Topological constraints in nucleic acid hybridization kinetics

Nucleic Acids Research

Volumn 33, Issue 13, 2005, Pages 4090-4095

  Bois, Justin S ^a   Venkataraman, Suvir ^b   Choi, Harry M T ^b   Spakowitz, Andrew J ^a   Wang, Zhen Gang ^a   Pierce, Niles A ^b,c  

^a California Institute of Technology   (United States)

^b California Institute of Technology   (United States)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; SINGLE STRANDED DNA; RNA;

ARTICLE; BASE PAIRING; DNA SEQUENCE; MOLECULAR DYNAMICS; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THEORETICAL STUDY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; KINETICS;

BASE PAIRING; DNA, SINGLE-STRANDED; KINETICS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; RNA;

EID: 23444454487     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki721     Document Type: Article

References (33)

1. deGennes,P.-G. (1968) Statistics of branching and hairpin helices for the dAT polymer. Biopolymers, 6, 715-729.
2. Chen,S.-J. and Dill,K.A. (1995) Statistical thermodynamics of double-stranded polymer molecules. J. Chem. Phys., 103, 5802-5813.
3. SantaLucia,J.,Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
4. Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
5. Flamm,C., Fontana,W., Hofacker,I.L. and Schuster,P. (2000) RNA folding at elementary step resolution. RNA, 6, 325-338.
6. Isambert,H. and Siggia,E.D. (2000) Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
7. Seeman,N.C. (1998) Nucleic acid nanostructures and topology. Angew. Chem. Int. Ed., 37, 3220-3238.
8. Wasserman,S.A. and Cozzarelli,N.R. (1986) Biochemical topology: applications to DNA recombination and replication. Science, 232, 951-960.
9. Brunel,C., Marquet,R., Romby,P. and Ehresmann,C. (2002) RNA loop-loop interactions as dynamic functional motifs. Biochimie, 84, 925-944.
10. Turberfield,A.J., Mitchell,J.C., Yurke,B., Mills,A.P.,Jr, Blakey,M.I. and Simmel,F.C. (2003) DNA fuel for free-running nanomachines. Phys. Rev. Lett., 90, 118102.
11. Seelig,G., Yurke,B. and Winfree,E. (2005) DNA hybridization catalysts and catalyst circuits. In DNA Computing: 10th International Meeting on DNA Based Computers. Lecture Notes in Computer Science, Springer, In press.
12. Dirks,R.M., Lin,M., Winfree,E. and Pierce,N.A. (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res., 32, 1392-1403.
13. Seeman,N.C. (1982) Nucleic acid junctions and lattices. J. Theor. Biol., 99, 237-247.
14. McCaskill,J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119.
15. Goddard,N.L., Bonnet,G., Krichevsky,O. and Libchaber,A. (2000) Sequence dependent rigidity of single stranded DNA. Phys. Rev. Lett., 85, 2400-2403.
16. Pastor,R.W., Zwanzig,R. and Szabo,A. (1996) Diffusion limited first contact of the ends of a polymer: Comparison of theory with simulation. J. Chem. Phys., 105, 3878-3882.
17. Grosberg,A.Y. and Kholkhlov,A.R. (1994) Statistical Physics of Macromolecules. American Institute of Physics Press, NY, pp. 75.
18. Kholodenko,A.L. and Vilgis,T.A. (1998) Some geometrical and topological problems in polymer physics. Phys. Rep., 298, 251-370.
19. Smith,S.B., Cui,Y.J. and Bustamante,C. (1996) The overstretching of B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
20. Wiegel,F.W. (1983) Conformational phase transitions in a macromolecule: exactly solvable models. In Domb,C. and Lebowitz,D.L. (eds), Phase Transitions and Critical Phenomena. Academic Press, London, Vol. 7, pp. 101-149.
21. Onuchic,J.N., Luthey-Schulten,Z. and Wolynes,P.G. (1997) Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem., 48, 545-600.
22. Chen,S.-J. and Dill,K.A. (2000) RNA folding energy landscapes. Proc. Natl Acad. Sci. USA, 97, 646-651.
23. Adams,C.C. (1994) The Knot Book: An Elementary Introduction to the Mathematical Theory of Knots. W.H. Freeman, NY.
24. White,J.H. and Cozzarelli,N.R. (1984) A simple toplogical method for describing stereoisomers of DNA catenanes and knots. Proc. Natl Acad. Sci. USA, 81, 3322-3326.
25. White,J.H., Millett,K.C. and Cozzarelli,N.R. (1987) Description of the topological entanglement of DNA catenanes and knots by a powerful method involving strand passage and recombination. J. Mol. Biol., 197, 585-603.
26. Kolb,F.A., Malmgren,C., Westhof,E., Ehresmann,C., Ehresmann,B., Wagner,E.G.H. and Romby,P. (2000) An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment. RNA, 6, 311-324.
27. Kolb,F.A., Engdahl,H.M., Slagter-Jager,J.G., Ehresmann,B., Ehresmann,C., Westhof,E., Wagner,E.G.H. and Romby,P. (2000) Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA. EMBO J., 19, 5905-5915.
28. Malmgren,C., Wagner,E.G.H., Ehresmann,C., Ehresmann,B. and Romby,P. (1997) Antisense RNA control of plasmid R1 replication. J. Biol. Chem., 272, 12508-12512.
29. Wagner,E.G.H. and Brantl,S. (1998) Kissing and RNA stability in antisense control of plasmid replication. Trends Biochem. Sci., 23, 451-454.
30. Kolb,F.A., Westhof,E., Ehresmann,B., Ehresmann,C., Wagner,E.G.H. and Romby,P. (2001) Four-way junctions in antisense RNA-mRNA complexes involved in plasmid replication control: A common theme? J. Mol. Biol., 309, 605-614.
31. Asano,K. and Mizobuchi,K. (2000) Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. J. Biol. Chem., 275, 1269-1274.
32. Herschlag,D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem., 270, 20871-20874.
33. Zhang,W. and Chen, S.-J. (2002) RNA hairpin-folding kinetics. Proc. Natl Acad. Sci. USA, 99, 1931-1936.