The initial step of DNA hairpin folding: A kinetic analysis using fluorescence correlation spectroscopy

Nucleic Acids Research

Volumn 34, Issue 9, 2006, Pages 2516-2527

  Kim, Jiho ^a,b   Doose, Sören ^a   Neuweiler, Hannes ^a   Sauer, Markus ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b Institute Pasteur Korea   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; GUANOSINE PHOSPHATE; NUCLEOTIDE; OLIGONUCLEOTIDE; OXAZINE DERIVATIVE; SINGLE STRANDED DNA; FLUORESCENT DYE; GUANOSINE; MR121 OXAZINE FLUOROPHORE;

AQUEOUS SOLUTION; ARTICLE; BASE PAIRING; COMPLEX FORMATION; CONTROLLED STUDY; DNA CONFORMATION; DNA HYBRIDIZATION; DNA STRUCTURE; ENTHALPY; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE SPECTROSCOPY; KINETICS; MOLECULAR INTERACTION; MOLECULAR STABILITY; PRIORITY JOURNAL; STEADY STATE; CHEMISTRY; CONFORMATION; METHODOLOGY; SPECTROFLUOROMETRY;

5'-GUANYLIC ACID; BASE PAIRING; DNA, SINGLE-STRANDED; FLUORESCENT DYES; GUANOSINE; KINETICS; NUCLEIC ACID CONFORMATION; OXAZINES; SPECTROMETRY, FLUORESCENCE;

EID: 33744502886     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl221     Document Type: Article

References (56)

1. Varani,G. (1995) Exceptionally stable nucleic acid hairpins. Annu. Rev. Biophys. Biomol. Struct., 24, 379-404.
2. Uhlenbeck,O.C. (1990) Tetraloops and RNA folding. Nature, 346, 613-614.
3. Tyagi,S. and Kramer,F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
4. Kostrikis,L.G., Tyagi,S., Mhlanga,M.M., Ho,D.D. and Kramer,R.F. (1998) Molecular beacons: Spectral genotyping of human alleles. Science, 279, 1228-1229.
5. Bonnet,G., Tyagi,S., Libchaber,A. and Kramer,F.R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl Acad. Sci. USA, 96, 6171-6176.
6. Ansari,A. and Kuznetsov,S.V. (2005) Is hairpin formation in single-stranded polynucleotide diffusion-controlled? J. Phys. Chem. B, 109, 12982-12989.
7. Wang,X. and Nau,W.M. (2004) Kinetics of end-to-end collision in short single-stranded nucleic acids. J. Am. Chem. Soc., 126, 808-813.
8. Jung,J. and VanOrden,A. (2006) A three-state mechanism for dna hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy. J. Am. Chem. Soc., 128, 1240-1249.
9. Elson,E.L., Scheffler,I.E. and Baldwin,R.L. (1970) Helix formation by d(TA) oligomers. 3. Electrostatic effects. J. Mol. Biol., 54, 401-415.
10. Gralla,J. and Crothers,D.M. (1973) Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol., 73, 497-511.
11. Uhlenbeck,O.C., Borer,P.N., Dengler,B. and Tinoco,I.Jr (1973) Stability of RNA hairpin loops: A6-Cm-U6. J. Mol. Biol., 73, 483-496.
12. Haasnoot,C.A., Hilbers,C.W., van der Marel,G.A., van Boom,J.H., Singh,U.C., Pattabiraman,N. and Kollman,P.A. (1986) On loop folding in nucleic acid hairpin-type structures. J. Biomol. Struct. Dyn., 3, 843-857.
13. Hilbers,C.W., Haasnoot,C.A., de Bruin,S.H., Joordens,J.J., van der Marel,G.A. and van Boom,J.H. (1985) Hairpin formation in synthetic oligonucleotides. Biochimie, 67, 685-695.
14. Wemmer,D.E., Chou,S.H., Hare,D.R. and Reid,B.R. (1985) Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res., 13, 3755-3772.
15. Senior,M.M., Jones,R.A. and Breslauer,K.J. (1988) Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc. Natl Acad. Sci. USA, 85, 6242-6246.
16. Zuker,M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.
17. Paner,T.M., Amaratunga,M., Doktycz,M.J. and Benight,A.S. (1990) Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X = A, T, G, C). Biopolymers, 29, 1715-1734.
18. Vallone,P.M., Paner,T.M., Hilario,J., Lane,M.J., Faldasz,B.D. and Benight,A.S. (1999) Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability. Biopolymers, 50, 425-442.
19. Rentzeperis,D., Alessi,K. and Marky,L.A. (1993) Thermodynamics of DNA hairpins: Contribution of loop size to hairpin stability and ethidium binding. Nucleic Acids Res., 21, 2683-2689.
20. Serra,M.J., Axenson,T.J. and Turner,D.H. (1994) A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry, 33, 14289-14296.
21. Hirao,I., Kawai,G., Yoshizawa,S., Nishimura,Y., Ishido,Y., Watanabe,K. and Miura,K. (1994) Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res., 22, 576-582.
22. Ma,H., Proctor,D.J., Kierzek,E., Kierzek,R., Bevilacqua,P.C. and Gruebele,M. (2006) Exploring the energy landscape of a small RNA hairpin. J. Am. Chem. Soc., 128, 1523-1530.
23. Bonnet,G., Krichevsky,O. and Libchaber,A. (1998) Kinetics of conformal fluctuations in DNA hairpin loops. Proc. Natl Acad. Sci. USA, 95, 8602-8606.
24. Goddard,N.L., Bonnet,G., Krichevsky,O. and Libchaber,A. (2000) Sequence dependent rigidity of single stranded DNA. Phys. Rev. Lett., 85, 2400-2403.
25. Ansari,A., Kuznetsov,S.V. and Shen,Y. (2001) Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc. Natl Acad. Sci. USA, 98, 7771-7776.
26. Ansari,A., Shen,Y. and Kuznetsov,S.V. (2002) Misfolded loops decrease the effective rate of DNA hairpin formation. Phys. Rev. Lett., 88, 069801.
27. Shen,Y.Q., Kuznetsov,S.V. and Ansari,A. (2001) Loop dependence of the dynamics of DNA hairpins. J. Phys. Chem. B, 105, 12202-12211.
28. Kuznetsov,S.V., Shen,Y., Benight,A.S. and Ansari,A. (2001) A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys. J., 81, 2864-2875.
29. Wallace,M.I., Ying,L., Balasubramanian,S. and Klenerman,D. (2001) Non-Arrhenius kinetics for the loop closure of a DNA hairpin. Proc. Natl Acad. Sci. USA, 98, 5584-5589.
30. Wallace,M.I., Ying,L.M., Balasubramanian,S. and Klenerman,D. (2000) FRET fluctuation spectroscopy: Exploring the conformational dynamics of a DNA hairpin loop. J. Phys. Chem. B, 104, 11551-11555.
31. Ying,L.M., Wallace,M.I. and Klenerman,D. (2001) Two-state model of conformational fluctuation in a DNA hairpin-loop. Chem. Phys. Lett., 334, 145-150.
32. Heinlein,T., Knemeyer,J.P., Piestert,O. and Sauer,M. (2003) Photoinduced electron transfer between fluorescent dyes and guanosine residues in DNA-hairpins. J. Phys. Chem. B, 107, 7957-7964.
33. Knemeyer,J.P., Marme,N. and Sauer,M. (2000) Probes for detection of specific DNA sequences at the single-molecule level. Anal. Chem., 72, 3717-3724.
34. Widengren,J., Dapprich,J. and Rigler,R. (1997) Fast interactions between R6G and dGTP in water studied by fluorescence correlation spectroscope. Chem. Phys., 216, 417-426.
35. Seidel,C.A.M., Schulz,A. and Sauer,M.H.M. (1996) Nucleobasespecific quenching of fluorescent dyes .1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J. Phys. Chem. B, 100, 5541-5553.
36. Edman,L., Mets,U. and Rigler,R. (1996) Conformational transitions monitored for single molecules in solution. Proc. Natl Acad. Sci. USA, 93, 6710-6715.
37. Neuweiler,H., Doose,S. and Sauer,M. (2005) A microscopic view of miniprotein folding: Enhanced folding efficiency through formation of an intermediate. Proc. Natl Acad. Sci. USA, 102, 16650-16655.
38. Neuweiler,H. and Sauer,M. (2004) Using photoinduced charge transfer reactions to study conformational dynamics of biopolymers at the single-molecule level. Curr. Pharm. Biotechnol., 5, 285-298.
39. Piestert,O., Barsch,H., Buschmann,V., Heinlein,T., Knemeyer,J.P., Weston,K.D. and Sauer,M. (2003) A single-molecule sensitive DNA hairpin system based on intramolecular electron transfer. Nano Letters, 3, 979-982.
40. Stöhr,K., Hafner,B., Nolte,O., Wolfrum,J., Sauer,M. and Herten,D.P. (2005) Species-specific identification of mycobacterial 16S rRNA PCR amplicons using smart probes. Anal. Chem., 77, 7195-7203.
41. Magde,D., Elson,E.L. and Webb,W.W. (1974) Fluorescence correlation spectroscopy. II. An experimental realization. Biopolymers, 13, 29-61.
42. Rigler,R., Mets,U., Widengren,J. and Kask,P. (1993) Fluorescence correlation spectroscopy with high count rate and low background-analysis of translational diffusion. Eur. Biophys. J., 22, 169-175.
43. Li,H., Ren,X., Ying,L., Balasubramanian,S. and Klenerman,D. (2004) Measuring single-molecule nucleic acid dynamics in solution by two-color filtered ratiometric fluorescence correlation spectroscopy. Proc. Natl Acad. Sci. USA, 101, 14425-14430.
44. Chattopadhyay,K., Elson,E.L. and Frieden,C. (2005) The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. Proc. Natl Acad. Sci. USA, 102, 2385-2389.
45. Hess,S.T., Huang,S., Heikal,A.A. and Webb,W.W. (2002) Biological and chemical applications of fluorescence correlation spectroscopy: A review. Biochemistry, 41, 697-705.
46. Berne,B.J. and Pecora,R. (1976) Dynamic Light Scattering. Wiley, NY.
47. Klafter,J. and Shlesinger,M.F. (1986) On the relationship among three theories of relaxation in disordered systems. Proc. Natl Acad. Sci. USA, 83, 848-851.
48. Lakowicz,J.R. (1999) Principles of Fluorescence Spectroscopy. Kluwer Academic/Plenum Publishers, NY.
49. Lide,D.R. (1994) CRC Handbook of Chemistry and Physics. 75th edn. CRC Press, Boca Raton, FI.
50. Fiebig,T., Wan,C., Kelley,S.O., Barton,J.K. and Zewail,A.H. (1999) Femtosecond dynamics of the DNA intercalator ethidium and electron transfer with mononucleotides in water. Proc. Natl Acad. Sci. USA, 96, 1187-1192.
51. Wan,C., Fiebig,T., Kelley,S.O., Treadway,C.R., Barton,J.K. and Zewail,A.H. (1999) Femtosecond dynamics of DNA-mediated electron transfer. Proc. Natl Acad. Sci. USA, 96, 6014-6019.
52. Widengren,J., Mets,U. and Rigler,R. (1995) Flourescence correlation spectroscopy of triplets in solution - a theoretical and experimental study. J. Phys. Chem. B, 99, 13368-13379.
53. Metzler,R., Klafter,J., Jortner,J. and Volk,M. (1998) Multiple time scales for dispersive kinetics in early events of peptide folding. Chem. Phys. Lett., 293, 477-484.
54. Doose,S., Neuweiler,H. and Sauer,M. (2005) A close look at fluorescence quenching of organic dyes by tryptophan. Chem. Phys. Chem., 6, 2277-2285.
55. Vaiana,A.C., Neuweiler,H., Schulz,A., Wolfrum,J., Sauer,M. and Smith,J.C. (2003) Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation. J. Am. Chem. Soc., 125, 14564-14572.
56. Murphy,M.C., Rasnik,I., Cheng,W., Lohman,T.M. and Ha,T. (2004) Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J., 86, 2530-2537.