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Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition pp 1–22Cite as

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Abstract

Deoxyribo-nucleic acids (DNA), which carry genetic information, and proteins which execute and regulate life process are two important biomolecules in any living organisms. The dynamical interactions between proteins and DNA play a central role in many biological processes such as DNA replication, transcription, recombination, gene regulation, repair, and even the packaging of DNA into chromosomes. In order to interact with DNA and perform their designated functions, proteins must first recognize and bind specifically to their target site on DNA. The study of the dynamics of protein–DNA interactions aimed at unraveling the mechanisms of binding-site recognition is a fascinating research field in biophysics and the central focus of this dissertation.

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References

  1. W. Yang, Structure and mechanism for DNA lesion recognition. Cell Res. 18(1), 184–197 (2008)

    Article  Google Scholar 

  2. T.J. Richmond, C.A. Davey, The structure of DNA in the nucleosome core. Nature 423(6936), 145–150 (2003)

    Article  ADS  Google Scholar 

  3. P.A. Rice et al., Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87(7), 1295–1306 (1996)

    Article  Google Scholar 

  4. M. Lewis, Response: DNA looping and Lac repressor—CAP interaction. Science 274(5294), 1931–1932 (1996)

    Article  Google Scholar 

  5. Y. Kim et al., Crystal structure of a yeast TBP/TATA-box complex. Nature 365(6446), 512–520 (1993)

    Article  ADS  Google Scholar 

  6. F.K. Winkler et al., The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12(5), 1781–1795 (1993)

    Google Scholar 

  7. G. Obmolova et al., Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407(6805), 703–710 (2000)

    Article  ADS  Google Scholar 

  8. M.H. Lamers et al., The crystal structure of DNA mismatch repair protein MutS binding to a G × T mismatch. Nature 407(6805), 711–717 (2000)

    Article  ADS  Google Scholar 

  9. K. Luger et al., Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389(6648), 251–260 (1997)

    Article  ADS  Google Scholar 

  10. J. Howard, Mechanics of Motor Proteins and the Cytoskeleton (Sinauer Associates, Sunderland, 2001)

    Google Scholar 

  11. P.A. Rice, C.C. Correll, Protein-Nucleic Acid Interactions (The Royal Society of Chemistry, Cambridge, 2008)

    Book  Google Scholar 

  12. J. Widom, Role of DNA sequence in nucleosome stability and dynamics. Q. Rev. Biophys. 34(3), 269–324 (2001)

    Article  Google Scholar 

  13. P.T. Lowary, J. Widom, New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276(1), 19–42 (1998)

    Article  Google Scholar 

  14. Y. Zhang, D.M. Crothers, High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc. Natl. Acad. Sci. U. S. A. 100(6), 3161–3166 (2003)

    Article  ADS  Google Scholar 

  15. T.M. Okonogi et al., Sequence-dependent dynamics in duplex DNA. Biophys. J. 78(5), 2560–2571 (2000)

    Article  ADS  Google Scholar 

  16. T.E. Cloutier, J. Widom, Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14(3), 355–362 (2004)

    Article  Google Scholar 

  17. R. Vafabakhsh, T. Ha, Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337, 1097–1101 (2012)

    Article  ADS  Google Scholar 

  18. Q. Du et al., Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. U. S. A. 102(15), 5397–5402 (2005)

    Article  ADS  Google Scholar 

  19. Q. Du, A. Kotlyar, A. Vologodskii, Kinking the double helix by bending deformation. Nucleic Acids Res. 36(4), 1120–1128 (2008)

    Article  Google Scholar 

  20. A. Vologodskii, Q. Du, M.D. Frank-Kamenetskii, Bending of short DNA helices. Artif. DNA PNA XNA 4, 1–3 (2013)

    Article  Google Scholar 

  21. D. Skoko et al., Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. J. Mol. Biol. 364(4), 777–798 (2006)

    Article  Google Scholar 

  22. P.A. Wiggins, R. Phillips, P.C. Nelson, Exact theory of kinkable elastic polymers. Phys. Rev. E 71(2 Pt 1), 021909 (2005)

    Article  ADS  MathSciNet  Google Scholar 

  23. P.A. Wiggins et al., High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol. 1(2), 137–141 (2006)

    Article  ADS  MathSciNet  Google Scholar 

  24. A. Travers, DNA dynamics: bubble ‘n’ flip for DNA cyclisation? Curr. Biol. 15(10), R377–R379 (2005)

    Article  Google Scholar 

  25. J. Yan, J.F. Marko, Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93(10), 108108 (2004)

    Article  ADS  Google Scholar 

  26. J.B. Mills, P.J. Hagerman, Origin of the intrinsic rigidity of DNA. Nucleic Acids Res. 32(13), 4055–4059 (2004)

    Article  Google Scholar 

  27. P. Yakovchuk, E. Protozanova, M.D. Frank-Kamenetskii, Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34(2), 564–574 (2006)

    Article  Google Scholar 

  28. O.T. Gotoh, Y. Tagashira, Locations of frequently opening regions on natural DNAs and their relation to functional loci. Biopolymers 20, 1033–1042 (1981)

    Article  Google Scholar 

  29. A.V. Vologodskii, B.R. Amirikyan, Y.L. Lyubchenko, M.D. Frank-Kamenetskii, Allowance for heterogeneous stacking in the DNA helix-coil transition theory. J. Biomol. Struct. Dyn. 2, 131–148 (1984)

    Article  Google Scholar 

  30. S.G. Delcourt, R.D. Blake, Stacking energies in DNA. J. Biol. Chem. 266, 15160–15169 (1991)

    Google Scholar 

  31. M.J. Doktycz et al., Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: evaluation of the nearest-neighbor stacking interactions in DNA. Biopolymers 32(7), 849–864 (1992)

    Article  Google Scholar 

  32. J. SantaLucia Jr., H. Allawi, P.A. Seneviratne, Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562 (1996)

    Article  Google Scholar 

  33. N. Sugimoto, S. Nakano, M. Yoneyama, K. Honda, Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 24, 4501–4505 (1996)

    Article  Google Scholar 

  34. J. SantaLucia Jr., A unified view of polymer, dumbbell, and oligonucleotide DNA nearest- neighbor thermodynamics. Proc. Natl. Acad. Sci. U. S. A. 95(4), 1460–1465 (1998)

    Article  ADS  Google Scholar 

  35. A. Ansari, S.V. Kuznetsov, Dynamics and mechanism of DNA-bending proteins in binding site recognition, in Biophysics of DNA-Protein Interactions, ed. by M.C. Williams, L.J. Maher III (Springer, New York, 2010)

    Google Scholar 

  36. E. Protozanova, P. Yakovchuk, M.D. Frank-Kamenetskii, Stacked–unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775–785 (2004)

    Article  Google Scholar 

  37. H. Arthanari et al., Effects of HU binding on the equilibrium cyclization of mismatched, curved, and normal DNA. Biophys. J. 86(3), 1625–1631 (2004)

    Article  ADS  Google Scholar 

  38. W.K. Olson et al., DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. U. S. A. 95(19), 11163–11168 (1998)

    Article  ADS  Google Scholar 

  39. W.K. Olson, V.B. Zhurkin, Modeling DNA deformations. Curr. Opin. Struct. Biol. 10(3), 286–297 (2000)

    Article  Google Scholar 

  40. D. Coman, I.M. Russu, A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys. J. 89(5), 3285–3292 (2005)

    Article  ADS  Google Scholar 

  41. J.B. Parker et al., Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 449(7161), 433–437 (2007)

    Article  ADS  Google Scholar 

  42. J.G. Moe, I.M. Russu, Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G.T mismatches. Biochemistry 31(36), 8421–8428 (1992)

    Article  Google Scholar 

  43. M.A. de la Rosa, E.F. Koslover, P.J. Mulligan, A.J. Spakowitz, Dynamic strategies for target-site search by DNA-binding proteins. Biophys. J. 98, 2943–2953 (2010)

    Article  ADS  Google Scholar 

  44. A.D. Riggs, S. Bourgeois, M. Cohn, The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 53(3), 401–417 (1970)

    Article  Google Scholar 

  45. A. Tafvizi, L.A. Mirny, A.M. van Oijen, Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem 12(8), 1481–1489 (2011)

    Article  Google Scholar 

  46. P.H. Richter, M. Eigen, Diffusion controlled reaction rates in spheroidal geometry. Application to repressor–operator association and membrane bound enzymes. Biophys. Chem. 2(3), 255–263 (1974)

    Article  Google Scholar 

  47. R.B. Winter, O.G. Berg, P.H. von Hippel, Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor–operator interaction: kinetic measurements and conclusions. Biochemistry 20(24), 6961–6977 (1981)

    Article  Google Scholar 

  48. N.P. Stanford et al., One- and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J. 19(23), 6546–6557 (2000)

    Article  Google Scholar 

  49. A. Revzin (ed.), The Biology of Nonspecific DNA Protein Interactions (CRC Press, Boca Raton, 1990).

    Google Scholar 

  50. S.E. Halford, J.F. Marko, How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32(10), 3040–3052 (2004)

    Article  Google Scholar 

  51. D.M. Gowers, G.G. Wilson, S.E. Halford, Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. 102, 15883–15888 (2005)

    Article  ADS  Google Scholar 

  52. J. Widom, Target site localization by site-specific, DNA-binding proteins. Proc. Natl. Acad. Sci. U. S. A. 102(47), 16909–16910 (2005)

    Article  ADS  Google Scholar 

  53. J.D. Schonhoft, J.T. Stivers, Timing facilitated site transfer of an enzyme on DNA. Nat. Chem. Biol. 8, 205–210 (2012)

    Article  Google Scholar 

  54. C.L. Lawson, H.M. Berman, Indirect readout of DNA sequence by proteins, in Protein-Nucleic Acid Interactions, ed. by P.A. Rice, C.C. Correl (Royal Society of Chemistry, Cambridge, 2008)

    Google Scholar 

  55. C.G. Kalodimos et al., Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305(5682), 386–389 (2004)

    Article  ADS  Google Scholar 

  56. D.E. Koshland, Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. 44, 98–104 (1958)

    Article  ADS  Google Scholar 

  57. R.S. Spolar, M.T. Record Jr., Coupling of local folding to site-specific binding of proteins to DNA. Science 263(5148), 777–784 (1994)

    Article  ADS  Google Scholar 

  58. C.W. Garvie, C. Wolberger, Recognition of specific DNA sequences. Mol. Cell 8(5), 937–946 (2001)

    Article  Google Scholar 

  59. M. Andrabi, K. Mizugushi, S. Ahmad, Conformational changes in DNA-binding proteins: relationships with precomplex features and contributions to specificity and stability. Proteins 82, 841–857 (2014)

    Article  Google Scholar 

  60. J.P. Changeux, S. Edelstein, Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol. Rep. 3, 19 (2011)

    Article  Google Scholar 

  61. G.M. Perez-Howard, P.A. Weil, J.M. Beechem, Yeast TATA binding protein interaction with DNA: fluorescence determination of oligomeric state, equilibrium binding, on-rate, and dissociation kinetics. Biochemistry 34(25), 8005–8017 (1995)

    Article  Google Scholar 

  62. K.M. Parkhurst, M. Brenowitz, L.J. Parkhurst, Simultaneous binding and bending of promoter DNA by the TATA binding protein: real time kinetic measurements. Biochemistry 35(23), 7459–7465 (1996)

    Article  Google Scholar 

  63. G.M. Dhavan et al., Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol. 315(5), 1027–1037 (2002)

    Article  Google Scholar 

  64. D.A. Hiller et al., Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence. Biochemistry 42(49), 14375–14385 (2003)

    Article  Google Scholar 

  65. S. Sugimura, D.M. Crothers, Stepwise binding and bending of DNA by Escherichia coli integration host factor. Proc. Natl. Acad. Sci. U. S. A. 103(49), 18510–18514 (2006)

    Article  ADS  Google Scholar 

  66. S.N. Huang, D.M. Crothers, The role of nucleotide cofactor binding in cooperativity and specificity of MutS recognition. J. Mol. Biol. 384(1), 31–47 (2008)

    Article  Google Scholar 

  67. S.P. Hancock et al., The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein. J. Mol. Biol. 406(2), 285–312 (2011)

    Article  MathSciNet  Google Scholar 

  68. B. van den Broek, M.C. Noom, G.J. Wuite, DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway. Nucleic Acids Res. 33(8), 2676–2684 (2005)

    Article  Google Scholar 

  69. S. Dixit et al., Mechanics of binding of a single integration-host-factor protein to DNA. Phys. Rev. Lett. 94(11), 118101 (2005)

    Article  ADS  Google Scholar 

  70. S.F. Tolic-Norrelykke et al., Stepwise bending of DNA by a single TATA-box binding protein. Biophys. J. 90(10), 3694–3703 (2006)

    Article  Google Scholar 

  71. B.M. Reinhard et al., Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes. Proc. Natl. Acad. Sci. U. S. A. 104(8), 2667–2672 (2007)

    Article  ADS  Google Scholar 

  72. S.V. Kuznetsov et al., Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc. Natl. Acad. Sci. U. S. A. 103(49), 18515–18520 (2006)

    Article  ADS  Google Scholar 

  73. J.T. Stivers, K.W. Pankiewicz, K.A. Watanabe, Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 38(3), 952–963 (1999)

    Article  Google Scholar 

  74. P.C. Blainey et al., A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. U. S. A. 103(15), 5752–5757 (2006)

    Article  ADS  Google Scholar 

  75. Y.M. Wang, R.H. Austin, E.C. Cox, Single molecule measurements of repressor protein 1D diffusion on DNA. Phys. Rev. Lett. 97(4), 048302 (2006)

    Article  ADS  Google Scholar 

  76. A. Tafvizi et al., Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys. J. 95(1), L01–L03 (2008)

    Article  Google Scholar 

  77. I. Bonnet et al., Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res. 36(12), 4118–4127 (2008)

    Article  ADS  Google Scholar 

  78. J. Gorman et al., Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell 28(3), 359–370 (2007)

    Article  Google Scholar 

  79. D. Barsky, T.A. Laurence, C. Venclovas, How proteins slide on DNA, in Biophysics of DNA-Protein Interactions, ed. by M.C. Williams, L.J. Maher (Springer, New York, 2010), pp. 39–68

    Chapter  Google Scholar 

  80. V.V. Koval et al., Real-time studies of conformational dynamics of the repair enzyme E. coli formamidopyrimidine-DNA glycosylase and its DNA complexes during catalytic cycle. Mutat. Res. 685(1–2), 3–10 (2010)

    Article  Google Scholar 

  81. N.A. Kuznetsov et al., Conformational dynamics of DNA repair by Escherichia coli Endonuclease III. J. Biol. Chem. 290(23), 14338–14349 (2015)

    Article  Google Scholar 

  82. M. Slutsky, L.A. Mirny, Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J. 87(6), 4021–4035 (2004)

    Article  ADS  Google Scholar 

  83. Y. Savir, T. Tlusty, Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition. PLoS One 2(5), e468 (2007)

    Article  ADS  Google Scholar 

  84. J.I. Friedman, J.T. Stivers, Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry 49(24), 4957–4967 (2010)

    Article  Google Scholar 

  85. R. Zhou et al., SSB functions as a sliding platform that migrates on DNA via reptation. Cell 146(2), 222–232 (2011)

    Article  Google Scholar 

  86. J.E. Wibley et al., Structure and specificity of the vertebrate anti-mutator uracil-DNA glycosylase SMUG1. Mol. Cell 11(6), 1647–1659 (2003)

    Article  Google Scholar 

  87. A. Banerjee et al., Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434(7033), 612–618 (2005)

    Article  ADS  Google Scholar 

  88. A. Banerjee, W.L. Santos, G.L. Verdine, Structure of a DNA glycosylase searching for lesions. Science 311(5764), 1153–1157 (2006)

    Article  ADS  Google Scholar 

  89. A. Banerjee, G.L. Verdine, A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex. Proc. Natl. Acad. Sci. U. S. A. 103(41), 15020–15025 (2006)

    Article  ADS  Google Scholar 

  90. J. Iwahara, M. Zweckstetter, G.M. Clore, NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA. Proc. Natl. Acad. Sci. U. S. A. 103(41), 15062–15067 (2006)

    Article  ADS  Google Scholar 

  91. J. Iwahara, G.M. Clore, Detecting transient intermediates in macromolecular binding by paramagnetic NMR. Nature 440(7088), 1227–1230 (2006)

    Article  ADS  Google Scholar 

  92. A. Maiti et al., Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition. Proc. Natl. Acad. Sci. U. S. A. 105(26), 8890–8895 (2008)

    Article  ADS  Google Scholar 

  93. Y. Qi et al., Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature 462(7274), 762–766 (2009)

    Article  ADS  Google Scholar 

  94. J.I. Friedman, A. Majumdar, J.T. Stivers, Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage. Nucleic Acids Res. 37(11), 3493–3500 (2009)

    Article  Google Scholar 

  95. J.S. Leith et al., Sequence-dependent sliding kinetics of p53. Proc. Natl. Acad. Sci. U. S. A. 109(41), 16552–16557 (2012)

    Article  ADS  Google Scholar 

  96. H. Ghodke et al., Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates. Proc. Natl. Acad. Sci. U. S. A. 111(18), E1862–E1871 (2014)

    Article  ADS  Google Scholar 

  97. S.R. Nelson et al., Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases. Proc. Natl. Acad. Sci. U. S. A. 111(20), E2091–E2099 (2014)

    Article  ADS  Google Scholar 

  98. C. Gell, D. Brockwell, A. Smith, Handbook of Single Molecule Fluorescence Spectroscopy (Oxford University Press, Oxford, 2006)

    Google Scholar 

  99. N. Jalili, K. Laxminarayana, A review of atomic force microscopy imaging systems: application to molecular metrology and biological sciences. Mechatronics 14, 907–945 (2004)

    Article  Google Scholar 

  100. I. Heller, T.P. Hoekstra, G.A. King, E.J.G. Peterman, G.J.L. Wuite, Optical tweezers analysis of DNA–protein complexes. Chem. Rev. 114, 3087–3119 (2014)

    Article  Google Scholar 

  101. J.R. Moffitt, Y.R. Chemla, S.B. Smith, C. Bustamante, Recent advances in optical tweezers. Annu. Rev. Biochem. 77, 205–228 (2008)

    Article  Google Scholar 

  102. I. De Vlaminck, C. Dekker, Recent advances in magnetic tweezers. Annu. Rev. Biophys. 41, 453–472 (2012)

    Article  Google Scholar 

  103. A. Van Orden, K. Fogarty, J. Jung, Fluorescence fluctuation spectroscopy: a coming of age story. Appl. Spectrosc. 58(5), 122A–137A (2004)

    Article  ADS  Google Scholar 

  104. L.E. Sass et al., Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes. Biochemistry 49(14), 3174–3190 (2010)

    Article  Google Scholar 

  105. G. Bonnet et al., Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. U. S. A. 96(11), 6171–6176 (1999)

    Article  ADS  Google Scholar 

  106. H.D. Kim et al., Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. U. S. A. 99(7), 4284–4289 (2002)

    Article  ADS  Google Scholar 

  107. G. Altan-Bonnet, A. Libchaber, O. Krichevsky, Bubble dynamics in double-stranded DNA. Phys. Rev. Lett. 90(13), 138101 (2003)

    Article  ADS  Google Scholar 

  108. G. Li et al., Rapid spontaneous accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol. 12(1), 46–53 (2005)

    Article  Google Scholar 

  109. J. Kubelka, Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. Photochem. Photobiol. Sci. 8(4), 499–512 (2009)

    Article  Google Scholar 

  110. P.A. Thompson, W.A. Eaton, J. Hofrichter, Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a ‘kinetic zipper’ model. Biochemistry 36(30), 9200–9210 (1997)

    Article  Google Scholar 

  111. L. Qiu et al., Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros. J. Am. Chem. Soc. 124(44), 12952–12953 (2002)

    Article  Google Scholar 

  112. W.Y. Yang, M. Gruebele, Folding at the speed limit. Nature 423(6936), 193–197 (2003)

    Article  ADS  Google Scholar 

  113. J. Kubelka et al., Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc. Natl. Acad. Sci. U. S. A. 105(48), 18655–18662 (2008)

    Article  ADS  Google Scholar 

  114. R. Narayanan et al., Fast folding of RNA pseudoknots initiated by laser temperature-jump. J. Am. Chem. Soc. 133(46), 18767–18774 (2011)

    Article  Google Scholar 

  115. S.V. Kuznetsov et al., Microsecond dynamics of protein-DNA interactions: direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E. coli SSB tetramer. J. Mol. Biol. 359(1), 55–65 (2006)

    Article  Google Scholar 

  116. P. Vivas et al., Mapping the transition state for DNA bending by IHF. J. Mol. Biol. 418(5), 300–315 (2012)

    Article  Google Scholar 

  117. X. Chen et al., Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat. Commun. 6, 5849 (2015)

    Article  ADS  Google Scholar 

  118. D. Anunciado et al., Multistep kinetics of the U1A-SL2 RNA complex dissociation. J. Mol. Biol. 408(5), 896–908 (2011)

    Article  Google Scholar 

  119. J.H. Min, N.P. Pavletich, Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature 449(7162), 570–575 (2007)

    Article  ADS  Google Scholar 

  120. C.C. Yang, H.A. Nash, The interaction of E. coli IHF protein with its specific binding sites. Cell 57(5), 869–880 (1989)

    Article  Google Scholar 

  121. K.K. Swinger, P.A. Rice, IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 14(1), 28–35 (2004)

    Article  Google Scholar 

  122. S. Khrapunov et al., Binding then bending: a mechanism for wrapping DNA. Proc. Natl. Acad. Sci. U. S. A. 103(51), 19217–19218 (2006)

    Article  ADS  Google Scholar 

  123. P. Vivas, Mechanism of integration host factor, a DNA-bending protein, probed with laser temperature-jump. Ph.D. Thesis, 2009

    Google Scholar 

  124. H. Zheng et al., Base flipping free energy profiles for damaged and undamaged DNA. Chem. Res. Toxicol. 23(12), 1868–1870 (2010)

    Article  ADS  Google Scholar 

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    Yogambigai Velmurugu

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Velmurugu, Y. (2017). Introduction. In: Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-45129-9_1

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