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

Kim J, Doose S, Neuweiler H, Sauer M (2006)
Nucleic Acids Research 34(9): 2516-2527.

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Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides.
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Kim J, Doose S, Neuweiler H, Sauer M. The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Research. 2006;34(9):2516-2527.
Kim, J., Doose, S., Neuweiler, H., & Sauer, M. (2006). The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Research, 34(9), 2516-2527.
Kim, J., Doose, S., Neuweiler, H., and Sauer, M. (2006). The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Research 34, 2516-2527.
Kim, J., et al., 2006. The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Research, 34(9), p 2516-2527.
J. Kim, et al., “The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy”, Nucleic Acids Research, vol. 34, 2006, pp. 2516-2527.
Kim, J., Doose, S., Neuweiler, H., Sauer, M.: The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Research. 34, 2516-2527 (2006).
Kim, Jiho, Doose, Soren, Neuweiler, Hannes, and Sauer, Markus. “The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy”. Nucleic Acids Research 34.9 (2006): 2516-2527.
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PMID: 25068376
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Conformational flexibility of glycosylated peptides.
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Direct monitoring of formation and dissociation of individual metal complexes by single-molecule fluorescence spectroscopy.
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56 References

Data provided by Europe PubMed Central.

Femtosecond dynamics of DNA-mediated electron transfer.
Wan C, Fiebig T, Kelley SO, Treadway CR, Barton JK, Zewail AH., Proc. Natl. Acad. Sci. U.S.A. 96(11), 1999
PMID: 10339533
Fluorescence correlation spectroscopy of triplet states in solution—a theoretical and experimental study
Widengren J., Mets U., Rigler R.., 1995
Multiple time scales for dispersive kinetics in early events of peptide folding
Metzler R., Klafter J., Jortner J., Volk M.., 1998
A close look at fluorescence quenching of organic dyes by tryptophan.
Doose S, Neuweiler H, Sauer M., Chemphyschem 6(11), 2005
PMID: 16224752
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation.
Vaiana AC, Neuweiler H, Schulz A, Wolfrum J, Sauer M, Smith JC., J. Am. Chem. Soc. 125(47), 2003
PMID: 14624606
Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.
Murphy MC, Rasnik I, Cheng W, Lohman TM, Ha T., Biophys. J. 86(4), 2004
PMID: 15041689

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