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. 1975 Mar;2(3):327–345. doi: 10.1093/nar/2.3.327

On the statistical significance of primary structural features found in DNA-protein interaction sites

Gene Dykes 1, Robert Bambara 1, Kenneth Marians 1, Ray Wu 1
PMCID: PMC342839  PMID: 1093137

Abstract

Probabilities of occurrence for a number of the symmetries and other sequence regularities found in DNA-protein interaction site sequences have been calculated for segments of random DNA sequence. Results show that many of the symmetrical and repetitive features seen in these interaction sites are likely to have occurred by chance. Other features are so unlikely to have occurred by chance that they are probably involved in the DNA-protein interaction processes.

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Selected References

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  1. Adler K., Beyreuther K., Fanning E., Geisler N., Gronenborn B., Klemm A., Müller-Hill B., Pfahl M., Schmitz A. How lac repressor binds to DNA. Nature. 1972 Jun 9;237(5354):322–327. doi: 10.1038/237322a0. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Chandrasekaran R., Hukins D. W., Smith P. J., Watts L. Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J Mol Biol. 1974 Sep 15;88(2):523–533. doi: 10.1016/0022-2836(74)90499-9. [DOI] [PubMed] [Google Scholar]
  3. Bambara R., Padmanabhan R., Wu R. Nucleotide sequence analysis of DNA. X. Complete nucleotide sequence of the cohesive ends of bacteriophage phi80 DNA. J Mol Biol. 1973 Apr 25;75(4):741–744. doi: 10.1016/0022-2836(73)90305-7. [DOI] [PubMed] [Google Scholar]
  4. Bernardi G. Mechanism of action and structure of acid deoxyribonuclease. Adv Enzymol Relat Areas Mol Biol. 1968;31:1–49. doi: 10.1002/9780470122761.ch1. [DOI] [PubMed] [Google Scholar]
  5. Crick F. General model for the chromosomes of higher organisms. Nature. 1971 Nov 5;234(5323):25–27. doi: 10.1038/234025a0. [DOI] [PubMed] [Google Scholar]
  6. Ghangas G. S., Jay E., Bambara R., Wu R. Nucleotide sequence analysis of DNA. XI. The 3' terminal sequences of bacteriophage lambda and phi 80 DNA. Biochem Biophys Res Commun. 1973 Oct 1;54(3):998–1007. doi: 10.1016/0006-291x(73)90793-6. [DOI] [PubMed] [Google Scholar]
  7. Gilbert W., Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3581–3584. doi: 10.1073/pnas.70.12.3581. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gilbert W., Müller-Hill B. Isolation of the lac repressor. Proc Natl Acad Sci U S A. 1966 Dec;56(6):1891–1898. doi: 10.1073/pnas.56.6.1891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gilbert W., Müller-Hill B. The lac operator is DNA. Proc Natl Acad Sci U S A. 1967 Dec;58(6):2415–2421. doi: 10.1073/pnas.58.6.2415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gralla J., DeLisi C. mRNA is expected to form stable secondary structures. Nature. 1974 Mar 22;248(446):330–332. doi: 10.1038/248330a0. [DOI] [PubMed] [Google Scholar]
  11. JACOB F., MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318–356. doi: 10.1016/s0022-2836(61)80072-7. [DOI] [PubMed] [Google Scholar]
  12. Lebowitz P., Weissman S. M., Radding C. M. Nucleotide sequence of a ribonucleic acid transcribed in vitro from lambda phage deoxyribonucleic acid. J Biol Chem. 1971 Aug 25;246(16):5120–5139. [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. Ptashne M. ISOLATION OF THE lambda PHAGE REPRESSOR. Proc Natl Acad Sci U S A. 1967 Feb;57(2):306–313. doi: 10.1073/pnas.57.2.306. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ptashne M. Specific binding of the lambda phage repressor to lambda DNA. Nature. 1967 Apr 15;214(5085):232–234. doi: 10.1038/214232a0. [DOI] [PubMed] [Google Scholar]
  17. Sekiya T., Khorana H. G. Nucleotide sequence in the promoter region of the Escherichia coli tyrosine tRNA gene. Proc Natl Acad Sci U S A. 1974 Aug;71(8):2978–2982. doi: 10.1073/pnas.71.8.2978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sobell H. M. Molecular mechanism for genetic recombination. Proc Natl Acad Sci U S A. 1972 Sep;69(9):2483–2487. doi: 10.1073/pnas.69.9.2483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Wang J. C., Barkley M. D., Bourgeois S. Measurements of unwinding of lac operator by repressor. Nature. 1974 Sep 20;251(5472):247–249. doi: 10.1038/251247a0. [DOI] [PubMed] [Google Scholar]
  20. Weigel P. H., Englund P. T., Murray K., Old R. W. The 3'-terminal nucleotide sequences of bacteriophage lambda DNA. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1151–1155. doi: 10.1073/pnas.70.4.1151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Wells R. D., Larson J. E., Grant R. C., Shortle B. E., Cantor C. R. Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J Mol Biol. 1970 Dec 28;54(3):465–497. doi: 10.1016/0022-2836(70)90121-x. [DOI] [PubMed] [Google Scholar]
  22. Wu R., Taylor E. Nucleotide sequence analysis of DNA. II. Complete nucleotide sequence of the cohesive ends of bacteriophage lambda DNA. J Mol Biol. 1971 May 14;57(3):491–511. doi: 10.1016/0022-2836(71)90105-7. [DOI] [PubMed] [Google Scholar]
  23. 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]

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