Effect of Mg2+ on kinetics of oxidation of pyrimidines in duplex DNA by potassium permanganate

Acta Biochimica Polonica

Volumn 48, Issue 2, 2001, Pages 511-523

  ŁozińSki, Tomasz ^a   Wierzchowski, Kazimierz L ^a  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

Author keywords

Magnesium ions; Oxidation of pyrimidines; pDS3 plasmid DNA; Quantitative permanganate footprinting; Rate constant of oxidation; Thymine glycol

Indexed keywords

ESCHERICHIA COLI;

BACTERIAL DNA; DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASES; MAGNESIUM; PERMANGANATE POTASSIUM; PYRIMIDINE DERIVATIVE;

ARTICLE; CHEMISTRY; DNA FOOTPRINTING; DRUG EFFECT; ESCHERICHIA COLI; KINETICS; METABOLISM; OXIDATION REDUCTION REACTION;

DNA FOOTPRINTING; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; KINETICS; MAGNESIUM; OXIDATION-REDUCTION; POTASSIUM PERMANGANATE; PYRIMIDINES; SUPPORT, NON-U.S. GOV'T;

EID: 0035232509     PISSN: 0001527X     EISSN: None     Source Type: Journal    
DOI: 10.18388/abp.2001_3934     Document Type: Article

References (45)

1. Hayatsu, H. & Ukita, T. (1967) The selective degradation of pyrimidines in nucleic acids by permanganate oxidation. Biochem. Biophys. Res. Commun. 29, 556-561.
2. Iida, S. & Hayatsu, H. (1971) The permanganate oxidation of deoxyribonucleic acid. Biochim. Biophys. Acta 240, 370-375.
3. McCarthy, J.G., Williams, L.D. & Rich, A. (1990) Chemical reactivity of potassium permanganate and diethyl pyrocarbonate with B DNA: Specific reactivity with short A-tracts. Biochemistry 29, 6071-6081.
4. Jeppsen, C. & Nielsen, P.E. (1988) Detection of intercalation-induced changes in DNA structure by reaction with diethyl pyrocarbonate and potassium permanganate. FEBS Lett. 231, 172-176.
5. Sasse-Dwight, S. & Gralla, J.D. (1991) Foot printing of protein-DNA complexes in vivo. Methods Enzymol. 208, 146-168.
6. Nielsen, P.E., Egholm, M., Berg, R.H. & Buchardt, O. (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254, 1497-1500.
7. Nielsen, P.E., Egholm, M. & Buchardt, O. (1994) Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement. J. Mol. Recognit. 7, 165-170.
8. 4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 8074-8081.
9. 4 footprinting study. Acta Biochim. Polon. 48, 495-510.
10. Łoziński, T., Markiewicz, W.T., Wyrzykiewicz, T.K. & Wierzchowski, K.L. (1989) Effect of the sequence-dependent structure of the 17 bp AT spacer on the strength of consensus-like E. coli promoters in vivo. Nucleic Acids Res. 17, 3855-3863.
11. Łoziński, T., Adrych-Rożek, K., Markiewicz, W.T. & Wierzchowski, K.L. (1991) Effect of DNA bending in various regions of a consensus-like Escherichia coli promoter on its strength in vivo and structure of the open complex in vitro. Nucleic Acids Res. 19, 2947-2953.
12. Ide, H., Kow, Y.W. & Wallace, S.S. (1985) Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro. Nucleic Acids Res. 13, 8035-8052.
13. 70 RNA polymerase. J. Mol. Biol. 283, 757-769.
14. 15. Nucleic Acids Res. 23, 1050-1059.
15. Boutonnet, N., Hui, X. & Zakrzewska, K. (1993) Looking into the grooves of DNA. Biopolymers 33, 479-490.
16. Gorin, A.A., Zhurkin, V.B. & Olson, W. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247, 34-48.
17. Zakrzewska, K. (1992) Static and dynamic properties of AT sequences. J. Biomol. Struct. Dynam. 9, 681-693.
18. Breslauer, K.J., Frank, R., Blöcker, H. & Marky, L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750.
19. Leroy, J.L., Charretier, E., Kochoyan, M. & Gueron, M. (1988) Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA structure. Biochemistry 27, 8894-8898.
20. n] duplexes in solution. Biochemistry 24, 926-935.
21. Patel, D.J. & Kozlowski, S.A. (1985) Conformation and dynamics of the Pribnow box region of the self-complementary d(C-G-A-T-T-A-T-A-A-T-C-G) duplex in solution. Biochemistry 24, 936-944.
22. 3 tract. Nucleic Acids Res. 23, 1984-1989.
23. Lu, P., Cheung, S. & Arndt, K. (1983) Possible molecular determinants in the DNA structure of regulatory sequences. J. Biomol. Struct. Dyn. 1, 509-521.
24. Ramstein, J. & Lavery, R. (1988) Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. U.S.A. 85, 7231-7235.
25. 2+ binding isotherms for nucleic acids using Poisson-Boltzmann theory. J. Mol. Biol. 294, 1135-1147.
26. Paulsen, M.D., Andersen, C.F. & Record, Jr., M.T. (1988) Counterion exchange reactions on DNA: Monte Carlo and Poisson-Boltzmann analysis. Biopolymers 27, 1249-1265.
27. Manning, G.S. (1978) The molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides. Q. Rev. Biophys. 11, 179-246.
28. Duguid, J., Bloomfield, V.A., Benevides, J. & Thomas, Jr., G.J. (1993) Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd and Cd. Biophysical J. 65, 1916-1928.
29. 2+. Biophysical J. 69, 2623-2641.
30. Li, A.Z., Huang, H., Re, X., Qi, L.J. & Marx, K.A. (1998) A gel electrophoretic study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA. Biophys. J. 74, 964-973.
31. 2+ recognizes the sequence of DNA through its hydration shell. J. Am. Chem. Soc. 116, 9423-9429.
32. MacKerell, A.D. (1997) Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J. Phys. Chem. B, 101, 646-650.
33. Brukner, I., Susic, S., Dlakic, M., Savic, A. & Pongor, S. (1994) Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J. Mol. Biol. 236, 26-32.
34. McFail-Isom, L., Shui, X. & Williams, L.D. (1998) Divalent cations stabilize unstacked conformations of DNA and RNA by interact ing with base π systems. Biochemistry 37, 17105-17111.
35. Sines, C.C., McFail-Isom, L., Howerton, S.B., VanDerveer, D. & Williams, L.D. (2000) Cations mediate B-DNA conformational heterogenity. J. Am. Chem. Soc. 122, 11048-11056.
36. Minasov, G., Tereshko, V. & Egli, M. (1999) Atomic-resolution structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. J. Mol. Biol. 291, 83-99.
37. Chiu, T.K. & Dickerson, R.E. (2000) 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J. Mol. Biol. 301, 915-945.
38. Halle, B. & Denisov, V.P. (1998) Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR. Biopolymers, Nucl. Acid Sci. 48, 210-233.
39. Denisov, V.P. & Halle, B. (2000) Sequence-specific binding of counterions to B-DNA. Proc. Natl. Acad. Sci. U.S.A. 97, 629-633.
40. Hammelberg, D., McFail-Isom, L., Williams, L.D. & Wilson, W.D. (2000) Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics. J. Am. Chem. Soc. 122, 10513-10520.
41. Stellwagen, N.C., Magnusdottir, S., Gelfi, C. & Righetti, P.G. (2001) Preferential counterion binding to A-T tract DNA oligomers. J. Mol. Biol. 305, 1025-1033.
42. Rybenkov, V.V., Vologodskii, A.V. & Cozzarelli, N.R. (1997) The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Res. 25, 1412-1418.
43. 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.
44. Kao, J.Y., Goljer, I., Phan, T.A. & Bolton, P.H. (1993) Characterization of the effects of a thymine glycol residue on the structure, dynamics, and stability of duplex DNA by NMR. J. Biol. Chem. 268, 17787-17793.
45. Kung, H.C. & Bolton, P.H. (1997) Structure of duplex DNA containing a thymine glycol residue in solution. J. Biol. Chem. 272, 9227-9236.