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A DNA-centered explanation of the DNA polymerase translocation mechanism

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A DNA-centered explanation of the DNA polymerase translocation mechanism

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Arias-Gonzalez, JR. (2017). A DNA-centered explanation of the DNA polymerase translocation mechanism. Scientific Reports. 7:1-8. https://doi.org/10.1038/s41598-017-08038-2

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Title: A DNA-centered explanation of the DNA polymerase translocation mechanism
Author: Arias-Gonzalez, J. R.
UPV Unit: Universitat Politècnica de València. Departamento de Física Aplicada - Departament de Física Aplicada
Issued date:
[EN] DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA ...[+]
Subjects: DNA , Polymerase , Single molecule , Mechano-chemistry
Copyrigths: Reconocimiento (by)
Scientific Reports. (issn: 2045-2322 )
DOI: 10.1038/s41598-017-08038-2
Nature Publishing Group
Publisher version: https://doi.org/10.1038/s41598-017-08038-2
Project ID:
The author thanks B. Ibarra and F.J. Cao for fruitful discussion and H.Rodriguez-Rodriguez for critical reading of the manuscript. This work was supported the Spanish Ministry of Economy and Competitiveness (grant number ...[+]
Type: Artículo


Bustamante, C., Cheng, C. & Mejia, Y. X. Revisiting the central dogma one molecule at a time. Cell 144, 480–497 (2011).

van Oijen, A. M. & Loparo, J. J. Single-molecule studies of the replisome. Annu. Rev. Biophys. 39, 429–448 (2010).

Wang, H.-Y., Elston, T., Mogilner, A. & Oster, G. Force generation in RNA polymerase. Biophys. J. 74, 1186–1202 (1998). [+]
Bustamante, C., Cheng, C. & Mejia, Y. X. Revisiting the central dogma one molecule at a time. Cell 144, 480–497 (2011).

van Oijen, A. M. & Loparo, J. J. Single-molecule studies of the replisome. Annu. Rev. Biophys. 39, 429–448 (2010).

Wang, H.-Y., Elston, T., Mogilner, A. & Oster, G. Force generation in RNA polymerase. Biophys. J. 74, 1186–1202 (1998).

Julicher, F. & Bruinsma, R. Motion of RNA polymerase along DNA: A stochastic model. Biophys. J. 74, 1169–1185 (1998).

Voliotis, M., Cohen, N., Molina-París, C. & Liverpool, T. B. Fluctuations, pauses, and backtracking in DNA transcription. Biophys. J. 94, 334–348 (2008).

Arias-Gonzalez, J. R. Entropy involved in fidelity of DNA replication. PLoS One 7, e42272 (2012).

Morin, J. A. et al. Active DNA unwinding dynamics during processive DNA replication. Proc. Natl. Acad. Sci. USA 109, 8115–8120 (2012).

Manosas, M. et al. Mechanism of strand displacement synthesis by DNA replicative polymerases. Nucleic Acids Res. 40, 6174–6186 (2012).

Yasuda, R., Noji, H., Kinosita, K. Jr. & Yoshida, M. f 1-atpase is a highly efficient molecular motor that rotates wit h discrete 120° steps. Cell 93, 1117–1124 (1998).

Oster, G. & Wang, H. How protein motors convert chemical energy into mechanical work, 1 edn. (ed. Schliwa, M.) (Wiley-VCH, 2003).

Chemla, Y. R. & Smith, D. E. Single-molecule studies of viral dna packaging. Adv. Exp. Med. Biol. 726, 549–584 (2012).

Arias-Gonzalez, J. R. Optical tweezers to study viruses. Subcell. Biochem. 68, 273–304 (2013).

Visscher, K., Schnitzer, M. J. & Block, S. M. Single kinesin molecules studied with a molecular force clamp. Nature 400, 184–189 (1999).

Goel, A., Frank-Kamenetskii, M. D., Ellenberger, T. & Herschbach, D. Tuning DNA “strings”: Modulating the rate of DNA replication with mechanical tension. Proc. Natl. Acad. Sci. USA 98, 8485–8489 (2001).

Arias-Gonzalez, J. R. Single-molecule portrait of DNA and RNA double helices. Integr. Biol. 6, 904–925 (2014).

Herrero-Galan, E. et al. Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level. J. Am. Chem. Soc. 135, 122–131 (2013).

Saenger, W. Principles of nucleic acid structure, 2 edn. (Springer-Verlag, New York, 1984).

Calladine, C. R., Drew, H., Luisi, B. & Travers, A. Understanding DNA. The molecule and how it works, 3 edn. (Elsevier, Academic Press, 2004).

Hormeno, S. et al. Mechanical properties of high-g·c content DNA with a-type base-stacking. Biophys. J. 100, 1996–2005 (2011).

Berman, A. J. et al. Structures of phi29 dna polymerase complexed with substrate: the mechanism of translocation in b-family polymerases. EMBO J. 26, 3494–3505 (2007).

Hogg, M., Wallace, S. S. & Doublié, S. Crystallographic snapshots of a replicative dna polymerase encountering an abasic site. EMBO J. 23, 1483–1493 (2004).

Franklin, M. C., Wang, J. & Steitz, T. A. Structure of the replicating complex of a pol alpha family dna polymerase. Cell 105, 657–667 (2001).

Doublié, S., Tabor, S., Long, A. M., Richardson, C. C. & Ellenberger, T. Crystal structure of a bacteriophage t7 dna replication complex at 2.2 a resolution. Nature 391, 251–258 (1998).

Blasco, M. A., Lázaro, J. M., Bernad, A., Blanco, L. & Salas, M. Phi29 dna polymerase active site. J. Biol. Chem. 267, 19427–19434 (1992).

Kunkel, T. A. & Bebenek, K. DNA replication fidelity. Annu. Rev. Biochem. 69, 497–529 (2000).

Kunkel, T. A. DNA replication fidelity. J. Biol. Chem. 279, 16895–16898 (2004).

Santoso, Y. et al. Conformational transitions in DNA polymerase i revealed by single-molecule FRET. Proc. Natl. Acad. Sci. USA 107, 715–720 (2010).

Morin, J. A. et al. Mechano-chemical kinetics of dna replication: identification of the translocation step of a replicative dna polymerase. Nucleic Acids Res. 43, 3643–3652 (2015).

Hormeno, S., Ibarra, B., Valpuesta, J. M., Carrascosa, J. L. & Arias-Gonzalez, J. R. Mechanical stability of low humidity single dna molecules. Biopolymers 97, 199–208 (2012).

Hormeno, S. et al. Condensation prevails over b-a transition in the structure of DNA at low humidity. Biophys. J. 100, 2006–2015 (2011).

SantaLucia, J. & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).

Friedberg, E. C. & Fischhaber, P. L. DNA replication fidelity. eLS 69, 497–529 (2005).

Arias-Gonzalez, J. R. Information management in DNA replication modeled by directional, stochastic chains with memory. J. Chem. Phys. 145, 185103 (2016).

Petruska, J. et al. Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc Natl Acad Sci USA 85, 6252–6256 (1988).

Shu, Y.-G., Song, Y.-S., Ou-Yang, Z.-C. & Li, M. A general theory of kinetics and thermodynamics of steady-state copolymerization. J. Phys.: Condens. Matter 27, 235105 (2015).

Gaspard, P. Kinetics and thermodynamics of exonuclease-deficient DNA polymerases. Phys. Rev. E 93, 042419 (2016).

Gaspard, P. Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading. Phys. Rev. E 93, 042420 (2016).

Song, Y.-S., Shu, Y.-G., Zhou, X., Ou-Yang, Z.-C. & Li, M. Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects. J. Phys.: Condens. Matter 29, 025101 (2017).

Erie, D. A., Yager, T. D. & von Hippel, P. H. The single-nucleotide addition cycle in transcription: a biophysical and biochemical perspective. Annu. Rev. Biophys. Biomol. Struct. 21, 379–415 (1992).

Odijk, T. Stiff chains and filaments under tension. Macromolecules 28, 7016–7018 (1995).

Wang, M. D., Yin, H., Landick, R., Gelles, J. & Block, S. M. Stretching dna with optical tweezers. Biophys. J. 72, 1335–1346 (1997).

Saturno, J., Blanco, L., Salas, M. & Esteban, J. A. A novel kinetic analysis to calculate nucleotide affinity of proofreading DNA polymerases. application to phi 29 DNA polymerase fidelity mutants. J. Biol. Chem. 270, 31235–31243 (1995).

Esteban, J. A., Salas, M. & Blanco, L. Fidelity of ϕ29 dna polymerase. J. Biol. Chem. 268, 2713–2726 (1993).

Korzheva, N. & Mustaev, A. RNA and DNA Polymerases, 1 edn. (ed. Schliwa, M.) (Wiley-VCH, 2003).

Ibarra, B. et al. Proofreading dynamics of a processive DNA polymerase. EMBO J. 28, 2794–2802 (2009).

Nong, E. X., DeVience, S. J. & Herschbach, D. Minimalist model for force-dependent dna replication. Biophys. J. 102, 810–818 (2012).

Echols, H. & Goodman, M. F. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60, 477–511 (1991).

Roberts, J. D. & Kunkel, T. A. Fidelity of dna replication. Cold Spring Harbor Laboratory Press 31, 217–247 (1996).

Johnson, S. J. & Beese, L. S. Structures of mismatch replication errors observed in a dna polymerase. Cell 116, 803–816 (2004).

Cover, T. M. & Thomas, J. A. Elements of Information Theory (John Wiley & Sons, 1991).




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