Targeting the minor groove of DNA

Current Opinion in Structural Biology

Volumn 7, Issue 3, 1997, Pages 355-361

  Wemmer, David E ^a   Dervan, Peter B ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 METHYLIMIDAZOLE; AMINO ACID; DISTAMYCIN A; DNA; POLYAMIDE; PYRROLE DERIVATIVE;

ARTICLE; BINDING AFFINITY; DNA BINDING; DNA CONFORMATION; DNA SEQUENCE; DRUG DNA BINDING; DRUG TARGETING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL;

EID: 0030927763     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80051-6     Document Type: Article

References (47)

1. Seeman NC, Rosenberg JM, Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA. 73:1976;804-808.
2. Nikolov DB, Hu S-H, Lin J, Gasch A, Hoffman A, Horikoshi M, Chua N-H, Roeder RG, Burley SK. Crystal structure of TFIID TATA-box binding protein. Nature. 360:1992;40-46.
3. Werner MH, Huth JR, Bronenborn AM, Clore GM. Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY - DNA complex. Cell. 81:1995;705-714.
4. Billeter M, Qian YQ, Otting G, Müller M, Gehring W, Würich K. Determination of the NMR solution structure of an Antennapedia homeodomain - DNA complex. J Mol Biol. 234:1993;1084-1097.
5. Feng J-A, Johnson RC, Dickerson RE. Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. Science. 263:1994;348-355.
6. Schumacher MA, Choi KY, Zalkin H, Brennan RG. Crystal structure of Lacl member, PurR, bound to DNA: minor groove binding by α helices. Science. 266:1994;763-770.
7. Geierstanger BH, Wemmer DE. Complexes of the minor groove of DNA. Annu Rev Biophys Biomol Struct. 24:1995;463-493.
8. Breslauer KJ, Remata DP, Chou W-Y, Ferrante R, Curry J, Zaunczkowski D, Snyder JG, Marky LA. Enthalpy - entropy compensations in drug - DNA binding studies. Proc Natl Acad Sci USA. 84:1987;8922-8926.
9. Abu-Daya A, Brown PM, Fox KR. DNA sequence preferences of several AT-selective minor groove binding ligands. Nucleic Acids Res. 23:1995;3385-3392.
10. Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci USA. 78:1981;2179-2183.
11. Nelson HCM, Finch JT, Luisi BR, Klug A. The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature. 330:1987;221-226.
12. Chuprina VB, Lipanov AA, Federoff OYu, Kim SG, Kintanar A, Reid BR. Sequence effects on local DNA topology. Proc Natl Acad Sci USA. 88:1987;9087-9091.
13. Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE. Binding of an antitumor drug to DNA. J Mol Biol. 183:1985;553-563.
14. Coll M, Frederick CA, Wang AH-J, Rich A. A bifurcated hydrogen-bonded conformation in the d(A·T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl Acad Sci USA. 84:1987;8385-8389.
15. Pelton JG, Wemmer DE. Structural characterization of a 2:1 distamycin A-d(CGCAAATTGGC) complex by two-dimensional NMR. Proc Natl Acad Sci USA. 86:1989;5723-5727.
16. Rentzeperis D, Marky LA, Dwyer TJ, Geierstanger BH, Pelton JG, Wemmer DE. Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry. 34:1995;2937-2945.
17. Wemmer DE, Geierstanger BH, Fagan PA, Dwyer TJ, Jacobsen JP, Pelton JG, Ball GE, Leheny AR, Chang WH, Bathini Y, et al. Minor groove recognition of DNA by distamycin and its analogs. Sarma RH, Sarma MH. Structural Biology: The State of the Art, Proceedings of the 8th Conversation. 1994;301-323 Adenine Press, Albany, NY.
18. Chen X, Ramakrishnan B, Rao ST, Sundaralingam M. Binding of two Distamycin A molecules in the minor groove of an alternating B-DNA duplex. Nat Struct Biol. 1:1994;169-175.
19. Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE. The molecular origin of DNA - drug specificity in netropsin and distamycin. Proc Natl Acad Sci USA. 82:1985;1376-1380.
20. Lown JW, Krowicki K, Bhat UG, Skorobogaty A, Ward B, Dabrowiak JC. Molecular recognition between oligopeptides and nucleic acids: novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity. Biochemistry. 25:1986;7408-7416.
21. Wade WE, Mrksich M, Dervan PB. Design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif. J Am Chem Soc. 114:1992;8783-8794.
22. Mrksich M, Wade WS, Dwyer TJ, Geierstanger BH, Wemmer DE, Dervan PB. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci USA. 89:1992;7568-7590.
23. Geierstanger BH, Dwyer TJ, Bathini Y, Lown JW, Wemmer DE. NMR characterization of a heterocomplex formed by distamycin and its analog 2-ImD with d(CGCAAGTTGGC):d(GCCAACTTGCG): preference for the 1:1:1 2-ImD:Dst:DNA complex over the 2:1 2-ImD:DNA and the 2:1 Dst:DNA complexes. J Am Chem Soc. 115:1993;4474-4482.
24. Mrksich M, Dervan PB. Antiparallel side-by-side heterodimer for sequence-specific recognition in the minor groove of DNA by a distamycin / 1-methylimidazole-2-carboxamide-netropsin pair. J Am Chem Soc. 115:1993;2572-2576.
25. Geierstanger BH, Mrksich M, Dervan PB, Wemmer DE. Design of a G·C-specific DNA minor groove-binding peptide. Science. 266:1994;646-650.
26. Mrksich M, Dervan PB. Recognition in the minor groove of DNA at 5'-(A,T)GCGC(A,T)-3' by a four ring tripeptide dimer. Reversal of the specificity of the natural product distamycin. J Am Chem Soc. 117:1995;3325-3332.
27. White S, Baird EE, Dervan PB. Effects of the A·T/T·A degeneracy of th pyrrole-imidazole polyamide recognition in the minor groove of DNA. Biochemistry. 35:1996;12532-12537.
28. Youngquist RS, Dervan PB. Sequence-specific recognition of B-DNA by oligo(N-methylpyrrole-carboxamide)s. Proc Natl Acad Sci USA. 82:1985;2565-2569.
29. Youngquist RS, Dervan PB. A synthetic peptide binding 16 base pairs of A,T double helical DNA. J Am Chem Soc. 109:1987;7564-7566.
30. Mrksich M, Dervan PB. Design of a covalent peptide heterodimer for sequence-specific recognition in the minor groove of double helical DNA. J Am Chem Soc. 116:1994;3663-3664.
31. 3-6 in complex with 5'-TGACT-3' sites by two dimensional NMR. J Am Chem Soc. 115:1993;9900-9906.
32. Mrksich M, Parks ME, Dervan PB. Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA. J Am Chem Soc. 116:1994;7983-7988.
33. Parks ME, Baird EE, Dervan PB. Optimization of the hairpin polyamide design for recognition of the minor groove of DNA. J Am Chem Soc. 118:1996;6147-6152.
34. 2-3' sequence in the minor groove of DNA by an eight-ring hairpin polyamide. J Am Chem Soc. 118:1996;8198-8206.
35. Cho J, Parks ME, Dervan PB. Cyclic polyamides for recognition in the minor groove of DNA. Proc Natl Acad Sci. 92:1995;10389-10392.
36. Trauger JW, Baird EE, Mrksich M, Dervan PB. Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs. J Am Chem Soc. 118:1996;6160-6166 This paper describes extended binding motifs that show that sequence-specific recognition can be extended to rather long target sequences. of special interest.
37. Geierstanger BH, Mrksich M, Dervan PB, Wemmer DE. Extending the recognition site of designed minor groove binding molecules. Nat Struct Biol. 3:1996;321-324 A structural characterization of the 'slipped' extended binding motif is presented, which shows the importance of linkers, and the good fit of ligand and DNA throughout the complex. of special interest.
38. Trauger JW, Baird EE, Dervan PB. Recognition of DNA by designed ligands at subnanomolar concentrations. Nature. 382:1996;559-561 The authors show that four ring hairpin ligands bind with very high affinity and good specificity. of outstanding interest.
39. Trauger JW, Baird EE, Dervan PB. Extended hairpin polyamide motif for sequence-specific recognition in the minor groove of DNA. Chem Biol. 3:1996;369-377 This paper shows that one of the many possible extensions of the extended binding motif is functional, giving high affinity and specificity. of special interest.
40. Baird EE, Dervan PB. Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J Am Chem Soc. 118:1996;6141-6146 This paper describes the synthetic enhancements that make practical the exploration of the binding motifs of polyamides and their applications. of outstanding interest.
41. Gao X, Mirau P, Patel DJ. Structure refinement of the chromomycin dimer - DNA oligomer complex in solution. J Mol Biol. 223:1992;259-279.
42. Walker S, Murnick J, Kahne D. Structural characterization of a calicheamicin - DNA complex by NMR. J Am Chem Soc. 115:1994;7954-7961.
43. Ikemoto N, Kumar RA, Ling TT, Ellestad GA, Danishefsky SJ, Patel DJ. Calicheamicin - DNA complexes - warhead alignment and saccharide recognition of the minor groove. Proc Natl Acad Sci USA. 92:1995;10506-10510.
44. Paloma LG, Smith JA, Chazin WJ, Nicolaou KC. Interaction of calicheamicin with duplex DNA - role of the oligosaccharide domain and identification of multiple binding modes. J Am Chem Soc. 116:1994;3697-3708.
45. Kahne D. Strategies for the design of minor groove binders: a reevaluation based on the mergence of site-selective carbohydrate binders. Chem Biol. 2:1995;9-12.
46. 2. J Am Chem Soc. 118:1996;8817-8824.
47. Gottesfeld JM, Neely L, Trauger JW, Baird EE, Dervan PB. Regulation of gene expression by small molecules. Nature. 1997;. in press.