Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1995 Jun 25;23(12):2192–2197. doi: 10.1093/nar/23.12.2192

The interaction of DNA duplexes containing 2-aminopurine with restriction endonucleases EcoRII and SsoII.

O V Petrauskene 1, S Schmidt 1, A S Karyagina 1, I I Nikolskaya 1, E S Gromova 1, D Cech 1
PMCID: PMC307007  PMID: 7610047

Abstract

Oligonucleotides containing 2-aminopurine (2-AP) in place of G or A in the recognition site of EcoRII (CCT/AGG) or SsoII (CCNGG) restriction endonucleases have been synthesized in order to investigate the specific interaction of DNA with these enzymes. Physicochemical properties (CD spectra and melting behaviour) have shown that DNA duplexes containing 2-aminopurine exist largely in a stable B-like form. 2-Aminopurine base paired with cytidine, however, essentially influences the helix structure. The presence of a 2-AP-C mismatch strongly reduces the stability of the duplexes in comparison with the natural double strand, indicated by a biphasic melting behaviour. SsoII restriction endonuclease recognizes and cleaves the modified substrate with a 2-AP-T mismatch in the centre of the recognition site, but it does not cleave the duplexes containing 2-aminopurine in place of inner and outer G, or both. EcoRII restriction endonuclease does not cleave duplexes containing 2-aminopurine at all. The two-substrate mechanism of EcoRII-DNA interaction, however, allows hydrolysis of the duplex containing 2-aminopurine in place of adenine in the presence of the canonical substrate.

Full text

PDF
2192

Images in this article

2196Image
on p.2196
2196Image
on p.2196

Selected References

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

  1. Brennan C. A., Van Cleve M. D., Gumport R. I. The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J Biol Chem. 1986 Jun 5;261(16):7270–7278. [PubMed] [Google Scholar]
  2. Dolinnaya N. G., Sokolova N. I., Gryaznova O. I., Shabarova Z. A. Site-directed modification of DNA duplexes by chemical ligation. Nucleic Acids Res. 1988 May 11;16(9):3721–3738. doi: 10.1093/nar/16.9.3721. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Eritja R., Kaplan B. E., Mhaskar D., Sowers L. C., Petruska J., Goodman M. F. Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Nucleic Acids Res. 1986 Jul 25;14(14):5869–5884. doi: 10.1093/nar/14.14.5869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fliess A., Wolfes H., Seela F., Pingoud A. Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides. Nucleic Acids Res. 1988 Dec 23;16(24):11781–11793. doi: 10.1093/nar/16.24.11781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gabbara S., Bhagwat A. S. Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites. J Biol Chem. 1992 Sep 15;267(26):18623–18630. [PubMed] [Google Scholar]
  6. Gromova E. S., Kubareva E. A., Vinogradova M. N., Oretskaya T. S., Shabarova Z. A. Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII. J Mol Recognit. 1991 Jul-Dec;4(4):133–141. doi: 10.1002/jmr.300040405. [DOI] [PubMed] [Google Scholar]
  7. Krüger D. H., Barcak G. J., Reuter M., Smith H. O. EcoRII can be activated to cleave refractory DNA recognition sites. Nucleic Acids Res. 1988 May 11;16(9):3997–4008. doi: 10.1093/nar/16.9.3997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Kubareva E. A., Petrauskene O. V., Karyagina A. S., Tashlitsky V. N., Nikolskaya I. I., Gromova E. S. Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonuclease SsoII. Nucleic Acids Res. 1992 Sep 11;20(17):4533–4538. doi: 10.1093/nar/20.17.4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Mazzarelli J., Scholtissek S., McLaughlin L. W. Effects of functional group changes in the EcoRV recognition site on the cleavage reaction catalyzed by the endonuclease. Biochemistry. 1989 May 30;28(11):4616–4622. doi: 10.1021/bi00437a016. [DOI] [PubMed] [Google Scholar]
  10. McClarin J. A., Frederick C. A., Wang B. C., Greene P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. doi: 10.1126/science.3024321. [DOI] [PubMed] [Google Scholar]
  11. McLaughlin L. W., Benseler F., Graeser E., Piel N., Scholtissek S. Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease. Biochemistry. 1987 Nov 17;26(23):7238–7245. doi: 10.1021/bi00397a007. [DOI] [PubMed] [Google Scholar]
  12. McLaughlin L. W., Leong T., Benseler F., Piel N. A new approach to the synthesis of a protected 2-aminopurine derivative and its incorporation into oligodeoxynucleotides containing the Eco RI and Bam HI recognition sites. Nucleic Acids Res. 1988 Jun 24;16(12):5631–5644. doi: 10.1093/nar/16.12.5631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Newman P. C., Nwosu V. U., Williams D. M., Cosstick R., Seela F., Connolly B. A. Incorporation of a complete set of deoxyadenosine and thymidine analogues suitable for the study of protein nucleic acid interactions into oligodeoxynucleotides. Application to the EcoRV restriction endonuclease and modification methylase. Biochemistry. 1990 Oct 23;29(42):9891–9901. doi: 10.1021/bi00494a020. [DOI] [PubMed] [Google Scholar]
  14. Pein C. D., Reuter M., Cech D., Krüger D. H. Oligonucleotide duplexes containing CC(A/T)GG stimulate cleavage of refractory DNA by restriction endonuclease EcoRII. FEBS Lett. 1989 Mar 13;245(1-2):141–144. doi: 10.1016/0014-5793(89)80208-x. [DOI] [PubMed] [Google Scholar]
  15. Petrauskene O. V., Kubareva E. A., Gromova E. S., Shabarova Z. A. Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites. Probing of modified DNA duplexes as activators of the enzyme. Eur J Biochem. 1992 Sep 15;208(3):617–622. doi: 10.1111/j.1432-1033.1992.tb17226.x. [DOI] [PubMed] [Google Scholar]
  16. Sinha N. D., Biernat J., McManus J., Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sowers L. C., Eritja R., Chen F. M., Khwaja T., Kaplan B. E., Goodman M. F., Fazakerley G. V. Characterization of the high pH wobble structure of the 2-aminopurine.cytosine mismatch by N-15 NMR spectroscopy. Biochem Biophys Res Commun. 1989 Nov 30;165(1):89–92. doi: 10.1016/0006-291x(89)91037-1. [DOI] [PubMed] [Google Scholar]

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

RESOURCES