Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-848d4c4894-jbqgn Total loading time: 0 Render date: 2024-07-01T05:23:10.910Z Has data issue: false hasContentIssue false

4 - DNA dynamics

Published online by Cambridge University Press:  05 March 2015

Alexander Vologodskii
Alexander Vologodskii
Affiliation:
New York University
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Biophysics of DNA , pp. 137 - 164
Publisher: Cambridge University Press
Print publication year: 2015

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Allison, S., Austin, R. & Hogan, M. (1989). Bending and twisting dynamics of short DNAs: analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation. J. Chem. Phys. 90, 3843–54.CrossRefGoogle Scholar
Allison, S. A. (1986). Brownian dynamics simulation of wormlike chains: fluorescence depolarization and depolarized light scattering. Macromolecules 19, 118–24%.CrossRefGoogle Scholar
Allison, S. A., Sorlie, S. S. & Pecora, R. (1990). Brownian dynamics simulations of wormlike chains – dynamic light scattering from a 2311 base pair DNA fragment. Macromolecules 23, 1110–18.CrossRefGoogle Scholar
Anshelevich, V. V., Vologodskii, A. V., Lukashin, A. V. & Frank-Kamenetskii, M. D. (1984). Slow relaxational processes in the melting of linear biopolymers: a theory and its application to nucleic acids. Biopolymers 23, 39–58.CrossRefGoogle ScholarPubMed
Bao, X. R., Lee, H. J. & Quake, S. R. (2003). Behaviour of complex knots in single DNA molecules. Phys. Rev. Lett. 91, 265506.CrossRefGoogle ScholarPubMed
Barkley, M. D. & Zimm, B. H. (1979). Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70, 2991–3007.CrossRefGoogle Scholar
Berne, B. J. & Pecora, R. (1976). Dynamic Light Scattering: with Applications to Chemistry, Biology, and Physics. New York: Wiley.Google Scholar
Blake, R. D. & Fresco, J. R. (1966). Polynucleotides. VII. Spectrophotometric study of the kinetics of formation of the two-stranded helical complex resulting from the interaction of polyriboadenylate and polyribouridylate. J. Mol. Biol. 19, 145–60.Google ScholarPubMed
Bloomfield, V. A., Crothers, D. M. & Tinoco, I., Jr. (1999). Nucleic Acids: Structures, Properties, and Functions. Sausalito, CA: University Science Books.Google Scholar
Bonnet, G., Krichevsky, O. & Libchaber, A. (1998). Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl. Acad. Sci. U. S. A. 95, 8602–6.CrossRefGoogle ScholarPubMed
Cantor, C. R. & Schimmel, P. R. (1980). Biophysical Chemistry. New York: Freeman.Google Scholar
Cherf, G. M., Lieberman, K. R., Rashid, H., Lam, C. E., Karplus, K. & Akeson, M. (2012). Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–8.CrossRefGoogle Scholar
Chirico, G. & Langowski, J. (1994). Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers 34, 415–33.CrossRefGoogle Scholar
Chirico, G. & Langowski, J. (1996). Brownian dynamic simulations of supercoiled DNA with bent sequences. Biophys. J. 71, 955–71.CrossRefGoogle Scholar
Chu, J., Gonzalez-Lopez, M., Cockroft, S. L., Amorin, M. & Ghadiri, M. R. (2010). Realtime monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. Angew. Chem. Int. Ed. 49, 10106–9.CrossRefGoogle Scholar
Craig, M. E., Crothers, D. M. & Doty, P. (1971). Relaxation kinetics of dimer formation by self complementary oligonucleotidesJ. Mol. Biol. 62, 383–401.CrossRefGoogle ScholarPubMed
de Gennes, P. G. (1979). Scaling Concepts in Polymer Physics. Ithaca, NY: Cornell University Press.Google Scholar
Ermak, D. L. & McCammon, J. A. (1978). Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69, 1352–60.CrossRefGoogle Scholar
Fischer, S. G. & Lerman, L. S. (1979). Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16, 191–200.CrossRefGoogle ScholarPubMed
Freese, E. B. & Freese, E. (1963). Rate of DNA strand separation. Biochemistry 2, 707–15.CrossRefGoogle ScholarPubMed
Freier, S. M., Albergo, D. D. & Turner, D. H. (1983). Solvent effects on the dynamics of (dG-dC)3. Biopolymers 22, 1107–31.CrossRefGoogle ScholarPubMed
Friedman, B. & O'shaughnessy, B. (1994). Scaling and universality in polymer reaction kinetics. Int. J. Mod. Phys. B 8, 2555–91.CrossRefGoogle Scholar
Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344, 175–8.CrossRefGoogle ScholarPubMed
Geggier, S., Kotlyar, A. & Vologodskii, A. (2011). Temperature dependence of DNA persistence length. Nucleic Acids Res. 39, 1419–26.CrossRefGoogle ScholarPubMed
Gralla, J. & Crothers, D. M. (1973). Free energy of imperfect nucleic acidhelices. II. Small hairpin loopsJ. Mol. Biol. 73, 497–511.CrossRefGoogle ScholarPubMed
Grosberg, A. Y. & Khohlov, A. R. (1994). Statistical Physics of Macromolecules. New York: AIP Press.Google Scholar
Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers 20, 1503–35.CrossRefGoogle ScholarPubMed
Hagerman, P. J. & Zimm, B. H. (1981). Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers 20, 1481–502.CrossRefGoogle Scholar
Hayden, E. C. (2012). Nanopore genome sequencer makes its debut. Nature News and Comment. DOI: 10.1038/nature.2012.10051Google Scholar
Hearst, J. & Stockmayer, W. (1962). Sedimentation constants of broken chains and wormlike coils. J. Chem. Phys. 37, 1425–33.CrossRefGoogle Scholar
Hoff, A. J. & Roos, A. L. (1972). Hysteresis of denaturation of DNA in the melting range. Biopolymers 11, 1289–94.CrossRefGoogle ScholarPubMed
Huang, J., Schlick, T. & Vologodskii, T. (2001). Dynamics of site juxtaposition in supercoiled DNA. Proc. Natl. Acad. Sci. U. S. A. 98, 968–73.CrossRefGoogle ScholarPubMed
Ivanov, V. I. & Krylov, D. (1992). A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211, 111–27.Google ScholarPubMed
Jian, H., Schlick, T. & Vologodskii, A. (1998). Internal motion of supercoiled DNA: Brownian dynamics simulations ofsite juxtaposition. J. Mol. Biol. 284, 287–96.CrossRefGoogle ScholarPubMed
Jian, H., Vologodskii, A. V. & Schlick, T. (1997). Combined wormlike-chain and bead model for dynamic simulations of long linear DNA. J. Comput. Phys. 136, 168–79.CrossRefGoogle Scholar
Jose, D. & Porschke, D. (2004). Dynamics of the B-A transition of DNA double helices. Nucleic Acids Res. 32, 2251–8.CrossRefGoogle Scholar
Jose, D. & Porschke, D. (2005). The dynamics of the B-A transition of natural DNA double helices. J. Am. Chem. Soc. 127, 16120–8.
Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U. S. A. 93, 13770–3.CrossRefGoogle ScholarPubMed
Kirkwood, J. G. & Riseman, J. (1948). The intrinsic viscosities and diffusion constants of flexible macromolecules on solution. J. Chem. Phys. 16, 565–73.CrossRefGoogle Scholar
Klenin, K., Merlitz, H. & Langowski, J. (1998). A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J. 74, 780–8.CrossRefGoogle ScholarPubMed
Kovacic, R. T. & van Holde, K. E. (1977). Sedimentation of homogeneous double-stranded DNA molecules. Biochemistry 1977, 1490–8.Google Scholar
Krichevsky, O. & Bonnet, G. (2002). Fluorescence correlation spectroscopy: the technique and its applications. Rep. Prog. Phys. 65, 251–97.CrossRefGoogle Scholar
Kuznetsov, S. V. & Ansari, A. (2012). A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. Biophys. J. 102, 101–11.CrossRefGoogle ScholarPubMed
Kuznetsov, S. V., Ren, C. C., Woodson, S. A. & Ansari, A. (2008). Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res. 36, 1098–112.Google ScholarPubMed
Levinthal, C. & Crane, H. (1956). On the unwinding of DNA. Proc. Natl. Acad. Sci. 42, 436–8.CrossRefGoogle ScholarPubMed
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L. A., Lander, E. S. & Dekker, J. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–93.CrossRefGoogle ScholarPubMed
Lilley, D. M. J. (2000). Structures of helical junctions in nucleic acids. Q. Rev. Biophys. 33, 109–59.CrossRefGoogle ScholarPubMed
Lilley, D. M. J. & Clegg, R. M. (1993a). The structure of branched DNA species. Q. Rev. Biophys. 26, 131–75.CrossRefGoogle ScholarPubMed
Lilley, D. M. J. & Clegg, R. M. (1993b). The structure of the four-way junction in DNA. Annu. Rev. Biophys. Biomol. Struct. 22, 299–328.CrossRefGoogle ScholarPubMed
Liu, Y. G., Jun, Y. G. & Steinberg, V. (2007). Longest relaxation times of double-stranded and single-stranded DNA. Macromolecules 40, 2172–6.Google Scholar
Lyamichev, V. I., Panyutin, I. G. & Frank-Kamenetskii, M. D. (1983). Evidence of cruciform structures in superhelical DNA provided by two-dimensional gel electrophoresis. FEBS Lett. 153, 298–302.CrossRefGoogle ScholarPubMed
Marmur, J. & Doty, P. (1961). Thermal renaturation of deoxyribonucleic acids. J. Mol. Biol. 3, 585–94.CrossRefGoogle ScholarPubMed
Martin, R. (1996). Gel Electrophoresis: Nucleic Acids. Oxford: BIOS.Google Scholar
Millar, D. P., Robbins, R. J. & Zewail, A. H. (1980). Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 77, 5593–7.CrossRefGoogle ScholarPubMed
Nelson, J. W. & Tinoco, I., Jr. (1982). Comparison of the kinetics of ribooligonucleotide, deoxyri-booligonucleotide, and hybrid oligonucleotide double-strand formation by temperature-jump kinetics. Biochemistry 21, 5289–95.CrossRefGoogle ScholarPubMed
Neschastnova, A. A., Markina, V. K., Popenko, V. I., Danilova, O. A., Sidorov, R. A., Belitsky, G. A. & Yakubovskaya, M. G. (2002). Mechanism of spontaneous DNA-DNA interaction of homologous linear duplexes. Biochemistry 41, 7795–801.CrossRefGoogle ScholarPubMed
Panyutin, I. G. & Hsieh, P. (1994). The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. U. S. A. 91, 2021–5.CrossRefGoogle ScholarPubMed
Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. (1982). Flipping of cloned d(pCpG)n • d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl. Acad. Sci. U. S. A. 79, 4560–4.CrossRefGoogle ScholarPubMed
Perelroyzen, M. P., Lyamichev, V. I., Kalambet, Y. A., Lyubchenko, Y. L. & Vologodskii, A. V. (1981). A study of the reversibility of helix-coil transition in DNA. Nucleic Acids Res. 9, 4043–59.CrossRefGoogle ScholarPubMed
Perkins, T. T., Quake, S. R., Smith, D. E. & Chu, S. (1994). Relaxation of a single DNA molecule observed by optical microscopy. Science 264, 822–6.CrossRefGoogle ScholarPubMed
Podtelezhnikov, A. & Vologodskii, A. (1997). Simulation of polymer cyclization by Brownian dynamics. Macromolecules 30, 6668–73.CrossRefGoogle Scholar
Pohl, F. M. (1986). Dynamics of the B-to-Z transition in supercoiled DNA. Proc. Natl. Acad. Sci. U. S. A. 83, 4783–7.CrossRefGoogle ScholarPubMed
Pohl, F. M. & Jovin, T. M. (1972). Salt-induced cooperative conformational change of a synthetic DNA – equilibrium and kinetic studies with poly(dG-dC). J. Mol. Biol. 67, 375–96.CrossRefGoogle Scholar
Pörschke, D. (1974). Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. Biophys Chem 1, 381–6.CrossRefGoogle ScholarPubMed
Pörschke, D. & Eigen, M. (1971). Co-operative non-enzymic base recognition. 3. Kinetics of the helix–coil transition of the oligoribouridylic–oligoriboadenylic acid system and of oligori-boadenylic acid alone at acidic pH. J. Mol. Biol. 62, 361–81.CrossRefGoogle ScholarPubMed
Record, M. T. & Zimm, B. H. (1972). Kinetics of helix–coil transition in DNA. Biopolymers 11, 1435–84.CrossRefGoogle ScholarPubMed
Reynaldo, L. P., Vologodskii, A. V., Neri, B. P. & Lyamichev, V. I. (2000). The kinetics of oligonucleotide replacements. J. Mol. Biol. 297, 511–20.CrossRefGoogle ScholarPubMed
Rickwood, D. & Hames, B. D. (1982). Gel Electrophoresis of Nucleic Acids. London: IRL Press.Google Scholar
Rosa, A. & Everaers, R. (2008). Structure and dynamics of interphase chromosomes. PLoS Comput. Biol. 4, e1000153.CrossRefGoogle ScholarPubMed
Ross, P. D. & Sturtevant, J. M. (1960). The kinetics of double helix formation from polyriboadenylic acid and polyribouridylic acid. Proc. Natl. Acad. Sci. U. S. A. 46, 1360–5.CrossRefGoogle ScholarPubMed
Rotne, J. & Prager, S. (1969). Variational treatment of hydrodynamic interaction in polymers. J. Chem. Phys. 50, 4831–7.CrossRefGoogle Scholar
Rybenkov, V. V., Cozzarelli, N. R. & Vologodskii, A. V. (1993). Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. U. S. A. 90, 5307–11.CrossRefGoogle ScholarPubMed
Rybenkov, V. V., Vologodskii, A. V. & Cozzarelli, N. R. (1997). The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. J. Mol. Biol. 267, 299–311.Google ScholarPubMed
Shibata, J. M., Fujimoto, B. S. & Schurr, J. M. (1985). Rotational dynamics of DNA from 10-10 to 10-5 seconds: comparison of theory with optical experiments. Biopolymers 24, 1909–30.CrossRefGoogle ScholarPubMed
Song, L. Z., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H. & Gouaux, J. E. (1996). Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274, 1859–66.CrossRefGoogle ScholarPubMed
Spatz, H. C. & Crothers, D. M. (1969). The rate of DNA unwindingJ. Mol. Biol. 42, 191–219.CrossRefGoogle ScholarPubMed
Stoddart, D., Heron, A. J., Mikhailova, E., Maglia, G. & Bayley, H. (2009). Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc. Natl. Acad. Sci. U. S. A. 106, 7702–7.CrossRefGoogle ScholarPubMed
Studier, F. W. (1969). Effects of the conformation of single-stranded DNA on renaturation and aggregation. J. Mol. Biol. 41, 199–209.Google ScholarPubMed
Thomas, J. C., Allison, S. A., Appelof, C. J. & Schurr, J. M. (1980). Torsional dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral ϕ29 DNA. Biophys. Chem. 12, 177–88.CrossRefGoogle Scholar
Thompson, B. J., Camien, M. N. & Warner, R. C. (1976). Kinetics of branch migration in double-stranded DNA. Proc. Natl. Acad. Sci. U. S. A. 73, 2299–303.CrossRefGoogle ScholarPubMed
Vafabakhsh, R. & Ha, T. (2012). Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337, 1097–101.CrossRefGoogle ScholarPubMed
van Holde, K. E., Johnson, W. C. & Ho, P. S. (1998). Principles of Physical Biochemistry. Upper Saddle River, NJ: Prentice Hall.Google Scholar
Viovy, J. L. (2000). Electrophoresis of DNA and other polyelectrolytespp: physical mechanisms. Rev. Mod. Phys. 72, 813–72.CrossRefGoogle Scholar
Vologodskii, A. (2006). Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys. J. 90, 1594–7.CrossRefGoogle ScholarPubMed
Wada, H. & Netz, R. (2009). Rotational friction of a semiflexible polymer far from equilibrium. Europhys. Lett. 87, 38001.CrossRefGoogle Scholar
Wahl, P., Paoletti, J. & Le Pecq, J. B. (1970). Decay of fluorescence emission anisotropy of the ethidium bromide-DNA complex: evidence for an internal motion in DNA. Proc. Natl. Acad. Sci. U.S.A. 65, 417–21.CrossRefGoogle Scholar
Wang, J. C. & Davidson, N. (1966). Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. J. Mol. Biol. 15, 111–23.CrossRefGoogle ScholarPubMed
Wang, J. C. & Davidson, N. (1968). Cyclization of phage DNAs. Cold Spring Harbor Symp. Quant. Biol. 33, 409–15.CrossRefGoogle ScholarPubMed
Wanunu, M. (2012). Nanopores: a journey towards DNA sequencing. Phys. Life Rev. 9, 125–58.CrossRefGoogle ScholarPubMed
Wetmur, J. G. & Davidson, N. (1968). Kinetics of renaturation of DNA. J. Mol. Biol. 31, 349–70.CrossRefGoogle ScholarPubMed
Wilemski, G. & Fixman, M. (1974a). Diffusion-controlled intrachain reactions of polymers. I. Theory. J. Chem. Phys. 60, 866–77.Google Scholar
Wilemski, G. & Fixman, M. (1974b). Diffusion-controlled intrachain reactions of polymers. II. Results for a pair of terminal reactive groups. J. Chem. Phys. 60, 878–90.Google Scholar
Williams, A. P., Longfellow, C. E., Freier, S. M., Kierzek, R. & Turner, D. H. (1989). Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28, 4283–91.CrossRefGoogle ScholarPubMed
Wu, H. M. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509–13.CrossRefGoogle ScholarPubMed
Yamakawa, H. & Fujii, M. (1973). Translational friction coefficient of wormlike chains. Macro-molecules 6, 407–15.CrossRefGoogle Scholar
Zimm, B. H. (1980). Chain molecule hydrodynamics by the Monte-Carlo method and the validity of the Kirkwood–Riseman approximation. Macromolecules 13, 592–602.CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

  • DNA dynamics
  • Alexander Vologodskii, New York University
  • Book: Biophysics of DNA
  • Online publication: 05 March 2015
  • Chapter DOI: https://doi.org/10.1017/CBO9781139542371.005
Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

  • DNA dynamics
  • Alexander Vologodskii, New York University
  • Book: Biophysics of DNA
  • Online publication: 05 March 2015
  • Chapter DOI: https://doi.org/10.1017/CBO9781139542371.005
Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

  • DNA dynamics
  • Alexander Vologodskii, New York University
  • Book: Biophysics of DNA
  • Online publication: 05 March 2015
  • Chapter DOI: https://doi.org/10.1017/CBO9781139542371.005
Available formats
×