Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1975 Oct;2(10):1851–1865. doi: 10.1093/nar/2.10.1851

Sequences spanning the EcoRI substrate site.

D E Garfin, H W Boyer, H M Goodman
PMCID: PMC343552  PMID: 171627

Abstract

Substrate recognition by the EcoRI restriction endonuclease was investigated by analysis of the nucleotide sequences at the sites of enzymatic cleavage in various DNA molecules. 5'-end labeling and homochromatographic fingerprinting led to the determination of a 17-base-pair sequence spanning the EcoRI site of simian virus 40 DNA and a 15-base-pair sequence overlapping the EcoRI site of Col El plasmid DNA. Three other DNAs were similarly tested, although extended sequences were not determined in these cases. The EcoRI site was shown to be symmetric double-stranded equivalent of -N-G-A-A-T-T-C-N-.

Full text

PDF
1851

Images in this article

1858Image
on p.1858
1861Image
on p.1861
1862Image
on p.1862

Selected References

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

  1. Boyer H. W. DNA restriction and modification mechanisms in bacteria. Annu Rev Microbiol. 1971;25:153–176. doi: 10.1146/annurev.mi.25.100171.001101. [DOI] [PubMed] [Google Scholar]
  2. Boyer H. W. Restriction and modification of DNA: enzymes and substrates. Introductory remarks. Fed Proc. 1974 May;33(5):1125–1127. [PubMed] [Google Scholar]
  3. Brownlee G. G., Sanger F. Chromatography of 32P-labelled oligonucleotides on thin layers of DEAE-cellulose. Eur J Biochem. 1969 Dec;11(2):395–399. doi: 10.1111/j.1432-1033.1969.tb00786.x. [DOI] [PubMed] [Google Scholar]
  4. Chamberlin M. J., Ring J. Studies of the binding of Escherichia coli RNA polymerase to DNA. V. T7 RNA chain initiation by enzyme-DNA complexes. J Mol Biol. 1972 Sep 28;70(2):221–237. doi: 10.1016/0022-2836(72)90535-9. [DOI] [PubMed] [Google Scholar]
  5. Dugaiczyk A., Hedgpeth J., Boyer H. W., Goodman H. M. Physical identity of the SV40 deoxyribonucleic acid sequence recognized by the Eco RI restriction endonuclease and modification methylase. Biochemistry. 1974 Jan 29;13(3):503–512. doi: 10.1021/bi00700a016. [DOI] [PubMed] [Google Scholar]
  6. Ehrlich S. D., Bertazzoni U., Bernardi G. The specificity of pancreatic deoxyribonuclease. Eur J Biochem. 1973 Dec 3;40(1):143–147. doi: 10.1111/j.1432-1033.1973.tb03178.x. [DOI] [PubMed] [Google Scholar]
  7. Garfin D. E., Goodman H. M. Nucleotide sequences at the cleavage sites of two restriction endonucleases from Hemophilus parainfluenzae. Biochem Biophys Res Commun. 1974 Jul 10;59(1):108–116. doi: 10.1016/s0006-291x(74)80181-6. [DOI] [PubMed] [Google Scholar]
  8. Glynn I. M., Chappell J. B. A simple method for the preparation of 32-P-labelled adenosine triphosphate of high specific activity. Biochem J. 1964 Jan;90(1):147–149. doi: 10.1042/bj0900147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Guerry P., LeBlanc D. J., Falkow S. General method for the isolation of plasmid deoxyribonucleic acid. J Bacteriol. 1973 Nov;116(2):1064–1066. doi: 10.1128/jb.116.2.1064-1066.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hedgpeth J., Goodman H. M., Boyer H. W. DNA nucleotide sequence restricted by the RI endonuclease. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3448–3452. doi: 10.1073/pnas.69.11.3448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hershfield V., Boyer H. W., Yanofsky C., Lovett M. A., Helinski D. R. Plasmid ColEl as a molecular vehicle for cloning and amplification of DNA. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3455–3459. doi: 10.1073/pnas.71.9.3455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Jay E., Bambara R., Padmanabhan R., Wu R. DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping. Nucleic Acids Res. 1974 Mar;1(3):331–353. doi: 10.1093/nar/1.3.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ling V. Fractionation and sequences of the large pyrimidine oligonucleotides from bacteriophage fd DNA. J Mol Biol. 1972 Feb 28;64(1):87–102. doi: 10.1016/0022-2836(72)90322-1. [DOI] [PubMed] [Google Scholar]
  14. Lovett M. A., Guiney D. G., Helinski D. R. Relaxation complexes of plasmids ColE1 and ColE2: unique site of the nick in the open circular DNA of the relaxed complexes. Proc Natl Acad Sci U S A. 1974 Oct;71(10):3854–3857. doi: 10.1073/pnas.71.10.3854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maniatis T., Jeffrey A., Kleid D. G. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. doi: 10.1073/pnas.72.3.1184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Maniatis T., Ptashne M., Barrell B. G., Donelson J. Sequence of a repressor-binding site in the DNA of bacteriophage lamda. Nature. 1974 Aug 2;250(465):394–397. doi: 10.1038/250394a0. [DOI] [PubMed] [Google Scholar]
  17. Morrow J. F., Berg P. Cleavage of Simian virus 40 DNA at a unique site by a bacterial restriction enzyme. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3365–3369. doi: 10.1073/pnas.69.11.3365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Morrow J. F., Cohen S. N., Chang A. C., Boyer H. W., Goodman H. M., Helling R. B. Replication and transcription of eukaryotic DNA in Escherichia coli. Proc Natl Acad Sci U S A. 1974 May;71(5):1743–1747. doi: 10.1073/pnas.71.5.1743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mulder C., Delius H. Specificity of the break produced by restricting endonuclease R 1 in Simian virus 40 DNA, as revealed by partial denaturation mapping. Proc Natl Acad Sci U S A. 1972 Nov;69(11):3215–3219. doi: 10.1073/pnas.69.11.3215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Murray K., Murray N. E. Terminal nucleotide sequences of DNA from temperate coliphages. Nat New Biol. 1973 May 30;243(126):134–139. doi: 10.1038/newbio243134a0. [DOI] [PubMed] [Google Scholar]
  21. Murray K. Nucleotide sequence analysis with polynucleotide kinase and nucleotide "mapping" methods. 5'-Terminal sequences of deoxyribonucleic acid from bacteriophages lambda and 424. Biochem J. 1973 Mar;131(3):569–582. doi: 10.1042/bj1310569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Murray K., Old R. W. The primary structure of DNA. Prog Nucleic Acid Res Mol Biol. 1974;14(0):117–185. doi: 10.1016/s0079-6603(08)60207-x. [DOI] [PubMed] [Google Scholar]
  23. Rensing U. F., Schoenmakers G. G. A sequence of 50 nucleotides from coliphage R17 RNA. Eur J Biochem. 1973 Feb 15;33(1):8–18. doi: 10.1111/j.1432-1033.1973.tb02648.x. [DOI] [PubMed] [Google Scholar]
  24. Salser W. A. DNA sequencing techniques. Annu Rev Biochem. 1974;43(0):923–965. doi: 10.1146/annurev.bi.43.070174.004423. [DOI] [PubMed] [Google Scholar]
  25. Sanger F., Donelson J. E., Coulson A. R., Kössel H., Fischer D. Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1209–1213. doi: 10.1073/pnas.70.4.1209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Subramanian K. N., Pan J., Zain S., Weissman S. M. The mapping and ordering of fragments of SV40 DNA produced by restriction endonucleases. Nucleic Acids Res. 1974 Jun;1(6):727–752. doi: 10.1093/nar/1.6.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
  28. Zain B. S., Weissman S. M., Dhar R., Pan J. The nucleotide sequence preceding an RNA polymerase initiation site on SV40 DNA. Part 1. The sequence of the late strand transcript. Nucleic Acids Res. 1974 Apr;1(4):577–594. doi: 10.1093/nar/1.4.577. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES