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Nucleic Acids Res. 1979 August 10; 6(11): 3481–3490.
PMCID: PMC327950

Rapid RNA sequencing: nucleases from Staphylococcus aureus and Neurospora crassa discriminate between uridine and cytidine.


Using end-labelled RNA, significant changes in base specificity of three nucleases have been detected under defined conditions. Staphylococcus aureus nuclease at pH 3.5 without Ca++ cleaves all Pyr-N bonds more uniformly and efficiently than RNase A, without any preference for Pyr-A bonds. At pH 7.5 in 10 mM Ca++ this enzyme cleaves all N-C and N-G bonds slowly, whereas N-U and N-A bonds are hydrolyzed rapidly. Hence, the base at the 3'- or at the 5'-side of a phosphodiester bond can determine the base specificity of S. aureus nuclease. - In absence of urea, Neurospora crassa endonuclease cleaves all phosphodiester bonds, but leaves all C-N bonds intact in 7 M urea. - RNase U2 at pH 3.5 cleaves A-N bonds more efficiently than at pH 5.0.

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Selected References

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  • Donis-Keller H, Maxam AM, Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. [PMC free article] [PubMed]
  • Simoncsits A, Brownlee GG, Brown RS, Rubin JR, Guilley H. New rapid gel sequencing method for RNA. Nature. 1977 Oct 27;269(5631):833–836. [PubMed]
  • Ross A, Brimacombe R. Application of a rapid gel method to the sequencing of fragments of 16S ribosomal RNA from Escherichia coli. Nucleic Acids Res. 1978 Jan;5(1):241–256. [PMC free article] [PubMed]
  • Domdey H, Jank P, Sänger L, Gross HJ. Studies on the primary and secondary structure of potato spindle tuber viroid: products of digestion with ribonuclease A and ribonuclease T1, and modification with bisulfite. Nucleic Acids Res. 1978 Apr;5(4):1221–1236. [PMC free article] [PubMed]
  • Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sänger HL. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature. 1978 May 18;273(5659):203–208. [PubMed]
  • Pilly D, Niemeyer A, Schmidt M, Bargetzi JP. Enzymes for RNA sequence analysis. Preparation and specificity of exoplasmodial ribonucleases I and II from Physarum polycephalum. J Biol Chem. 1978 Jan 25;253(2):437–445. [PubMed]
  • Gupta RC, Randerath K. Use of specific endonuclease cleavage in RNA sequencing-an enzymic method for distinguishing between cytidine and uridine residues. Nucleic Acids Res. 1977 Oct;4(10):3441–3454. [PMC free article] [PubMed]
  • Stanley J, Vassilenko S. A different approach to RNA sequencing. Nature. 1978 Jul 6;274(5666):87–89. [PubMed]
  • Koper-Zwarthoff EC, Lockard RE, Alzner-deWeerd B, RajBhandary UL, Bol JF. Nucleotide sequence of 5' terminus of alfalfa mosaic virus RNA 4 leading into coat protein cistron. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5504–5508. [PubMed]
  • Domdey H, Gross HJ. RNA sequence determination in the nanogram range by a combination of in vitro labeling procedures. Anal Biochem. 1979 Mar;93(2):321–328. [PubMed]
  • Berridge MV, Loewensteiner DD, Aronson AI. Characterization of an endoribonuclease from Xenopus oocytes. Possible role in ribonucleic acid turnover. Biochemistry. 1974 Jun 4;13(12):2520–2527. [PubMed]
  • Silberklang M, Prochiantz A, Haenni AL, Rajbhandary UL. Studies on the sequence of the 3'-terminal region of turnip-yellow-mosaic-virus RNA. Eur J Biochem. 1977 Feb;72(3):465–478. [PubMed]
  • Lockard RE, Alzner-Deweerd B, Heckman JE, MacGee J, Tabor MW, RajBhandary UL. Sequence analysis of 5'[32P] labeled mRNA and tRNA using polyacrylamide gel electrophoresis. Nucleic Acids Res. 1978 Jan;5(1):37–56. [PMC free article] [PubMed]
  • Walker RT, RajBhandary UL. The nucleotide sequence of formylmethionine tRNA from Mycoplasma mycoides sp. capri. Nucleic Acids Res. 1978 Jan;5(1):57–70. [PMC free article] [PubMed]
  • Knecht ME, Busch H. Isolation of an electrophoretically homogeneous nonhistone nucleolar protein. Life Sci II. 1971 Nov 22;10(22):1297–1309. [PubMed]
  • Sanger F, Coulson AR. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. [PubMed]
  • Schmukler M, Jewett PB, Levy CC. The effects of polyamines on a residue-specific human plasma ribonuclease. J Biol Chem. 1975 Mar 25;250(6):2206–2212. [PubMed]
  • Mukai JI. An endonuclease from silkworm---purification and mode of action. Biochem Biophys Res Commun. 1965 Dec 21;21(6):562–567. [PubMed]
  • Mikulski AJ, Laskowski M., Sr Mung bean nuclease I. 3. Purification procedure and (3') omega monophosphatase activity. J Biol Chem. 1970 Oct 10;245(19):5026–5031. [PubMed]
  • Verdlov ED, Monastyrskaya GS, Guskova LI, Levitan TL, Sheichenko VI, Budowsky EI. Modification of cytidine residues with a bisulfite-O-methylhydroxylamine mixture. Biochim Biophys Acta. 1974 Mar 8;340(2):153–165. [PubMed]
  • Carbon P, Ehresmann C, Ehresmann B, Ebel JP. The sequence of Escherichia coli ribosomal 16 S RNA determined by new rapid gel methods. FEBS Lett. 1978 Oct 1;94(1):152–156. [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Gupta RC, Randerath K. Use of specific endonuclease cleavage in RNA sequencing. Nucleic Acids Res. 1977 Jun;4(6):1957–1978. [PMC free article] [PubMed]
  • Martin RP, Sibler AP, Schneller JM, Keith G, Stahl AJ, Dirheimer G. Primary structure of yeast mitochondrial DNA-coded phenylalanine-tRNA. Nucleic Acids Res. 1978 Dec;5(12):4579–4592. [PMC free article] [PubMed]
  • Winter G, Brownlee GG. 3'End labelling of RNA with 32P suitable for rapid gel sequencing. Nucleic Acids Res. 1978 Sep;5(9):3129–3139. [PMC free article] [PubMed]
  • Guilley H, Jonard G, Kukla B, Richards KE. Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA. Nucleic Acids Res. 1979 Apr;6(4):1287–1308. [PMC free article] [PubMed]
  • Tenenhouse H, Fraser MJ. The ribonuclease activities of the single-strand-specific nucleases of Neurospora crassa. Can J Biochem. 1973 May;51(5):569–580. [PubMed]
  • Forget BG, Weissman SM. The nucleotide sequence of ribosomal 5 S ribonucleic acid from KB cells. J Biol Chem. 1969 Jun 25;244(12):3148–3165. [PubMed]
  • Labrie F, Sanger F. 32P-labellingof haemoglobin messenger and other reticulocyte ribonucleic acids with polynucleotide phosphokinase in iro. Biochem J. 1969 Sep;114(2):29P–29P. [PubMed]
  • Peattie DA. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760–1764. [PubMed]

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