Skip to main content
SpringerLink
Log in

Hairpin Formation in Polynucleotides: A Simple Folding Problem?

  • Chapter
Biological Nanostructures and Applications of Nanostructures in Biology

Part of the book series: Bioelectric Engineering ((BEEG))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aalberts, D. P., Parman, J. M., and Goddard, N. L., 2003, Single-strand stacking free energy from DNA beacon kinetics., Biophys. J. 84:3212.

    Google Scholar 

  • Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J. D., 1989, Molecular Biology of the Cell, Garland Publishing, Inc., New York.

    Google Scholar 

  • Alifano, P., Bruni, C. B., and Carlomagno, M. S., 1994, Control of mRNA processing and decay in prokaryotes Genetica 94:157.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Ansari, A., Shen, Y., and Kuznetsov, S. V., 2002, Misfolded loops decrease the effective rate of DNA hairpin formation, Phys. Rev. Lett. 88:069801.

    Article  Google Scholar 

  • Armitage, B., Ly, D., Koch, T., Frydenlund, H., Orum, H., and Schuster, G. B., 1998, Hairpin-forming peptide nucleic acid oligomers, Biochemistry 37:9417.

    Article  Google Scholar 

  • Baldwin, R. L., 1996, Why is protein folding so fast?, Proc. Natl. Acad. Sci. USA 93:2627.

    Google Scholar 

  • Bianco, P. R., Brewer, L. R., Corzett, M., Balhorn, R., Yeh, Y., Kowalczykowski, S. C., and Baskin, R. J., 2001, Processive translocation and DNA unwinding by individual RecBCD enzyme molecules, Nature 409:374.

    Article  Google Scholar 

  • Bieri, O., Wirz, J., Hellrung, B., Schutkowski, M., Drewello, M., and Kiefhaber, T., 1999, The speed limit for protein folding measured by triplet-triplet energy transfer, Proc. Natl. Acad. Sci. USA 96:9597.

    Article  Google Scholar 

  • Bockelmann, U., Thomen, P., Essevaz-Roulet, B., Viasnoff, V., and Heslot, F., 2002, Unzipping DNA with optical tweezers: high sequence sensitivity and force flips, Biophys. J. 82:1537.

    Google Scholar 

  • Bonnet, G., Krichevsky, O., and Libchaber, A., 1998, Kinetics of conformational fluctuations in DNA hairpinloops, Proc. Natl. Acad. Sci. USA 95:8602.

    Article  Google Scholar 

  • 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.

    Google Scholar 

  • Bryngelson, J. D., Onuchic, J. N., Socci, N. D., and Wolynes, P. G., 1995, Funnels, pathways, and the energy landscape of protein folding: a synthesis, Proteins 21:167.

    Article  Google Scholar 

  • Bryngelson, J. D., and Wolynes, P. G., 1989, Intermediates and barrier crossing in a random energy model (with applications to protein folding), J. Phys. Chem. 93:6902.

    Article  Google Scholar 

  • Bustamante, C., Marko, J. F., Siggia, E. D., and Smith, S., 1994, Entropic elasticity of lambda-phage DNA, Science 265:1599.

    Google Scholar 

  • Bustamante, C., Smith, S. B., Liphardt, J., and Smith, D., 2000, Single-molecule studies of DNA mechanics, Curr. Opin. Struct. Biol. 10:279.

    Article  Google Scholar 

  • Cantor, C. R., and Schimmel, P. R., 1980, The behavior of biological macromolecules, W. H. Freeman and Company, New York.

    Google Scholar 

  • Caskey, C. T., Pizzuti, A., Fu, Y. H., Fenwick, R. G. J., and Nelson, D. L., 1992, Triplet repeat mutations in human disease, Science 256:784.

    Google Scholar 

  • Cech, T. R., Zaug, A. J., and Grabowski, P. J., 1981, In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence, Cell. 27:487.

    Article  Google Scholar 

  • Chalikian, T. V., Volker, J., Plum, G. E., and Breslauer, K. J., 1999, A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques, Proc. Natl. Acad. Sci. USA 96:7853.

    Article  Google Scholar 

  • Chen, S. J., and Dill, K. A., 2000, RNA folding energy landscapes, Proc. Natl. Acad. Sci. USA 97:646.

    Google Scholar 

  • Cheng, J. C., Moore, T. B., and Sakamoto, K. M., 2003, RNA interference and human disease., Mol. Genet. Metab. 80:121.

    Article  Google Scholar 

  • Cheong, C., Varani, G., and Tinoco, I. J., 1990, Solution structure of an unusually stable RNA hairpin, 5’GGAC(UUCG)GUCC, Nature 346:680.

    Article  Google Scholar 

  • Chu, Y. G., and Tinoco, I., 1983, Temperature-jump kinetics of the dC-G-T-G-A-A-T-T-C-G-C-G double helix containing a G.T base-pair and the dC-G-C-A-G-A-A-T-T-C-G-C-G double helix containing an extra adenine, Biopolymers 22:1235.

    Article  Google Scholar 

  • Cocco, S., Marko, J. F., and Monasson, R., 2003a, Slow nucleic acid unzipping kinetics from sequence-defined barriers, Eur. Phys. J. E. 10:153.

    Google Scholar 

  • Cocco, S., Marko, J. F., Monasson, R., Sarkar, A., and Yan, J., 2003b, Force-extension behavior of folding polymers, Eur. Phys. J. E. 10:249.

    Google Scholar 

  • Cohen, R. J., and Crothers, D. M., 1971, Rate of unwinding small DNA, J. Mol. Biol. 61:525.

    Article  Google Scholar 

  • Coutts, S. M., 1971, Thermodynamics and kinetics of G-C base pairing in the isolated extra arm of serinespecific transfer RNA from yeast, Biochim. Biophys. Acta 232:94.

    Google Scholar 

  • Craig, M. E., Crothers, D. M., and Doty, P., 1971, Relaxation kinetics of dimer formation by self complementary oligonucleotides, J. Mol. Biol. 62:383.

    Article  Google Scholar 

  • Crews, S., Ojala, D., Posakony, J., Nishiguchi, J., and Attardi, G., 1979, Nucleotide sequence of a region of human mitochondrial DNA containing the precisely identified origin of replication, Nature 277:192.

    Article  Google Scholar 

  • Dai, X., Greizerstein, M. B., Nadas-Chinni, K., and Rothman-Denes, L. B., 1997, Supercoil-induced extrusion of a regulatory DNA hairpin, Proc. Natl. Acad. Sci. USA 94:2174.

    Article  Google Scholar 

  • Dai, X., Kloster, M., and Rothman-Denes, L. B., 1998, Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters, J. Mol. Biol. 283:43.

    Article  Google Scholar 

  • DeGennes, P. G., 1979, Scaling Concepts in Polymer Physics, Cornell University Press, Ithaca, N.Y.

    Google Scholar 

  • Deniz, A. A., Dahan, M., Grunwell, J. R., Ha, T., Faulhaber, A. E., Chemla, D. S., Weiss, S., and Schultz, P. G., 1999, Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Forster distance dependence and subpopulations, Proc. Natl. Acad. Sci. USA 96:3670.

    Article  Google Scholar 

  • Dill, K. A., 1990, Dominant forces in protein folding, Biochemistry 29:7133.

    Article  Google Scholar 

  • Dill, K. A., and Bromberg, S., 2003, Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology, Garland Science Publishing, New York.

    Google Scholar 

  • Dill, K. A., and Chan, H. S., 1997, From Levinthal to pathways to funnels, Nat. Struct. Biol. 4:10.

    Article  Google Scholar 

  • Doi, M., 1975, Diffusion-controlled reaction of polymers, Chem. Phys. 9:455.

    Article  Google Scholar 

  • Doudna, J. A., and Doherty, E. A., 1997, Emerging themes in RNA folding, Fold Des. 2:R65.

    Article  Google Scholar 

  • Draper, D. E., 1999, Themes in RNA-protein recognition, J. Mol. Biol. 293:255.

    Article  Google Scholar 

  • Dyer, R. B., Gai, F., Woodruff, W. H., Gilmanshin, R., and Callender, R. H., 1998, Infrared studies of fast events in protein folding, Acc. Chem. Res. 31:709.

    Article  Google Scholar 

  • Dykxhoorn, D. M., Novina, C. D., and Sharp, P. A., 2003, Killing the messenger: short RNAs that silence gene expression, Nature Rev. Mol. Cell Biol. 4:457.

    Article  Google Scholar 

  • Eaton, W. A., Munoz, V., Thompson, P. A., Henry, E. R., and Hofrichter, J., 1998, Kinetics and dynamics of loops, alpha-helices, and fast-folding proteins, Acc. Chem. Res., 31:745.

    Article  Google Scholar 

  • Eigen, M., and de Maeyer, L., 1963, Relaxation Methods, Interscience, New York, 895.

    Google Scholar 

  • Eisenberg, H., and Felsenfeld, G., 1967, Studies of the temperature-dependent conformation and phase separation of polyriboadenylic acid solutions at neutral pH, J. Mol. Biol. 30:17.

    Article  Google Scholar 

  • Essevaz-Roulet, B., Bockelmann, U., and Heslot, F., 1997, Mechanical separation of the complementary strands of DNA, Proc. Natl. Acad. Sci. USA 94:11935.

    Article  Google Scholar 

  • Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., and Mello, C. C., 1998, Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans, Nature 391:806.

    Article  Google Scholar 

  • Flamm, C., Fontana, W., Hofacker, I. L., and Schuster, P., 2000, RNA folding at elementary step resolution, RNA 6:325.

    Article  Google Scholar 

  • Friedman, B., and O’Shaughnessy, B., 1989, Theory of polymer cyclization, Phys. Rev. A. 40:5950.

    Article  Google Scholar 

  • Gacy, A. M., Goellner, G., Juranic, N., Macura, S., and McMurray, C. T., 1995, Trinucleotide repeats that expand in human disease form hairpin structures in vitro, Cell 81:533.

    Google Scholar 

  • Gerland, U., Bundschuh, R., and Hwa, T., 2001, Force-induced denaturation of RNA, Biophys. J. 81:1324.

    Google Scholar 

  • Glucksmann-Kuis, M. A., Dai, X., Markiewicz, P., and Rothman-Denes, L. B., 1996, E. coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition, Cell 84:147.

    Google Scholar 

  • Goddard, N. L., Bonnet, G., Krichevsky, O., and Libchaber, A., 2000, Sequence dependent rigidity of singlestranded DNA, Phys. Rev. Lett. 85:2400.

    Article  Google Scholar 

  • Goddard, N. L., Bonnet, G., Krichevsky, O., and Libchaber, A., 2002, Goddard et al. reply, Phys. Rev. Lett. 88:069802.

    Article  Google Scholar 

  • Gralla, J., and Crothers, D. M., 1973, Free energy of imperfect nucleic acid helices. II. Small hairpin loops, J. Mol. Biol. 73:497.

    Article  Google Scholar 

  • Gregorian, R. S., Jr., and Crothers, D. M., 1995, Determinants of RNA hairpin loop-loop complex stability, J. Mol. Biol. 248:968.

    Google Scholar 

  • Gruebele, M., Sabelko, J., Ballew, R., and Ervin, J., 1998, Laser temperature jump induced protein refolding, Acc. Chem. Res. 31:699.

    Article  Google Scholar 

  • Grunwell, J. R., Glass, J. L., Lacoste, T. D., Deniz, A. A., Chemla, D. S., and Schultz, P. G., 2001, Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer, J. Am. Chem. Soc. 123:4295.

    Article  Google Scholar 

  • Guo, Z., and Thirumalai, D., 1995, Kinetics of protein folding: Nucleation mechanism, time scales, and pathways, Biopolymers 36:83.

    Article  Google Scholar 

  • Hagen, S. J., Carswell, C. W., and Sjolander, E. M., 2001, Rate of intrachain contact formation in an unfolded protein: temperature and denaturant effects, J. Mol. Biol. 305:1161.

    Article  Google Scholar 

  • Hagen, S. J., Hofrichter, J., Szabo, A., and Eaton, W. A., 1996, Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding, Proc. Natl. Acad. Sci. USA 93:11615.

    Article  Google Scholar 

  • Hagerman, P. J., 1988, Flexibility of DNA, Annu. Rev. Biophys. Biophys. Chem. 17:265.

    Article  Google Scholar 

  • Hamilton, A. J., and Baulcombe, D. C., 1999, A species of small antisense RNA in posttranscriptional gene silencing in plants, Science 286:950.

    Article  Google Scholar 

  • Heus, H. A., and Pardi, A., 1991, Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops, Science 253:191.

    Google Scholar 

  • Hoffman, G. W., 1971, A Nanosecond Temperature-Jump Apparatus, Rev. Sci. Instruments 42:1643.

    Article  Google Scholar 

  • Hofrichter, J., 2001, Laser Temperature-Jump Methods for Studying Folding Dynamics, in: Methods in Molecular Biology, K P. Murphy, ed., Humana Press, Totowa, New Jersey.

    Google Scholar 

  • Hudgins, R. R., Huang, F., Gramlich, G., and Nau, W.M., 2002, A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides, J. Am. Chem. Soc. 124:556.

    Article  Google Scholar 

  • Inners, L. D., and Felsenfeld, G., 1970, Conformation of polyribouridylic acid in solution, J. Mol. Biol. 50:373.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Jacob, M., Schindler, T., Balbach, J., and Schmid, F. X., 1997, Diffusion control in an elementary protein folding reaction, Proc. Natl. Acad. Sci. USA 94:5622.

    Article  Google Scholar 

  • Jaeger, J. A., SantaLucia, J., Jr., and Tinoco, I., Jr., 1993, Determination of RNA structure and thermodynamics, Annu. Rev. Biochem. 62:255.

    Article  Google Scholar 

  • Jaeger, J. A., Turner, D. H., and Zuker, M., 1990, Predicting optimal and suboptimal secondary structure for RNA, Methods Enzymol. 183:281.

    Google Scholar 

  • Jager, M., Nguyen, H., Crane, J. C., Kelly, J. W., and Gruebele, M., 2001, The folding mechanism of a The WW domain, J. Mol. Biol. 311:373.

    Article  Google Scholar 

  • Klausner, R. D., Rouault, T. A., and Harford, J. B., 1993, Regulating the fate of mRNA: the control of cellular iron metabolism, Cell. 72:19.

    Article  Google Scholar 

  • Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M., and Ansari, A., 2004, Kinetics of wrapping/unwrapping of single-stranded DNA around the Escherichia coli SSB tetramer, Biophys. J. 86:588a.

    Google Scholar 

  • 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.

    Google Scholar 

  • Landau, L. D., and Lifshitz, E. M., 1980, Statistical Physics, Pergamon Press, New York.

    Google Scholar 

  • Lapidus, L. J., Eaton, W. A., and Hofrichter, J., 2000, Measuring the rate of intramolecular contact formation in polypeptides, Proc. Natl. Acad. Sci. USA 97:7220.

    Article  Google Scholar 

  • Levinthal, C., 1969, How to Fold Graciously?, in: Mossbauer Spectroscopy in Biological Systems: Proceedings of a meeting held at Allerton House, Monticello, Illinois., P. DeBrunner, J. C. M. Tsibris and E. Munck, eds., Univ. of Illinois Bulletin, Urbana, IL, pp. 22–24.

    Google Scholar 

  • Lilley, D. M., 1981, Hairpin-loop formation by inverted repeats in supercoiled DNA is a local and transmissible property, Nucleic Acids Res. 9:1271.

    Google Scholar 

  • Lilley, D. M., 2003, The origins of RNA catalysis in ribozymes, Trends Biochem. Sci. 28:495.

    Article  Google Scholar 

  • Liphardt, J., Onoa, B., Smith, S. B., Tinoco, I. J., and Bustamante, C., 2001, Reversible unfolding of single RNA molecules by mechanical force, Science 292:733.

    Article  Google Scholar 

  • Lohman, T. M., and Bjornson, K. P., 1996, Mechanisms of helicase-catalyzed DNA unwinding, Annu. Rev. Biochem. 65:169.

    Article  Google Scholar 

  • Maier, B., Bensimon, D., and Croquette, V., 2000, Replication by a single DNA polymerase of a stretched single-stranded DNA, Proc. Natl. Acad. Sci. USA 97:12002.

    Article  Google Scholar 

  • Marino, J. P., Gregorian, R. S., Csankovszki, G., and Crothers, D. M., 1995, Bent helix formation between RNA hairpins with complementary loops, Science 268:1448.

    Google Scholar 

  • Marko, J. F., and Siggia, E. D., 1994, Fluctuations and supercoiling of DNA, Science 265:506.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Miller, J. L., and Kollman, P. A., 1997a, Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics, Biophys. J. 73:2702.

    Google Scholar 

  • Miller, J. L., and Kollman, P. A., 1997b, Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics, J. Mol. Biol. 270:436.

    Article  Google Scholar 

  • Miller, W. G., Brant, D. A., and Flory, P. J., 1967, Random coil configurations of polypeptide copolymers, J. Mol. Biol. 23:67.

    Google Scholar 

  • Mills, J. B., Vacano, E., and Hagerman, P. J., 1999, Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA), J. Mol. Biol. 285:245.

    Article  Google Scholar 

  • Montanari, A., and Mezard, M., 2001, Hairpin formation and elongation of biomolecules, Phys. Rev. Lett. 86:2178.

    Article  Google Scholar 

  • Munoz, V., and Eaton, W. A., 1999, A simple model for calculating the kinetics of protein folding from threedimensional structures, Proc. Natl. Acad. Sci. USA 96:11311.

    Article  Google Scholar 

  • Munoz, V., Thompson, P. A., Hofrichter, J., and Eaton, W. A., 1997, Folding dynamics and mechanism of β-hairpin formation, Nature 390:196.

    Google Scholar 

  • Nielsen, P. E., 1999, Peptide nucleic acids as therapeutic agents, Current opinion in structural biology. 9:353.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Pan, J., Thirumalai, D., and Woodson, S. A., 1997, Folding of RNA involves parallel pathways, J. Mol. Biol. 273:7.

    Article  Google Scholar 

  • Pan, T., and Sosnick, T. R., 1997, Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity, Nat. Struct. Biol. 4:931.

    Article  Google Scholar 

  • Plaxco, K. W., and Baker, D., 1998, Limited internal friction in the rate-limiting step of a two-state protein folding reaction, Proc. Natl. Acad. Sci. USA 95:13591.

    Article  Google Scholar 

  • Podtelezhnikov, A., and Vologodskii, A., 1997, Simulations of polymer cyclization by brownian dynamics, Macromolecules 30:6668.

    Article  Google Scholar 

  • Poland, D., and Scheraga, H. A., 1970, Theory of helix-coil transitions in biopolymers; statistical mechanical theory of order-disorder transitions in biological macromolecules, Academic Press, New York,, xvii.

    Google Scholar 

  • Porschke, D., 1974a, A direct measure of the unzippering rate of a nucleic acid double helix, Biophys. Chem. 2:97.

    Google Scholar 

  • Porschke, D., 1974b, Thermodynamics and Kinetics Parameters of an Oligonucleotide Hairpin Helix, Biophys. Chem. 1:381.

    Google Scholar 

  • Porschke, D., 1977, Elementary steps of base recognition and helix-coil transitions in nucleic acids, Mol. Biol. Biochem. Biophys. 24:191.

    Google Scholar 

  • Porschke, D., and Eigen, M., 1971, Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic—oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH, J. Mol. Biol. 62:361.

    Article  Google Scholar 

  • Porschke, D., Uhlenbeck, O. C., and Martin, F. H., 1973, Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs., Biopolymers 12:1313.

    Google Scholar 

  • Rief, M., Clausen-Schaumann, H., and Gaub, H. E., 1999, Sequence-dependent mechanics of single DNA molecules, Nat. Struct. Biol. 6:346.

    Google Scholar 

  • Rivetti, C., Walker, C., and Bustamante, C., 1998, Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility, J. Mol. Biol. 280:41.

    Article  Google Scholar 

  • Romer, R., Schomburg, U., Krauss, G., and Maass, G., 1984, Escherichia coli single-stranded DNA binding protein is mobile on DNA: 1H NMR study of its interaction with oligo-and polynucleotides, Biochemistry 23:6132.

    Google Scholar 

  • Roth, D. B., Menetski, J. P., Nakajima, P. B., Bosma, M. J., and Gellert, M., 1992, V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes, Cell 70:983.

    Article  Google Scholar 

  • Rouzina, I., and Bloomfield, V. A., 1999, Heat capacity effects on the melting of DNA. 1. General aspects, Biophys. J. 77:3242.

    Google Scholar 

  • Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferre-D’Amare, A. R., 2002, Transition state stabilization by a catalytic RNA, Science 298:1421.

    Article  Google Scholar 

  • Sali, A., Shakhnovich, E., and Karplus, M., 1994a, How does a protein fold?, Nature 369:248.

    Google Scholar 

  • Sali, A., Shakhnovich, E., and Karplus, M., 1994b, Kinetics of protein folding. A lattice model study of the requirements for folding to the native state, J. Mol. Biol. 235:1614.

    Article  Google Scholar 

  • Sarzynska, J., Kulinski, T., and Nilsson, L., 2000, Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge, Biophys. J. 79:1213.

    Google Scholar 

  • Schindler, T., and Schmid, F. X., 1996, Thermodynamic properties of an extremely rapid protein folding reaction, Biochemistry 35:16833.

    Google Scholar 

  • Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., and Woodson, S. A., 1998, RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting, Science 279:1940.

    Article  Google Scholar 

  • Serra, M. J., and Turner, D. H., 1995, Predicting thermodynamic properties of RNA, Methods Enzymol. 259:242.

    Google Scholar 

  • Shen, Y., Kuznetsov, S. V., and Ansari, A., 2001, Loop dependence of the dynamics of DNA hairpins, J. Phys. Chem. B. 105:12202.

    Google Scholar 

  • Shirts, M. R., and Pande, V. S., 2001, Mathematical analysis of coupled parallel simulations, Phys. Rev. Lett. 86:4983.

    Article  Google Scholar 

  • Smith, S. B., Cui, Y., and Bustamante, C., 1996, Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules, Science 271:795.

    Google Scholar 

  • Smolke, C. D., Carrier, T. A., and Keasling, J. D., 2000, Coordinated, differential expression of two genes through directed mRNA cleavage and stabilization by secondary structures, Appl. Environ. Microbiol. 66:5399.

    Article  Google Scholar 

  • Socci, N. D., Onuchic, J. N., and Wolynes, P. G., 1996, Diffusive dynamics of the reaction coordinate for protein folding funnels, J. Chem. Phys. 104:5860.

    Article  Google Scholar 

  • Sorin, E. J., Engelhardt, M. A., Herschlag, D., and Pande, V. S., 2002, RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop, J. Mol. Biol. 317:493.

    Article  Google Scholar 

  • Sorin, E. J., Rhee, Y. M., Nakatani, B. J., and Pande, V. S., 2003, Insights into nucleic acid Conformational dynamics from massively parallel stochastic simulations, Biophys. J. 85:790.

    Google Scholar 

  • Spatz, H., and Baldwin, R. L., 1965, Study of the folding of the dAT copolymer by kinetics measurements of melting, J. Mol. Biol. 11:213.

    Google Scholar 

  • Srinivasan, J., Miller, J., Kollman, P. A., and Case, D. A., 1998, Continuum solvent studies of the stability of RNA hairpin loops and helices, J. Biomol. Struct. Dyn. 16:671.

    Google Scholar 

  • Stannard, B. S., and Felsenfeld, G., 1975, The conformation of polyriboadenylic acid at low temperature and neutral pH. A single-stranded rodlike structure, Biopolymers 14:299.

    Article  Google Scholar 

  • Steinfeld, J. I., Francisco, J. S., and Haas, W. L., 1999, Chemical Kinetics and Dynamics, Prentice Hall, New Jersey.

    Google Scholar 

  • Szabo, A., Schulten, K., and Schulten, Z., 1980, First passage time approach to diffusion controlled reactions, J. Chem. Phys. 72:4350.

    Google Scholar 

  • Tan, Y. J., Oliveberg, M., and Fersht, A. R., 1996, Titration properties and thermodynamics of the transition state for folding: comparison of two-state and multi-state folding pathways, J. Mol. Biol. 264:377.

    Article  Google Scholar 

  • Thirumalai, D., 1998, Native secondary structure formation in RNA may be a slave to tertiary folding, Proc. Natl. Acad. Sci. USA 95:11506.

    Article  Google Scholar 

  • Thirumalai, D., Lee, N., Woodson, S. A., and Klimov, D., 2001, Early events in RNA folding, Annu. Rev. Phys. Chem. 52:751.

    Article  Google Scholar 

  • Thirumalai, D., and Woodson, S. A., 1996, Kinetics of folding of proteins and RNA, Acc. Chem. Res. 29:433.

    Article  Google Scholar 

  • Thomen, P., Bockelmann, U., and Heslot, F., 2002, Rotational drag on DNA: a single molecule experiment, Phys. Rev. Lett. 88:248102.

    Article  Google Scholar 

  • Tinland, B., Pluen, A., Sturm, J., and Weill, G., 1997, Persistence length of single-stranded DNA, Macromolecules 30:5763.

    Article  Google Scholar 

  • Turner, D. H., 2000, Conformational Changes, in: Nucleic Acids: Structures, Properties, and Functions, V. A. Bloomfield, D. M. Crothers and I. J. Tinoco, ed., University Science Books, Sausalito, California.

    Google Scholar 

  • Turner, D. H., and Sugimoto, N., 1988, RNA structure prediction, Annu. Rev. Biophys. Biophys. Chem. 17:167.

    Article  Google Scholar 

  • Uhlenbeck, O. C., 1990, Tetraloops and RNA folding, Nature 346:613.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Vallone, P. M., and Benight, A. S., 1999, Melting studies of short DNA hairpins containing the universal base 5-nitroindole, Nucleic Acids Res. 27:3589.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Varani, G., 1995, Exceptionally stable nucleic acid hairpins, Annu. Rev. Biophys. Biomol. Struct. 24:379.

    Article  Google Scholar 

  • Vesnaver, G., and Breslauer, K. J., 1991, The contribution of DNA single-stranded order to the thermodynamics of duplex formation, Proc. Natl. Acad. Sci. USA 88:3569.

    Google Scholar 

  • Wallace, M. I., Ying, L., Balasubramanian, S., and Klenerman, D., 2000, FRET fluctuation spectroscopy: exploring the conformational dynamics of a DNA hairpin loop, J. Phys. Chem. B. 104:11551.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • Wang, J. C., and Davidson, N., 1966a, On the probability of ring closure of lambda DNA, J. Mol. Biol. 19:469.

    Google Scholar 

  • Wang, J. C., and Davidson, N., 1966b, Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA, J. Mol. Biol. 15:111.

    Article  Google Scholar 

  • Wang, J. C., and Davidson, N., 1968, Cyclization of phage DNAs, Cold. Spring Harb. Symp. Quant. Biol. 33:409.

    Google Scholar 

  • Wartell, R. M., and Benight, A. S., 1985, Thermal denaturation of DNA molecules: a comparison of theory with experiment, Phys. Rep. 126:67.

    Article  Google Scholar 

  • Wetmur, J. G., and Davidson, N., 1968, Kinetics of renaturation of DNA, J. Mol. Biol. 31:349.

    Article  Google Scholar 

  • Wilemski, G., and Fixman, M., 1974, Diffusion-controlled intrachain reactions of polymers. I. Theory, J. Chem. Phys. 60:866.

    Google Scholar 

  • Williams, A. P., Longfellow, C. E., Freier, S. M., Kierzek, R., and Turner, D. H., 1989, Laser temperaturejump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC, Biochemistry 28:4283.

    Article  Google Scholar 

  • Williams, D. J., and Hall, K. B., 1999, Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model, Biophys. J. 76:3192.

    Google Scholar 

  • Williams, M. C., Wenner, J. R., Rouzina, I., and Bloomfield, V. A., 2001, Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching, Biophys. J. 80:1932.

    Google Scholar 

  • Wilson, K. S., and von Hippel, P. H., 1995, Transcription termination at intrinsic terminators: the role of the RNA hairpin, Proc. Natl. Acad Sci. USA 92:8793.

    Google Scholar 

  • Winnik, M. A., 1986, Cyclic Polymers, Elsevier, New York.

    Google Scholar 

  • Wolynes, P. G., Onuchic, J. N., and Thirumalai, D., 1995, Navigating the folding routes, Science 267:1619.

    Google Scholar 

  • Wu, M., and Tinoco, I., Jr., 1998, RNA folding causes secondary structure rearrangement, Proc. Natl. Acad. Sci. USA 95:11555.

    Google Scholar 

  • Wuite, G. J., Smith, S. B., Young, M., Keller, D., and Bustamante, C., 2000, Single-molecule studies of the effect of template tension on T7 DNA polymerase activity, Nature 404:103.

    Google Scholar 

  • Xodo, L. E., Manzini, G., Quadrifoglio, F., van der Marel, G. A., and van Boom, J. H., 1988, The duplexhairpin conformational transition of d(CGCGCGATCGCGCG) and d(CGCGCGTACGCGCG): a thermodynamic and kinetic study, J. Biomol. Struct. Dyn. 6:139.

    Google Scholar 

  • Young, M. A., Ravishanker, G., and Beveridge, D. L., 1997, A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation, Biophys. J. 73:2313.

    Google Scholar 

  • Zacharias, M., 2001, Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model, Biophys. J. 80:2350.

    Article  Google Scholar 

  • Zagrovic, B., Sorin, E. J., and Pande, V., 2001, β-hairpin folding simulations in atomistic detail using an implicit solvent model, J. Mol. Biol. 313:151.

    Article  Google Scholar 

  • Zarrinkar, P. P., Wang, J., and Williamson, J. R., 1996, Slow folding kinetics of RNase P RNA, RNA 2:564.

    Google Scholar 

  • Zarrinkar, P. P., and Williamson, J. R., 1994, Kinetic intermediates in RNA folding, Science 265:918.

    Google Scholar 

  • Zhang, W., and Chen, S. J., 2002, RNA Hairpin Folding Kinetics, Proc. Natl. Acad. Sci. USA 99:1931.

    Google Scholar 

  • Zhang, Y., Zhou, H., and Ou-Yang, Z. C., 2001, Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions, Biophys. J. 81:1133.

    Google Scholar 

  • Zhuang, X., Bartley, L. E., Babcock, H. P., Russell, R., Ha, T., Herschlag, D., and Chu, S., 2000, A singlemolecule study of RNA catalysis and folding, Science 288:2048.

    Article  Google Scholar 

  • Zichi, D. A., 1995, Molecular dynamics of RNA with the OPLS force field. Aqueous simulations of a hairpin containing a tetranucleotide loop, J. Am. Chem. Soc. 117:2957.

    Article  Google Scholar 

  • Zuker, M., 1989, On finding all suboptimal foldings of an RNA molecule, Science 244:48.

    MathSciNet  Google Scholar 

  • Zwanzig, R., 1988, Diffusion in a rough potential, Proc. Natl. Acad. Sci. USA 85:2029.

    MathSciNet  Google Scholar 

  • Zwanzig, R., Szabo, A., and Bagchi, B., 1992, Levinthal’s paradox, Proc. Natl. Acad. Sci. USA 89:20.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607

    Anjum Ansari

  2. Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607

    Serguei V. Kuznetsov

Authors
  1. Anjum Ansari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Serguei V. Kuznetsov
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of Illinois at Chicago, Chicago, Illinois

    Michael A. Stroscio  & Mitra Dutta  & 

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer Science + Business Media, Inc.

About this chapter

Cite this chapter

Ansari, A., Kuznetsov, S.V. (2004). Hairpin Formation in Polynucleotides: A Simple Folding Problem?. In: Stroscio, M.A., Dutta, M. (eds) Biological Nanostructures and Applications of Nanostructures in Biology. Bioelectric Engineering. Springer, Boston, MA. https://doi.org/10.1007/0-306-48628-8_5

Download citation

  • DOI: https://doi.org/10.1007/0-306-48628-8_5

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-306-48627-2

  • Online ISBN: 978-0-306-48628-9

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation