Sequence-specific minor groove binding by bis-benzimidazoles: Water molecules in ligand recognition

Nucleic Acids Research

Volumn 31, Issue 5, 2003, Pages 1514-1524

  Bailly, Christian ^d   Chessari, Gianni ^a   Carrasco, Carolina ^c   Joubert, Alexandra ^d   Mann, John ^b   Wilson, W David ^c   Neidle, Stephen ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^c GEORGIA STATE UNIVERSITY   (United States)

^d CENTRE OSCAR LAMBRET   (France)

Author keywords

[No Author keywords available]

Indexed keywords

4 [5 (4 METHYL 1 PIPERAZINYL)[2,5' BI 1H BENZIMIDAZOL] 2' YL]PHENOL; ADENINE; ANTHELMINTIC AGENT; BENZIMIDAZOLE DERIVATIVE; DEOXYRIBONUCLEASE I; LIGAND; OXYGEN; PIPERIDINE DERIVATIVE; THYMINE; WATER;

BINDING AFFINITY; CONTROLLED STUDY; DNA FOOTPRINTING; DNA SEQUENCE; DRUG BINDING; DRUG DNA INTERACTION; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; REVIEW; SURFACE PLASMON RESONANCE;

BASE SEQUENCE; BENZIMIDAZOLES; BINDING SITES; BINDING, COMPETITIVE; DEOXYRIBONUCLEASE I; DNA FOOTPRINTING; HYDROGEN BONDING; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; SURFACE PLASMON RESONANCE; WATER;

EID: 0037337378     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg237     Document Type: Review

References (51)

1. Bailly,C. and Chaires,J.B. (1998) Design of sequence-specific DNA minor groove binders. Netropsin and distamycin analogues. Bioconjug. Chem., 9, 513-538.
2. Neidle,S. (2001) DNA minor-groove recognition by small molecules. Natural Products Rep., 18, 291-309.
3. Dervan,P.B. and Bürli, RW. (1999) Sequence-specific DNA recognition by polyamides. Curr. Opin. Chem. Biol., 3, 688-693
4. Dervan,P.B. (2001) Molecular recognition of DNA by small molecules. Bioorg. Med. Chem., 9, 2215-2235.
5. Gong,B. and Yan,Y. (1997) New DNA minor-groove binding molecules with high sequence-selectivities and binding affinities. Biochem. Biophys. Res. Commun., 240, 557-560.
6. Hawkins,C.A., Watson,C., Yan,Y., Gong,B. and Wemmer,D.E. (2001) Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes. Nucleic Acids Res., 29, 936-942.
7. Stephens,C.E., Tanious,F.A., Kim,S., Wilson,W.D., Schell,W., Perfect,J., Franzblau,S. and Boykin,D.W. (2001) Diguanidino and 'reversed' diamidino 2,5-diarylfurans as antimicrobial agents. J. Med. Chem., 44, 1741-1748.
8. Wilson,W.D., Tanious,F.A., Ding,D., Kumar,A., Boykin,D.W., Colson,P., Houssier,C. and Bailly,C. (1998) Nucleic acid interactions of unfused aromatic cations: evaluation of proposed minor-groove, major-groove and intercalation binding modes. J. Am. Chem. Soc., 120, 10310-10321.
9. Mazur, S., Tanious,F.A., Ding,D., Kumar,A., Boykin,D.W., Simpson,I.J., Neidle,S. and Wilso.,W.D. (2000) A thermodynamic and structural analysis of DNA minor groove complex formation. J. Mol. Biol., 300, 321-337.
10. Tanious,F.A., Ding,D., Patrick,D.A., Tidwell,R.R. and Wilson,W.D. (1997) A new type of DNA minor groove complex: carbazole dication-DNA interactions. Biochemistry, 36, 15315-15325.
11. Reddy,B.S.P., Sondhi,S.M. and Lown,J.W. (1999) Synthetic DNA minor groove-binding drugs. Pharmacol. Ther., 84, 1-111.
12. Pjura,P.E., Grzeskoniak,K. and Dickerson,R.E. (1987) Binding of Hoechst 33258 to the minor groove of B-DNA. J. Mol. Biol., 197, 257-271.
13. Teng,M.-K., Usman,N., Frederick,C.A. and Wang,A.H.-J. (1988) The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res., 16, 2671-2690.
14. Carrondo,M.A.A. de C.T., Coll,M., Aymami,J., Wang,A.H.-J., Van der Marel,G.A., Van Boom,J.H. and Rich,A. (1989) Binding of a Hoechst dye to d(CGCGATATCGCG) and its influence on the conformation of the DNA fragment. Biochemistry, 28, 7849-7859.
15. 2 by Hoechst 33258: a high-field NMR study. Biochemistry, 29, 10181-10190.
16. 1H NMR spectroscopy. Nucleic Acids Res., 18, 3753-3762.
17. Quintana,J.R., Lipanov,A.A. and Dickerson,R.E. (1991) Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer CGCGAATTCGCG. Biochemistry, 30, 10294-10306.
18. 6G]AATTCGCG) complexed with Hoechst 33258 or Hoechst 33342. EMBO J., 11, 225-232
19. 2 complex and comparison with the X-ray crystal structure. Structure, 1, 177-186.
20. 1H NMR. Biochemistry, 30, 11377-11388.
21. 2 studied in solution by NMR spectroscopy. Eur. J. Biochem., 211, 437-447
22. 2 duplex. Nucleic Acids Res., 22, 1607-1612.
23. Vega,M.C., Garcia Saez,I., Aymami,J., Eritja,R., Van der Marel,G.A., van Boom,J.H., Rich,A. and Coll,M. (1994) The three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258. Eur. J. Biochem., 222, 721-726.
24. Czamy,A., Boykin,D.W., Wood,A.A., Nunn,C.M., Neidle,S., Zhao,M. and Wilson,W.D. (1995) Analysis of van der Waals and electrostatic contributions in the interactions of minor groove binding benzimidazoles with DNA. J. Am. Chem. Soc., 117, 4716-4717.
25. 2 duplex: calorimetric and spectroscopic studies. J. Mol. Biol., 271, 244-257.
26. Drobyshev,A.L., Zasedatelev,A.S., Yershov,G.M. and Mirzabekov,A.D. (1999) Massive parallel analysis of DNA-Hoechst 33258 binding specificity with a generic oligodeoxyribonucleotide microchip. Nucleic Acids Res., 27, 4100-4105.
27. Rao,K.E. and Lown,J.W. (1991) Molecular recognition between ligands and nucleic acids: DNA binding characteristics of analogues of Hoechst 33258 designed to exhibit altered base and sequence recognition. Chem. Res. Toxicol., 4, 661-669.
28. 1H-NMR studies. J. Biomol. Struct. Dyn., 8, 331-357.
29. 2. Biochemistry, 33, 8442-8452.
30. Clark,G.R., Gray,E.J., Neidle,S., Li,Y.-H. and Leupin,W. (1996) Isohelicity and phasing in drug-DNA sequence-recognition: crystal structure of a tris(benzimidazole)-oligonucleotide complex. Biochemistry, 35, 13745-13752.
31. 2. Nucleic Acids Res., 24, 4882-4889.
32. Pilch,D.S., Xu,Z., Sun,Q., LaVoie,E., Liu,L.F. and Breslauer,K.J. (1997) A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning. Proc. Natl Acad. Sci. USA, 94, 13565-13570
33. 2. Nucleic Acids Res., 23, 3678-3684.
34. Aymami,J., Nunn,C.M. and Neidle,S. (1999) DNA minor-groove recognition of a tris-benzimidazole drug by a non-self-complementary AT-rich sequence. Nucleic Acids Res., 27, 2691-2698.
35. Bathini,Y., Rao,K.E., Shea,R.G. and Lown,J.W. (1990) Molecular recognition between ligands and nucleic acids: novel pyridine- and benzoxazole-containing agents related to Hoechst 33258 that exhibit altered DNA sequence specificity deduced from footprinting and spectroscopic studies. Chem. Res. Toxicol., 3, 268-280.
36. 2: the role of hydrogen bonding in minor groove drug-DNA recognition. Nucleic Acids Res., 25, 1510-1515.
37. 2. Nucleic Acids Res., 26, 1660-1667.
38. Mann,J., Baron,A., Opoku-Boahen,Y., Johansson,E., Parkinson,G., Kelland,L.R. and Neidle,S. (2001) A new class of symmetric bisbenzimidazole-based DNA minor groove-binding agents showing antitumor activity. J. Med. Chem., 44, 138-144.
39. Bailly,C. Tardy,C., Wang L., Armitage B., Hopkins K., Kumar A., Schuster G.B., Boykin D.W. and Wilson W.D. (2001) Recognition of ATGA sequences by the unfused aromatic dication DB293 forming stacked dimers in the DNA minor groove. Biochemistry, 40, 9770-9779.
40. Davis,T.M. and Wilson,W.D. (2000) Determination of the refractive index increments of small molecules for correction of surface plasmon resonance data. Anal. Biochem., 284, 348-353.
41. Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys., 23, 327-341.
42. Read,M.A., Wood,A.A., Harrison,J.R., Gowan,S.M., Kelland,L.R., Dosanjh,H.S. and Neidle,S. (1999) Molecular modeling studies on G-quadruplex complexes of telomerase inhibitors: structure-activity relationships. J. Med. Chem., 42, 4538-4546.
43. Fox,K.R. and Waring,M.J. (2001) High-resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes. Methods Enzymol., 340, 412-430.
44. Wilson,W.D. (2002) Analyzing biomolecular interactions. Science, 295, 2103-2105.
45. Carrasco,C., Facompré,M., Chisholm,J.D., Van Vranken,D.L., Wilson,W.D. and Bailly,C. (2002) DNA sequence recognition by the indolocarbazole antitumor antibiotic AT2433-B1 and its diastereoisomer. Nucleic Acids Res., 30, 1774-1781.
46. Ngyen,B., Lee,M.P.H., Hamelberg,D., Joubert,A., Bailly,C., Brun,R., Neidle,S. and Wilson,W.D. (2002) Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove. J. Am. Chem. Soc., 124, 13680-13681.
47. Wilson,W.D., Wang,L., Tanious,F., Kumar,A., Boykin,D.W., Carrasco,C. and Bailly,C. (2001) BIAcore and DNA footprinting for discovery and development of new DNA targeted therapeutics and reagents. BIAcore J., 1, 15-19.
48. Brown,D.G., Sanderson,M.R., Skelly,J.V., Jenkins,T.C., Brown,T., Garman,E., Stuart,D.I. and Neidle,S. (1990) Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding. EMBO J., 9, 1329-1334.
49. 2 complex determined by NMR and molecular dynamics simulations in solution. J. Mol. Biol., 290, 699-716.
50. Chiu,T.K., Sohn,C., Dickerson,R.E. and Johnson,R.C. (2002) Testing water-mediated DNA recognition by the Hin recombinase. EMBO J., 21, 801-814.
51. Frelon,S., Douki,T. and Cadet,J. (2002) Radical oxidation of the adenine moiety of nucleoside and DNA: 2-hydroxy-2′-deoxyadenosine is a minor decomposition product. Free