Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1981 May 25;9(10):2397–2410. doi: 10.1093/nar/9.10.2397

The properties of ATP-analogs in initiation of RNA synthesis catalyzed by RNA polymerase from E coli.

W J Smagowicz, K H Scheit
PMCID: PMC326853  PMID: 7019855

Abstract

Various base and sugar modified derivatives of ATP and UTP were used as substrate analogs for the steady state initiation reaction ATP+UTP=pppApU and the single step addition reaction ApC+ATP=ApCpA. These reactions were carried out by E. coli RNA polymerase on T7 DNA in the presence of rifampicin. The steady state kinetic parameters of the analogs, either as substrates or inhibitors, were determined. On the basis of the obtained results it is concluded that purine NTP s in initiation require anti-conformation about the glycosidic bonds as well as gauche-gauche conformation of the C(4')-C(5') bonds. The latter conformation is also a prerequisite for substrates in elongation, whereas strict anti-conformation of glycosidic bonds is not.

Full text

PDF
2397

Selected References

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

  1. Darlix J. L., Fromageot P., Reich E. Analysis of transcription in vitro using purine nucleotide analogs. Biochemistry. 1971 Apr 27;10(9):1525–1531. doi: 10.1021/bi00785a003. [DOI] [PubMed] [Google Scholar]
  2. Evans F. E., Kaplan N. O. 8-Alkylaminoadenyl nucleotides as probes of dehydrogenase interactions with nucleotide analogs of different glycosyl conformation. J Biol Chem. 1976 Nov 10;251(21):6791–6797. [PubMed] [Google Scholar]
  3. Freist W., von der Haar F., Sprinzl M., Cramer F. Phenylalanyl-tRNA and seryl-tRNA synthetases from baker's yeast. Substrate specificity with regard to ATP analogs and mechanism of the aminoacylation reaction. Eur J Biochem. 1976 May 1;64(2):389–393. doi: 10.1111/j.1432-1033.1976.tb10313.x. [DOI] [PubMed] [Google Scholar]
  4. Hattori M., Frazier J., Miles H. T. Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid). Biochemistry. 1975 Nov 18;14(23):5033–5045. doi: 10.2196/50814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hattori M., Ikehara M., Miles H. T. Poly(2-methyl-N6-methyladenylic acid): synthesis, properties, and interaction with poly(uridylic acid). Biochemistry. 1974 Jun 18;13(13):2754–2761. doi: 10.1021/bi00710a015. [DOI] [PubMed] [Google Scholar]
  6. Kapuler A. M., Monny C., Michelson A. M. The relationship of mono- and polynucleotide conformation to catalysis by polynucleotide phosphorylase. Biochim Biophys Acta. 1970 Sep 17;217(1):18–29. doi: 10.1016/0005-2787(70)90118-8. [DOI] [PubMed] [Google Scholar]
  7. Kapuler A. M., Reich E. Some stereochemical requirements of Escherichia coli ribonucleic acid polymerase. Interaction with conformationally restricted ribonucleoside 5'-triphosphates: 8-bromoguanosine, 8-ketoguanosine, and 6-methylcytidine triphosphates. Biochemistry. 1971 Oct 26;10(22):4050–4061. doi: 10.1021/bi00798a007. [DOI] [PubMed] [Google Scholar]
  8. McClure W. R., Cech C. L., Johnston D. E. A steady state assay for the RNA polymerase initiation reaction. J Biol Chem. 1978 Dec 25;253(24):8941–8948. [PubMed] [Google Scholar]
  9. McClure W. R., Cech C. L. On the mechanism of rifampicin inhibition of RNA synthesis. J Biol Chem. 1978 Dec 25;253(24):8949–8956. [PubMed] [Google Scholar]
  10. Rackwitz H. R., Scheit K. H. The stereochemical basis of template function. Eur J Biochem. 1977 Jan 3;72(1):191–200. doi: 10.1111/j.1432-1033.1977.tb11239.x. [DOI] [PubMed] [Google Scholar]
  11. Saenger W., Suck D. 6-Azauridine-5'-phosphoric acid: unusual molecular structure and functional mechanism. Nature. 1973 Apr 27;242(5400):610–612. doi: 10.1038/242610a0. [DOI] [PubMed] [Google Scholar]
  12. Smagowicz J. W., Scheit K. H. Steady state kinetic studies of initiation of RNA synthesis on T7 DNA in the presence of rifampicin. Nucleic Acids Res. 1977 Nov;4(11):3863–3876. doi: 10.1093/nar/4.11.3863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Smagowicz W. J., Scheit K. H. Primed abortive initiation of RNA synthesis by E. coli RNA polymerase on T7 DNA. Steady state kinetic studies. Nucleic Acids Res. 1978 Jun;5(6):1919–1932. doi: 10.1093/nar/5.6.1919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Stütz A., Scheit K. H. Properties of ATP and UTP analogues with P-S-C-5' bonds. Eur J Biochem. 1975 Jan 2;50(2):343–349. doi: 10.1111/j.1432-1033.1975.tb09809.x. [DOI] [PubMed] [Google Scholar]
  15. Tavale S. S., Sobell H. M. Crystal and molecular structure of 8-bromoguanosine and 8-bromoadenosine, two purine nucleosides in the syn conformation. J Mol Biol. 1970 Feb 28;48(1):109–123. doi: 10.1016/0022-2836(70)90222-6. [DOI] [PubMed] [Google Scholar]
  16. Zillig W., Zechel K., Halbwachs H. J. A new method of large scale preparation of highly purified DNA-dependent RNA-polymerase from E. coli. Hoppe Seylers Z Physiol Chem. 1970 Feb;351(2):221–224. doi: 10.1515/bchm2.1970.351.1.221. [DOI] [PubMed] [Google Scholar]

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

RESOURCES