Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 May 1;24(9):1594–1601. doi: 10.1093/nar/24.9.1594

The structure of 4-way DNA junctions: specific binding of bis-intercalators with rigid linkers.

M L Carpenter 1, G Lowe 1, P R Cook 1
PMCID: PMC145853  PMID: 8649974

Abstract

During replication and recombination, two DNA duplexes lie side by side. We have developed reagents that might be used to probe structure during these critical processes; they contain two intercalating groups connected by a rigid linker that forces those groups to point in opposite directions. If their stereochemistry proves appropriate, such structure-specific agents should intercalate specifically into adjacent duplexes in the Y- and X-shaped structures (i.e. 3- and 4-way junctions, now known as 3H and 4H junctions) found at replication and recombination sites. We prepared DNA structures in which four duplexes were arranged in all possible combinations around 2- and 4-way junctions and then probed the accessibility to DNase I of all their phosphodiester bonds. In the absence of any bis-intercalators, 7-9 nucleotides (nt) in each of the strands in 4-way junctions were protected from attack; protected regions were significantly offset to the 3' side of the junction in continuous strands, but only slightly offset, if at all, in exchanging strands. All the intercalators decreased accessibility throughout the structure, but none did so at specific points in the two adjacent arms of 4-way junctions. However, one bis-intercalator--but not its sister with a shorter linker--strikingly increased access to a particular CpT bond that lay 9 nt away from the centre of some 4-way junctions without reducing access to neighbouring bonds. Binding was both sequence and structure specific, and depended on complementary stereochemistry between bis-intercalator and junction.

Full Text

The Full Text of this article is available as a PDF (304.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Annan N. K., Cook P. R., Mullins S. T., Lowe G. Evidence for cross-linking DNA by bis-intercalators with rigid and extended linkers is provided by knotting and catenation. Nucleic Acids Res. 1992 Mar 11;20(5):983–990. doi: 10.1093/nar/20.5.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bailly C., Gentle D., Hamy F., Purcell M., Waring M. J. Localized chemical reactivity in DNA associated with the sequence-specific bisintercalation of echinomycin. Biochem J. 1994 May 15;300(Pt 1):165–173. doi: 10.1042/bj3000165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Canellakis E. S., Shaw Y. H., Hanners W. E., Schwartz R. A. Diacridines: bifunctional intercalators. I. Chemistry, physical chemistry and growth inhibitory properties. Biochim Biophys Acta. 1976 Feb 5;418(3):277–289. doi: 10.1016/0005-2787(76)90290-2. [DOI] [PubMed] [Google Scholar]
  4. Chen J. H., Churchill M. E., Tullius T. D., Kallenbach N. R., Seeman N. C. Construction and analysis of monomobile DNA junctions. Biochemistry. 1988 Aug 9;27(16):6032–6038. doi: 10.1021/bi00416a031. [DOI] [PubMed] [Google Scholar]
  5. Drew H. R. Structural specificities of five commonly used DNA nucleases. J Mol Biol. 1984 Jul 15;176(4):535–557. doi: 10.1016/0022-2836(84)90176-1. [DOI] [PubMed] [Google Scholar]
  6. Drew H. R., Travers A. A. DNA structural variations in the E. coli tyrT promoter. Cell. 1984 Jun;37(2):491–502. doi: 10.1016/0092-8674(84)90379-9. [DOI] [PubMed] [Google Scholar]
  7. Duckett D. R., Murchie A. I., Diekmann S., von Kitzing E., Kemper B., Lilley D. M. The structure of the Holliday junction, and its resolution. Cell. 1988 Oct 7;55(1):79–89. doi: 10.1016/0092-8674(88)90011-6. [DOI] [PubMed] [Google Scholar]
  8. Fox K. R., Waring M. J. Footprinting at low temperatures: evidence that ethidium and other simple intercalators can discriminate between different nucleotide sequences. Nucleic Acids Res. 1987 Jan 26;15(2):491–507. doi: 10.1093/nar/15.2.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fu T. J., Tse-Dinh Y. C., Seeman N. C. Holliday junction crossover topology. J Mol Biol. 1994 Feb 11;236(1):91–105. doi: 10.1006/jmbi.1994.1121. [DOI] [PubMed] [Google Scholar]
  10. Gao X. L., Patel D. J. NMR studies of echinomycin bisintercalation complexes with d(A1-C2-G3-T4) and d(T1-C2-G3-A4) duplexes in aqueous solution: sequence-dependent formation of Hoogsteen A1.T4 and Watson--Crick T1.A4 base pairs flanking the bisintercalation site. Biochemistry. 1988 Mar 8;27(5):1744–1751. doi: 10.1021/bi00405a054. [DOI] [PubMed] [Google Scholar]
  11. Guo Q., Lu M., Seeman N. C., Kallenbach N. R. Drug binding by branched DNA molecules: analysis by chemical footprinting of intercalation into an immobile junction. Biochemistry. 1990 Jan 16;29(2):570–578. doi: 10.1021/bi00454a034. [DOI] [PubMed] [Google Scholar]
  12. Guo Q., Seeman N. C., Kallenbach N. R. Site-specific interaction of intercalating drugs with a branched DNA molecule. Biochemistry. 1989 Mar 21;28(6):2355–2359. doi: 10.1021/bi00432a001. [DOI] [PubMed] [Google Scholar]
  13. Herrera J. E., Chaires J. B. Characterization of preferred deoxyribonuclease I cleavage sites. J Mol Biol. 1994 Feb 18;236(2):405–411. doi: 10.1006/jmbi.1994.1152. [DOI] [PubMed] [Google Scholar]
  14. Huang C. H., Mirabelli C. K., Mong S., Crooke S. T. Intermolecular cross-linking of DNA through bifunctional intercalation of an antitumor antibiotic, luzopeptin A (BBM-928A). Cancer Res. 1983 Jun;43(6):2718–2724. [PubMed] [Google Scholar]
  15. Jacobsen J. P., Pedersen J. B., Hansen L. F., Wemmer D. E. Site selective bis-intercalation of a homodimeric thiazole orange dye in DNA oligonucleotides. Nucleic Acids Res. 1995 Mar 11;23(5):753–760. doi: 10.1093/nar/23.5.753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kimball A., Guo Q., Lu M., Cunningham R. P., Kallenbach N. R., Seeman N. C., Tullius T. D. Construction and analysis of parallel and antiparallel Holliday junctions. J Biol Chem. 1990 Apr 25;265(12):6544–6547. [PubMed] [Google Scholar]
  17. Le Pecq J. B., Le Bret M., Barbet J., Roques B. DNA polyintercalating drugs: DNA binding of diacridine derivatives. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2915–2919. doi: 10.1073/pnas.72.8.2915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lilley D. M., Clegg R. M. The structure of the four-way junction in DNA. Annu Rev Biophys Biomol Struct. 1993;22:299–328. doi: 10.1146/annurev.bb.22.060193.001503. [DOI] [PubMed] [Google Scholar]
  19. Lu M., Guo Q., Kallenbach N. R. Effect of sequence on the structure of three-arm DNA junctions. Biochemistry. 1991 Jun 18;30(24):5815–5820. doi: 10.1021/bi00238a001. [DOI] [PubMed] [Google Scholar]
  20. Lu M., Guo Q., Kallenbach N. R. Interaction of drugs with branched DNA structures. Crit Rev Biochem Mol Biol. 1992;27(3):157–190. doi: 10.3109/10409239209082562. [DOI] [PubMed] [Google Scholar]
  21. Lu M., Guo Q., Pasternack R. F., Wink D. J., Seeman N. C., Kallenbach N. R. Drug binding by branched DNA: selective interaction of tetrapyridyl porphyrins with an immobile junction. Biochemistry. 1990 Feb 13;29(6):1614–1624. doi: 10.1021/bi00458a037. [DOI] [PubMed] [Google Scholar]
  22. Lu M., Guo Q., Seeman N. C., Kallenbach N. R. DNase I cleavage of branched DNA molecules. J Biol Chem. 1989 Dec 15;264(35):20851–20854. [PubMed] [Google Scholar]
  23. Lu M., Guo Q., Seeman N. C., Kallenbach N. R. Drug binding by branched DNA: selective interaction of the dye stains-all with an immobile junction. Biochemistry. 1990 Apr 3;29(13):3407–3412. doi: 10.1021/bi00465a038. [DOI] [PubMed] [Google Scholar]
  24. Mullins S. T., Annan N. K., Cook P. R., Lowe G. Bisintercalators of DNA with a rigid linker in an extended configuration. Biochemistry. 1992 Jan 28;31(3):842–849. doi: 10.1021/bi00118a029. [DOI] [PubMed] [Google Scholar]
  25. Murchie A. I., Carter W. A., Portugal J., Lilley D. M. The tertiary structure of the four-way DNA junction affords protection against DNase I cleavage. Nucleic Acids Res. 1990 May 11;18(9):2599–2606. doi: 10.1093/nar/18.9.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Peek M. E., Lipscomb L. A., Bertrand J. A., Gao Q., Roques B. P., Garbay-Jaureguiberry C., Williams L. D. DNA distortion in bis-intercalated complexes. Biochemistry. 1994 Apr 5;33(13):3794–3800. doi: 10.1021/bi00179a002. [DOI] [PubMed] [Google Scholar]
  27. Searle M. S., Hall J. G., Denny W. A., Wakelin L. P. Interaction of the antitumour antibiotic luzopeptin with the hexanucleotide duplex d(5'-GCATGC)2. One-dimensional and two-dimensional n.m.r. studies. Biochem J. 1989 Apr 15;259(2):433–441. doi: 10.1042/bj2590433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Seeman N. C., Kallenbach N. R. DNA branched junctions. Annu Rev Biophys Biomol Struct. 1994;23:53–86. doi: 10.1146/annurev.bb.23.060194.000413. [DOI] [PubMed] [Google Scholar]
  29. Suck D., Lahm A., Oefner C. Structure refined to 2A of a nicked DNA octanucleotide complex with DNase I. Nature. 1988 Mar 31;332(6163):464–468. doi: 10.1038/332464a0. [DOI] [PubMed] [Google Scholar]
  30. Veal J. M., Li Y., Zimmerman S. C., Lamberson C. R., Cory M., Zon G., Wilson W. D. Interaction of a macrocyclic bisacridine with DNA. Biochemistry. 1990 Dec 11;29(49):10918–10927. doi: 10.1021/bi00501a009. [DOI] [PubMed] [Google Scholar]
  31. Ward B., Rehfuss R., Goodisman J., Dabrowiak J. C. Rate enhancements in the DNase I footprinting experiment. Nucleic Acids Res. 1988 Feb 25;16(4):1359–1369. doi: 10.1093/nar/16.4.1359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Zhang S., Seeman N. C. Symmetric Holliday junction crossover isomers. J Mol Biol. 1994 May 20;238(5):658–668. doi: 10.1006/jmbi.1994.1327. [DOI] [PubMed] [Google Scholar]
  33. Zhang X. L., Patel D. J. Solution structure of the luzopeptin-DNA complex. Biochemistry. 1991 Apr 23;30(16):4026–4041. doi: 10.1021/bi00230a030. [DOI] [PubMed] [Google Scholar]
  34. von Kitzing E., Lilley D. M., Diekmann S. The stereochemistry of a four-way DNA junction: a theoretical study. Nucleic Acids Res. 1990 May 11;18(9):2671–2683. doi: 10.1093/nar/18.9.2671. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES