Single-molecule derivation of salt dependent base-pair free energies in DNA

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 35, 2010, Pages 15431-15436

  Huguet, Josep M ^a   Bizarro, Cristiano V ^a,b   Forns, Núria ^a,b   Smith, Steven B ^c   Bustamante, Carlos ^c   Ritort, Felix ^a,b  

^a UNIVERSITY OF BARCELONA   (Spain)

^b BIOMATERIALES Y NANOMEDICINA CIBER BBN   (Spain)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA thermodynamics; DNA unzipping; Nearest neighbor model; Optical tweezers

Indexed keywords

DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; SODIUM CHLORIDE;

ALGORITHM; ARTICLE; DNA REPAIR; ENERGY; ENTHALPY; PRIORITY JOURNAL; TEMPERATURE SENSITIVITY; THERMODYNAMICS;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; DNA; DNA, SINGLE-STRANDED; ENTROPY; MODELS, CHEMICAL; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; SODIUM CHLORIDE; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 77957269559     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1001454107     Document Type: Article

References (36)

1. Calladine C, Drew H, Luisi B, Travers A (2004) Understanding DNA: the molecule and how it works (Elsevier Academic Press, Amsterdam), 3rd Ed.
2. SantaLucia JJ (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460-1465. (Pubitemid 128624151)
3. Devoe H, Tinoco IJ (1962) The stability of helical polynucleotides: base contributions. J Mol Biol 4:500-517.
4. Crothers DM, Zimm BH (1964) Theory of the melting transition of synthetic polynucleotides: evaluation of the stacking free energy. J Mol Biol 9:1-9.
5. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297-302.
6. Douglas SM, et al. (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414-418.
7. Shoemaker DD, et al. (2001) Experimental annotation of the human genome using microarray technology. Nature 409:922-927.
8. Dorsett Y, Tuschl T (2004) siRNAs: applications in functional genomics and potential as therapeutics. Nat Rev Drug Discov 3:318-329.
9. Johnson DS, Bai1 L, Smith BY, Patel SS, Wang MD (2007) Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 129:1299-1309.
10. Russel R (2008) RNA misfolding and the action of chaperones. Front Biosci 13:1-20.
11. Nykypanchuk D, Maye MM, van der Lelie D, Gang O (2008) DNA-guided crystallization of colloidal nanoparticles. Nature 451:549-552.
12. Holbrook JA, Capp MW, Saecker RM, Record MTJ (1999) Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry 38:8409-8422.
13. Ritort F (2006) Single-molecule experiments in biological physics: methods and applications. J Phys Condens Mat 18:R531-R583. (Pubitemid 44159969)
14. Lubensky DK, Nelson DR (2000) Single molecule statistics and the polynucleotide unzipping transition. Phys Rev E 65:031917.
15. Essevaz-Roulet B, Bockelmann U, Heslot F (1997) Mechanical separation of the complementary strands of DNA. Proc Natl Acad Sci USA 94:11935-11940.
16. Rief M, Clausen-Schaumann H, Gaub HE (1999) Sequence-dependent mechanics of single DNA molecules. Nat Struct Biol 6:346-349. (Pubitemid 29166483)
17. Danilowicz C, et al. (2003) DNA unzipped under a constant force exhibits multiple metastable intermediates. Proc Natl Acad Sci USA 100:1694-1699.
18. Bockelmann U, Thomen P, Essevaz-Roulet B, Viasnoff V, Heslot F (2002) Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys J 82:1537-1553.
19. Shundrovsky A, Smith CL, Lis TJ, Peterson CL, Wang M (2006) Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Biol 13:549-554. (Pubitemid 43848910)
20. Bustamante C, Smith SB (2006) Light-force sensor and method for measuring axial optical-trap forces from changes in light momentum along an optical axis. U.S. Patent 7,133,132 B2.
21. Smith SB, Rivetti C (2010) TweezersLAB. http://tweezerslab.unipr.it.
22. Zhang Y, Zhou H, Ou-Yang Z-C (2001) Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions. Biophys J 81:1133-1143.
23. Dessinges M, et al. (2002) Stretching single stranded DNA, a model polyelectrolyte. Phys Rev Lett 89:248102.
24. ZukerM(2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415.
25. Peyret N (2000) Prediction of nucleic acid hybridization: parameters and algorithms. PhD dissertation (Wayne State University, Department of Chemistry, Detroit, MI).
26. Zuker M (2009) The Rensselaer bioinformatics web server. http://mfold.bioinfo.rpi.edu.
27. Tan Z-J, Chen S-J (2006) Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys J 90:1175-1190.
28. Alemayehu S, et al. (2009) Influence of buffer species on the thermodynamics of short DNA duplex melting: sodium phosphate versus sodium cacodylate. J Phys Chem B 113:2578-2586.
29. Nakano S, Fujimoto M, Hara H, Sugimoto N (1999) Nucleic acid duplex stability: influence of base composition on cation effects. Nucleic Acids Res 27:2957-2965.
30. Cheatham TE, III, Kollman PA (1997) MD simulations highlight the structural differences among DNA:DNA,RNA:RNA and DNA:RNA hybrid duplexes. J Am Chem Soc 119:4805-4825.
31. Owczarzy R, et al. (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43:3537-3554. (Pubitemid 38391709)
32. Owczarzy R (2005) Melting temperatures of nucleic acids: discrepancies in analysis. Biophys Chem 117:207-215.
33. Marky LA, Breslauer KJ (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26:1601-1620.
34. Smith SB, Cui Y, Bustamante C (1996) Overstretching B. DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271:795-799.
35. Seol Y, Skinner GM, Visscher K (2007) Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking. Phys Rev Lett 98:158103.
36. Manosas M, Ritort F (2005) Thermodynamic and kinetic aspects of RNA pulling experiments. Biophys J 88:3224-3242.