157
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations

&
Pages 3384-3397 | Received 02 Jul 2016, Accepted 24 Oct 2016, Published online: 16 Nov 2016

References

  • Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., … Schneider, B. (1992). The nucleic acid database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophysical Journal, 63, 751–759. doi:10.1016/S0006-3495(92)81649-1
  • Boschitsch, A. H., & Fenley, M. O. (2011). A fast and robust Poisson–Boltzmann solver based on adaptive cartesian grids. Journal of Chemical Theory and Computation, 7, 1524–1540. doi:10.1021/ct1006983
  • Burdett, V., Baitinger, C., Viswanathan, M., Lovett, S. T., & Modrich, P. (2001). In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proceedings of the National Academy of Sciences, 98, 6765–6770. doi:10.1073/pnas.121183298
  • Cherstvy, A. G. (2011). Electrostatic interactions in biological DNA-related systems. Physical Chemistry Chemical Physics, 13, 9942–9968. doi:10.1039/c0cp02796k
  • Chin, K., Sharp, K. A., Honig, B., & Pyle, A. M. (1999). Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nature Structural Biology, 6, 1055–1061. doi:10.1038/14940
  • Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Jr., … Kollman, P. A. (1995). A second generation force field for the simulation of proteins. Nucleic acids, and organic molecules. Journal of the American Chemical Society, 117, 5179–5197. doi:10.1021/ja955032e
  • Coulocheri, S. A., Pigis, D. G., Papavassiliou, K. A., & Papavassiliou, A. G. (2007). Hydrogen bonds in protein–DNA complexes: Where geometry meets plasticity. Biochimie, 89, 1291–1303. doi:10.1016/j.biochi.2007.07.020
  • Dermic, D. (2006). Functions of multiple exonucleases are essential for cell viability, DNA repair and homologous recombination in recD mutants of Eschirichia coli. Genetics, 172, 2057–2069. doi:10.1534/genetics.105.052076
  • Djuranovic, D., & Hartmann, B. (2003). Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: Evidence for sub-states. Journal of Biomolecular Structure and Dynamics, 20, 771–788. doi:10.1080/07391102.2003.10506894
  • Djuranovic, D., & Hartmann, B. (2004). DNA fine structure and dynamics in crystals and in solution: The impact of BI/BII backbone conformations. Biopolymers, 73, 356–368. doi:10.1002/bip.10528
  • El Hassan, M. A., & Calladine, C. R. (1998). Two distinct modes of protein-induced bending in DNA. Journal of Molecular Biology, 282, 331–343. doi:10.1006/jmbi.1998.1994
  • Fujii, S., Kono, H., Takenaka, S., Go, N., & Sarai, A. (2007). Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Research, 35, 6063–6074. doi:10.1093/nar/gkm627
  • Gorin, A. A., Zhurkin, V. B., & Olson, W. K. (1995). B-DNA twisting correlates with base-pair morphology. Journal of Molecular Biology, 247, 34–48. PMID:7897660.10.1006/jmbi.1994.0120
  • Harris, R. C., Mackoy, T., Dantas Machado, A., Xu, D., Rohs, R., & Fenley, M. O. (2012). Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes. Innovations in Biomolecular Modeling and Simulations, 2, 53–80. doi: 10.1039/9781849735056-00053
  • Harteis, S., & Schneider, S. (2014). Making the bend: DNA tertiary structure and protein-DNA interactions. International Journal of Molecular Sciences, 15, 12335–12363. doi:10.3390/ijms150712335
  • Hartmann, B., Piazzola, D., & Lavery, R. (1993). BI-BII transitions in B-DNA. Nucleic Acids Research, 21, 561–568. doi:10.1093/nar/21.3.561
  • Heddi, B., Abi-Ghanem, J., Lavigne, M., & Hartmann, B. (2010). Sequence-dependent DNA flexibility mediates DNase I cleavage. Journal of Molecular Biology, 395, 123–133. doi:10.1016/j.jmb.2009.10.023
  • Honig, B., & Rohs, R. (2011). Biophysics: Flipping Watson and Crick. Nature, 470, 472–473. doi:10.1038/470472a
  • Hud, N. V., & Plavec, J. (2003). A unified model for the origin of DNA sequence-directed curvature. Biopolymers, 69, 144–158. doi:10.1002/bip.10364
  • Jayaram, B., Sharp, K. A., & Honig, B. (1989). The electrostatic potential of B-DNA. Biopolymers, 28, 975–993. doi:10.1002/bip.360280506
  • Joshi, R., Passner, J. M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M. A., … Mann, R. S. (2007). Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell, 131, 530–543. doi:10.1016/j.cell.2007.09.024
  • Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B., & Shakked, Z. (2010). Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nature Structural & Molecular Biology, 17, 423–429. doi:10.1038/nsmb.1800
  • Lavery, R., & Pullman, B. (1982). The electrostatic field of DNA: The role of the nucleic acid conformation. Nucleic Acids Research, 10, 4383–4395. doi:10.1093/nar/10.14.4383
  • Li, L., Li, C., Sarkar, S., Zhang, J., Witham, S., Zhang, Z., … Wang, L. (2012). DelPhi: A comprehensive suite for DelPhi software and associated resources. BMC Biophysics, 5(1), 1–9. doi:10.1186/2046-1682-5-9
  • Locasale, J. W., Napoli, A. A., Chen, S., Berman, H. M., & Lawson, C. L. (2009). Signatures of protein-DNA recognition in free DNA binding sites. Journal of Molecular Biology, 386, 1054–1065. doi:10.1016/j.jmb.2009.01.007
  • Lu, X. J., & Olson, W. K. (2008). 3DNA: A versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid structures. Nature Protocols, 3, 1213–1227. doi:10.1038/nprot.2008.14
  • Manning, G. S. (1978). The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Quarterly Reviews of Biophysics, 11, 179–246. doi:10.1017/S0033583500002031
  • Matthew, J. B., & Ohlendorf, D. H. (1985). Electrostatic deformation of DNA by a DNA-binding protein. The Journal of Biological Chemistry, 260, 5860–5862. Retrieved from http://www.jbc.org/content/260/10/5860.long
  • Moravek, Z., Neidle, S., & Schneider, B. (2002). Protein and drug interactions in the minor groove of DNA. Nucleic Acids Research, 30, 1182–1191. doi:10.1093/nar/30.5.1182
  • Narayanan, B., Westbrook, J., Ghosh, S., Petrov, A. I., Sweeney, B., Zirbel, C. L., … Berman, H. M. (2014). The nucleic acid database: New features and capabilities. Nucleic Acids Research, 42, D114–D122. doi:10.1093/nar/gkt980
  • Nikolov, D. B., Chen, H., Halay, E. D., Hoffman, A., Roeder, R. G., & Burley, S. K. (1996). Crystal structure of a human TATA box-binding protein/TATA element complex. Proceedings of the National Academy of Sciences, 93, 4862–4867. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC39370/pdf/pnas01511-0352.pdf10.1073/pnas.93.10.4862
  • Oguey, C., Foloppe, N., & Hartmann, B. (2010). Understanding the sequence-dependence of DNA groove dimensions: Implications for DNA interactions. PLoS ONE, 5, e15931. doi:10.1371/journal.pone.0015931
  • Osypov, A. A., Krutinin, G. G., & Kamzolova, S. G. (2010). DEPPDB–DNA electrostatic potential properties database: Electrostatic properties of genome DNA. Journal of Bioinformatics and Computational Biology, 10, 1–19. doi:10.1142/S0219720010004811
  • Otwinowski, Z., Schevitz, R. W., Zhang, R. G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., … Sigler, P. B. (1988). Crystal structure of trp represser/operator complex at atomic resolution. Nature, 335, 321–329. doi:10.1038/335321a0
  • Pullman, A., & Pullman, B. (1981). Molecular electrostatic potential of the nucleic acids. Quarterly Reviews of Biophysics, 14, 289–380. doi:10.1017/S0033583500002341
  • Rhodes, D., & Klug, A. (1981). Sequence-dependent helical periodicity of DNA. Nature, 292, 378–380. doi:10.1038/292378a0
  • Rife, J. P., Stallings, S. C., Correll, C. C., Dallas, A., Steitz, T. A., & Moore, P. B. (1999). Comparison of the crystal and solution structures of two RNA oligonucleotides. Biophysical Journal, 76, 65–75. doi:10.1016/S0006-3495(99)77178-X
  • Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B., & Mann, R. S. (2010). Origins of specificity in protein-DNA recognition. Annual Review of Biochemistry, 79, 233–269. doi:10.1146/annurev-biochem-060408-091030
  • Rohs, R., West, S. M., Liu, P., & Honig, B. (2009). Nuance in the double-helix and its role in protein-DNA recognition. Current Opinion in Structural Biology, 19, 171–177. doi:10.1016/j.sbi.2009.03.002
  • Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009). The role of DNA shape in protein-DNA recognition. Nature, 461, 1248–1253. doi:10.1038/nature08473
  • Savelyev, A., Materese, C. K., & Papoian, G. A. (2011). Is DNA’s rigidity dominated by electrostatic or nonelectrostatic interactions? Journal of the American Chemical Society, 133, 19290–19293. doi:10.1021/ja207984z
  • Seeman, N. C., Rosenberg, J. M., & Rich, A. (1976). Sequence-specific recognition of double helical nucleic acids by proteins. Proceedings of the National Academy of Sciences, 73, 804–808. Retrieved from http://www.pnas.org/content/73/3/804.full.pdf10.1073/pnas.73.3.804
  • Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014). Absence of a simple code: How transcription factors read the genome. Trends in Biochemical Sciences, 39, 381–399. doi:10.1016/j.tibs.2014.07.002
  • Srinivasan, A. R., Sauers, R. R., Fenley, M. O., Boschitsch, A. H., Matsumoto, A., Colasanti, A. V., & Olson, W. K. (2009). Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states: Computational insights into the sequence-dependent features of double-helical DNA. Biophysical Reviews, 1, 13–20. doi:10.1007/s12551-008-0003-2
  • Svozil, D., Kalina, J., Omelka, M., & Schneider, B. (2008). DNA conformations and their sequence preferences. Nucleic Acids Research, 36, 3690–3706. doi:10.1093/nar/gkn260
  • Tolstorukov, M. Y., Jernigan, R. L., & Zhurkin, V. B. (2004). Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. Journal of Molecular Biology, 337, 65–76. doi:10.1016/j.jmb.2004.01.011
  • Travers, A. A. (1989). DNA conformation and protein binding. Annual Review of Biochemistry, 58, 427–452. doi:10.1146/annurev.bi.58.070189.002235
  • Tullius, T. (2009). Structural biology: DNA binding shapes up. Nature, 461, 1225–1226. doi:10.1038/4611225a
  • Ulyanov, N. B., & James, T. L. (1995). Statistical analysis of DNA duplex structural features. Methods in Enzymology, 261, 90–120. doi:10.1016/S0076-6879(95)61006-5
  • Viswanathan, M., Burdett, V., Baitinger, C., Modrich, P., & Lovett, S. T. (2001). Redundant exonuclease involvement in Escherichia coli methyl-directed mismatch repair. Journal of Biological Chemistry, 276, 31053–31058. doi:10.1074/jbc.M105481200
  • Wang, T., Sun, H. L., Cheng, F., Zhang, X. E., Bi, L., & Jiang, T. (2013). Recognition and processing of double-stranded DNA by ExoX, a distributive 3’-5’ exonuclease. Nucleic Acids Research, 41, 7556–7565. doi:10.1093/nar/gkt495
  • Watkins, S., van Pouderoven, G., & Sixma, T. K. (2004). Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA. Nucleic Acids Research, 32, 4306–4312. doi:10.1093/nar/gkh770
  • Weber, I. T., & Steitz, T. A. (1984). Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity. Proceedings of the National Academy of Sciences, 81, 3973–3977. Retrieved from http://www.pnas.org/content/81/13/3973.long10.1073/pnas.81.13.3973
  • Weiner, P. K., Langridge, R., Blaney, J. M., Schaefer, R., & Kollman, P. A. (1989). Electrostatic potential molecular surfaces. Proceedings of the National Academy of Sciences of the USA, 79, 3754–3758. Retrieved from http://www.pnas.org/content/79/12/3754.full.pdf
  • West, S. M., Rohs, R., Mann, R. S., & Honig, B. (2010). Electrostatic interactions between arginines and the minor groove in the nucleosome. Journal of Biomolecular Structure and Dynamics, 27, 861–866. doi:10.1080/07391102.2010.10508587
  • Winger, R. H., Liedl, K. R., Pichler, A., Hallbrucker, A., & Mayer, E. (1999). Helix morphology changes in B-DNA induced by spontaneous B I ⇌B II Substate Interconversion. Journal of Biomolecular Structure and Dynamics, 17, 223–235. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1056357210.1080/07391102.1999.10508355
  • Wynveen, A., Lee, D. J., & Kornyshev, A. A. (2008). Helical coherence of DNA in crystals and solution. Nucleic Acids Research, 36, 5540–5551. doi:10.1093/nar/gkh514
  • Zhitnikova, M. Y., Boryskina, O. P., & Shestopalova, A. V. (2014). Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. Journal of Biomolecular Structure and Dynamics, 32, 1670–1685. doi:10.1080/07391102.2013.830579

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.