIAM Review (Search for Journal in Brave)

Full work available at URL https://authors.library.caltech.edu/7706/

zbMATH Keywords

base pairconvexitydilute solutionDNAdynamic programmingequilibriummultiple strandsovercountingpartition functionredundancyRNAsecondary structuresymmetry

Mathematics Subject Classification ID

Exact enumeration problems, generating functions (05A15) Chemistry (general) in thermodynamics and heat transfer (80A50) Classical equilibrium statistical mechanics (general) (82B05) Convex programming (90C25) Dynamic programming (90C39) Optimality conditions and duality in mathematical programming (90C46) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

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Cited in

(23)

• Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
• Characterization of alpha helices interacting with nucleic acids
• A heuristic approach to RNA-RNA interaction prediction
• Energy and structural analysis of double nucleic acid triplets
• Intramolecular interactions in aminoacyl cyclic-3',5'-nucleotides
• Using temperature effects to predict the interactions between two RNAs
• On the local form and transitions of pre-symmetry sets
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• Stochastic simulation of the kinetics of multiple interacting nucleic acid strands
• Localized hybridization circuits
• Enumeration approach to computing chemical equilibria
• scientific article; zbMATH DE number 1342094 (Why is no real title available?)
• Strand algebras for DNA computing
• DNA Computing
• The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
• Computing properties of thermodynamic binding networks: an integer programming approach
• Predicting minimum free energy structures of multi-stranded nucleic acid complexes is APX-hard
• Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts.
• Computing with chemical reaction networks: a tutorial
• Combinatorial analysis of interacting RNA molecules
• Symmetric circular matchings and RNA folding
• RNA triplet repeats: improved algorithms for structure prediction and interactions
• Predicting RNA secondary structures with pseudoknots by MCMC sampling

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