Probe position-dependent counterion dynamics in DNA: Comparison of time-resolved stokes shift of groove-bound to base-stacked probes in the presence of different monovalent counterions

Journal of Physical Chemistry Letters

Volumn 3, Issue 18, 2012, Pages 2621-2626

  Verma, Sachin Dev ^a   Pal, Nibedita ^a   Singh, Moirangthem Kiran ^a   Sen, Sobhan ^a  

^a JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

Biophysical Chemistry and Biomolecules

Indexed keywords

COUNTERIONS; MINOR GROOVES; MOLECULAR DYNAMICS SIMULATIONS; MONOVALENT COUNTERIONS; STOKES SHIFT; TETRABUTYLAMMONIUM; TIME-CORRELATED SINGLE PHOTON COUNTING; TIME-RESOLVED; TIME-RESOLVED EMISSION SPECTRA; TIME-RESOLVED FLUORESCENCE; UP-CONVERSION;

BIOMOLECULES; DNA; EMISSION SPECTROSCOPY; MOLECULAR DYNAMICS; PROBES;

IONS;

EID: 84866615435     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz300934x     Document Type: Article

References (44)

1. Saenger, W. Principles of Nucleic Acid Structure; Springer: New York, 1984.
2. Anderson, C. F.; Record, M. T. Salt-Nucleic Acid Interactions Annu. Rev. Phys. Chem. 1995, 46, 657-700
3. Manning, G. S.; Ray, J. Counterion Condensation Revisited J. Biomol. Struct. Dyn. 1998, 16, 461-476
4. Young, M. A.; Jayaram, B.; Beveridge, D. L. Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA: Fractional Occupancy of Electronegative Pockets J. Am. Chem. Soc. 1997, 119, 59-69
5. Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L. Ion Motions in Molecular Dynamics Simulation on DNA Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14771-14775
6. Furse, K. E.; Corcelli, S. A. Effects of an Unnatural Base Pair Replacement on the Structure and Dynamics of DNA and Neighboring Water and Ions J. Phys. Chem. B 2010, 114, 9934-9945
7. Rouzina, I.; Bloomfield, V. A. DNA Bending by Small, Mobile Multivalent Cations Biophys. J. 1998, 74, 3152-3164
8. Shen, X.; Gu, B.; Che, S. A.; Zhang, F. S. Solvent Effects on the Conformation of DNA Dodecamer Segment: A Simulation Study J. Chem. Phys. 2011, 135, 034509
9. Tan, Z. J.; Chen, S. J. Electrostatic Free Energy Landscapes for DNA Helix Bending Biophys. J. 2008, 94, 3137-3149
10. Williams, L. D.; Maher, L. J., III. Electrostatic Mechanisms of DNA Deformation Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 497-521
11. Mol, C. D.; Izumi, T.; Mitra, S.; Tainer, J. A. DNA-Bound Structures and Mutants Reveal Abasic DNA Binding by APE1 DNA Repair and Coordination Nature 2000, 403, 451-456
12. Ho, M. H.; Vivo, M. D.; Peraro, M. D.; Klein, M. L. Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis? J. Am. Chem. Soc. 2010, 132, 13702-13712
13. Sen, S.; Paraggio, N. A.; Gearheart, L. A.; Connor, E. E.; Issa, A.; Coleman, R. S.; Wilson, D. M., III.; Wyatt, M. D.; Berg, M. A. Effect of Protein Binding on Ultrafast DNA Dynamics: Characterization of a DNA:APE1 Complex Biophys. J. 2005, 89, 4129-4138
14. Privalov, P. L.; Dragan, A. I.; Robinson, C. C. Interpreting Protein/DNA Interactions: Distinguishing Specific from Non-specific and Electrostatic from Non-electrostatic Components Nucleic Acids Res. 2011, 39, 2483-2491
15. Pal, N.; Verma, S. D.; Sen, S. Probe Position Dependence of DNA Dynamics: Comparison of the Time-Resolved Stokes Shift of Groove-Bound to Base-Stacked Probes J. Am. Chem. Soc. 2010, 132, 9277-9279
16. Sen, S.; Gearheart, L. A.; Rivers, E.; Liu, H.; Coleman, R. S.; Murphy, C. J.; Berg, M. A. Role of Monovalent Counterions in the Ultrafast Dynamics of DNA J. Phys. Chem. B 2006, 110, 13248-13255
17. Brauns, E. B.; Madaras, M. L.; Coleman, R. S.; Murphy, C. J.; Berg, M. A. Measurement of Local DNA Reorganization on the Picosecond and Nanosecond Time Scales J. Am. Chem. Soc. 1999, 121, 11644-11649
18. Andreatta, D.; Pérez Lustres, J. L.; Kovalenko, S. A.; Ernsting, N. P.; Murphy, C. J.; Coleman, R. S.; Berg, M. A. Power-Law Solvation Dynamics in DNA over Six Decades in Time J. Am. Chem. Soc. 2005, 127, 7270-7271
19. Andreatta, D.; Sen, S.; Pérez Lustres, J. L.; Kovalenko, S. A.; Ernsting, N. P.; Murphy, C. J.; Coleman, R. S.; Berg, M. A. Ultrafast Dynamics in DNA: "Fraying" at the End of the Helix J. Am. Chem. Soc. 2006, 128, 6885-6892
20. Pal, S. K.; Zhao, L.; Zewail, A. H. Water at DNA Surfaces: Ultrafast Dynamics in Minor Groove Recognition Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 8113-8118
21. Pal, S. K.; Zhao, L.; Xia, T.; Zewail, A. H. Site- and Sequence-Selective Ultrafast Hydration of DNA Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13746-13751
22. Dallmann, A.; Pfaffe, M.; Mugge, C.; Mahrwald, R.; Kovalenko, S. A.; Ernsting, N. P. Local THz Time Domain Spectroscopy of Duplex DNA via Fluorescence of an Embedded Probe J. Phys. Chem. B 2009, 113, 15619-15628
23. Sajadi, M.; Furse, K. E.; Zhang, X. X.; Dehmel, L.; Kovalenko, S. A.; Corcelli, S. A.; Ernsting, N. P. Detection of DNA-Ligand Binding Oscillations by Stokes-Shift Measurements Angew. Chem., Int. Ed. 2011, 50, 9501-9505
24. Banerjee, D.; Pal, S. K. Dynamics in the DNA Recognition by DAPI: Exploration of the Various Binding Modes J. Phys, Chem. B 2008, 112, 1016-1021
25. Abbyad, P.; Shi, X.; Childs, W.; McAnaney, T. B.; Cohen, B. E.; Boxer, S. G. Measurement of Solvation Responses at Multiple Sites in a Globular Protein J. Phys. Chem. B 2007, 111, 8269-8276
26. Zhang, L.; Yang, Y.; Kao, Y.-T.; Wang, L.; Zhong, D. Protein Hydration Dynamics and Molecular Mechanism of Coupled Water-Protein Fluctuations J. Am. Chem. Soc. 2009, 131, 10677-10691
27. Li, T.; Hassanali, A. A.; Kao, Y.-T.; Zhong, D.; Singer, S. Hydration Dynamics and Time Scales of Coupled Water-Protein Fluctuations J. Am. Chem. Soc. 2007, 129, 3376-3382
28. Mandal, D.; Sen, S.; Sukul, D.; Bhattacharrya, K.; Mandal, A. K.; Banerjee, R.; Roy, S. Solvation Dynamics of a Probe Covalently Bound to a Protein and in an AOT Microemulsion: 4-(n -Bromoacetylamino)-phthalimide J. Phys. Chem. B. 2002, 106, 10741-10747
29. Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Femtosecond Solvation Dynamics of Water Nature 1994, 369, 471-473
30. Pal, S.; Maiti, P. K.; Bagchi, B.; Hynes, J. T. Multiple Time Scales in Solvation Dynamics of DNA in Aqueous Solution: The Role of Water, Counterions, and Cross-Correlations J. Phys. Chem. B 2006, 110, 26396-26402
31. Furse, K. E.; Corcelli, S. A. The Dynamics of Water at DNA Interfaces: Computational Studies of Hoechst 33258 Bound to DNA J. Am. Chem. Soc. 2008, 130, 13103-13109
32. Sen, S.; Andreatta, D.; Ponomarev, S. Y.; Beveridge, D. L.; Berg, M. A. Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments J. Am. Chem. Soc. 2009, 131, 1724-1735
33. Mukherjee, A.; Lavery, R.; Bagchi, B.; Hynes, J. T. On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes J. Am. Chem. Soc. 2008, 130, 9747-9755
34. Furse, K. E.; Corcelli, S. A. Molecular Dynamics Simulations of DNA Solvation Dynamics J. Phys. Chem. Lett. 2010, 1, 1813-1820
35. Furse, K. E.; Corcelli, S. A. Dynamical Signature of Abasic Damage in DNA J. Am. Chem. Soc. 2011, 133, 720-723
36. Halle, B.; Nilsson, L. Does the Dynamic Stokes Shift Report on Slow Protein Hydration Dynamics? J. Phys. Chem. B 2009, 113, 8210-8213
37. Golosov, A. A.; Karplus, M. Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis J. Phys. Chem. B 2007, 111, 1482-1490
38. Tereshko, V.; Minasov, G.; Egli, M. A "Hydrat-Ion" Spine in a B-DNA Minor Groove J. Am. Chem. Soc. 1999, 121, 3590-3595
39. + Binding in the Minor Groove of DNA J. Am. Chem. Soc. 2004, 126, 6739-6750
40. Denisov, V. P.; Halle, B. Sequence-Specific Binding of Counterions to B-DNA Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 629-633
41. Fiala, R.; Spackova, N.; Foldynova-Trantirkova, S.; Sponer, J.; Sklenar, V.; Trantirek, L. NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA J. Am. Chem. Soc. 2011, 133, 13790-13793
42. 2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems J. Phys. Chem. Lett. 2012, 3, 45-50
43. Dong, Q.; Stellwagen, E.; Stellwagen, N. C. Monovalent Cation Binding in the Minor Groove of DNA A-Tracts Biochemistry 2009, 48, 1047-1055
44. Stellwagen, E.; Dong, Q.; Stellwagen, N. C. Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method Biochemistry 2007, 46, 2050-2058