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. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789

Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity.

M E Mulligan, D K Hawley, R Entriken, W R McClure
PMCID: PMC321093  PMID: 6364042

Abstract

We describe a simple algorithm for computing a homology score for Escherichia coli promoters based on DNA sequence alone. The homology score was related to 31 values, measured in vitro, of RNA polymerase selectivity, which we define as the product KBk2, the apparent second order rate constant for open complex formation. We found that promoter strength could be predicted to within a factor of +/-4.1 in KBk2 over a range of 10(4) in the same parameter. The quantitative evaluation was linked to an automated (Apple II) procedure for searching and evaluating possible promoters in DNA sequence files.

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Selected References

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

  1. Fristensky B., Lis J., Wu R. Portable microcomputer software for nucleotide sequence analysis. Nucleic Acids Res. 1982 Oct 25;10(20):6451–6463. doi: 10.1093/nar/10.20.6451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Harr R., Häggström M., Gustafsson P. Search algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Res. 1983 May 11;11(9):2943–2957. doi: 10.1093/nar/11.9.2943. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Hawley D. K., McClure W. R. In vitro comparison of initiation properties of bacteriophage lambda wild-type PR and x3 mutant promoters. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6381–6385. doi: 10.1073/pnas.77.11.6381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hawley D. K., McClure W. R. Mechanism of activation of transcription initiation from the lambda PRM promoter. J Mol Biol. 1982 May 25;157(3):493–525. doi: 10.1016/0022-2836(82)90473-9. [DOI] [PubMed] [Google Scholar]
  6. Larson R., Messing J. Apple II software for M13 shotgun DNA sequencing. Nucleic Acids Res. 1982 Jan 11;10(1):39–49. doi: 10.1093/nar/10.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. McClure W. R. Rate-limiting steps in RNA chain initiation. Proc Natl Acad Sci U S A. 1980 Oct;77(10):5634–5638. doi: 10.1073/pnas.77.10.5634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  9. Shih M. C., Gussin G. N. Mutations affecting two different steps in transcription initiation at the phage lambda PRM promoter. Proc Natl Acad Sci U S A. 1983 Jan;80(2):496–500. doi: 10.1073/pnas.80.2.496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Siebenlist U., Simpson R. B., Gilbert W. E. coli RNA polymerase interacts homologously with two different promoters. Cell. 1980 Jun;20(2):269–281. doi: 10.1016/0092-8674(80)90613-3. [DOI] [PubMed] [Google Scholar]
  11. Simons R. W., Hoopes B. C., McClure W. R., Kleckner N. Three promoters near the termini of IS10: pIN, pOUT, and pIII. Cell. 1983 Sep;34(2):673–682. doi: 10.1016/0092-8674(83)90400-2. [DOI] [PubMed] [Google Scholar]
  12. Stefano J. E., Gralla J. D. Mutation-induced changes in RNA polymerase-lac ps promoter interactions. J Biol Chem. 1982 Dec 10;257(23):13924–13929. [PubMed] [Google Scholar]

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