Logo of narLink to Publisher's site
Nucleic Acids Res. 1998 Jul 15; 26(14): 3392–3396.
PMCID: PMC147710

Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides.


Several chimeric ribo/2'- O -methylribo oligonucleotides were synthesized and their hydrolytic cleavage studied in the presence of Mg2+, Zn2+, Pb2+and the 1,4,9-triaza-cyclododecane chelate of Zn2+(Zn2+[12]aneN3) to evaluate the importance of RNA secondary structure as a factor determining the reactivity of phosphodiester bonds. In all the cases studied, a phosphodiester bond within a 4-7 nt loop was hydrolytically more stable than a similar bond within a linear single strand, but markedly less stable than that in a double helix. With Zn2+and Zn2+[12]aneN3, the hydrolytic stability of a phosphodiester bond within a hairpin loop gradually decreased on increasing the distance from the stem. A similar but less systematic trend was observed with Pb2+. Zn2+- and Pb2+-promoted cleavage was observed to be considerably more sensitive to the secondary structure of the chain than that induced by Zn2+[12]aneN3. This difference in behaviour may be attributed to bidentate binding of uncomplexed aquo ions to two different phosphodiester bonds. Mg2+was observed to be catalytically virtually inactive compared with the other cleaving agents studied.

Full Text

The Full Text of this article is available as a PDF (78K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Wilcox Dean E. Binuclear Metallohydrolases. Chem Rev. 1996 Nov 7;96(7):2435–2458. [PubMed]
  • Dismukes G Charles. Manganese Enzymes with Binuclear Active Sites. Chem Rev. 1996 Nov 7;96(7):2909–2926. [PubMed]
  • Lipscomb William N, Sträter Norbert. Recent Advances in Zinc Enzymology. Chem Rev. 1996 Nov 7;96(7):2375–2434. [PubMed]
  • Cech TR, Bass BL. Biological catalysis by RNA. Annu Rev Biochem. 1986;55:599–629. [PubMed]
  • Pan T, Dichtl B, Uhlenbeck OC. Properties of an in vitro selected Pb2+ cleavage motif. Biochemistry. 1994 Aug 16;33(32):9561–9565. [PubMed]
  • Pyle AM. Ribozymes: a distinct class of metalloenzymes. Science. 1993 Aug 6;261(5122):709–714. [PubMed]
  • Werner C, Krebs B, Keith G, Dirheimer G. Specific cleavages of pure tRNAs by plumbous ions. Biochim Biophys Acta. 1976 May 3;432(2):161–175. [PubMed]
  • Brown RS, Hingerty BE, Dewan JC, Klug A. Pb(II)-catalysed cleavage of the sugar-phosphate backbone of yeast tRNAPhe--implications for lead toxicity and self-splicing RNA. Nature. 1983 Jun 9;303(5917):543–546. [PubMed]
  • Brown RS, Dewan JC, Klug A. Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. Biochemistry. 1985 Aug 27;24(18):4785–4801. [PubMed]
  • Krzyzosiak WJ, Marciniec T, Wiewiorowski M, Romby P, Ebel JP, Giegé R. Characterization of the lead(II)-induced cleavages in tRNAs in solution and effect of the Y-base removal in yeast tRNAPhe. Biochemistry. 1988 Jul 26;27(15):5771–5777. [PubMed]
  • Behlen LS, Sampson JR, DiRenzo AB, Uhlenbeck OC. Lead-catalyzed cleavage of yeast tRNAPhe mutants. Biochemistry. 1990 Mar 13;29(10):2515–2523. [PubMed]
  • Michałowski D, Wrzesinski J, Krzyzosiak W. Cleavages induced by different metal ions in yeast tRNA(Phe) U59C60 mutants. Biochemistry. 1996 Aug 20;35(33):10727–10734. [PubMed]
  • Morrow JR. Hydrolytic cleavage of RNA catalyzed by metal ion complexes. Met Ions Biol Syst. 1996;33:561–592. [PubMed]
  • Hall J, Hüsken D, Häner R. Towards artificial ribonucleases: the sequence-specific cleavage of RNA in a duplex. Nucleic Acids Res. 1996 Sep 15;24(18):3522–3526. [PMC free article] [PubMed]
  • Kuusela S, Lönnberg H. Effect of metal ions on the hydrolytic reactions of nucleosides and their phosphoesters. Met Ions Biol Syst. 1996;32:271–300. [PubMed]
  • Wrzesinski J, Michałowski D, Ciesiołka J, Krzyzosiak WJ. Specific RNA cleavages induced by manganese ions. FEBS Lett. 1995 Oct 23;374(1):62–68. [PubMed]
  • Michałowski D, Wrzesinski J, Ciesiołka J, Krzyzosiak WJ. Effect of modified nucleotides on structure of yeast tRNA(Phe). Comparative studies by metal ion-induced hydrolysis and nuclease mapping. Biochimie. 1996;78(2):131–138. [PubMed]
  • Ciesiołka J, Lorenz S, Erdmann VA. Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA--ribosomal-protein complexes by means of Pb(II)-induced hydrolysis. Eur J Biochem. 1992 Mar 1;204(2):575–581. [PubMed]
  • Ciesiołlka J, Lorenz S, Erdmann VA. Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis. Eur J Biochem. 1992 Mar 1;204(2):583–589. [PubMed]
  • Ciesiolka J, Hardt WD, Schlegl J, Erdmann VA, Hartmann RK. Lead-ion-induced cleavage of RNase P RNA. Eur J Biochem. 1994 Jan 15;219(1-2):49–56. [PubMed]
  • Ciesiolka J, Krzyzosiak WJ. Structural analysis of two plant 5S rRNA species and fragments thereof by lead-induced hydrolysis. Biochem Mol Biol Int. 1996 May;39(2):319–328. [PubMed]
  • Ciesiołka J, Wrzesinski J, Górnicki P, Podkowiński J, Krzyzosiak WJ. Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages. Eur J Biochem. 1989 Dec 8;186(1-2):71–77. [PubMed]
  • Marciniec T, Ciesiołka J, Wrzesinski J, Krzyzosiak WJ. Identification of the magnesium, europium and lead binding sites in E. coli and lupine tRNAPhe by specific metal ion-induced cleavages. FEBS Lett. 1989 Jan 30;243(2):293–298. [PubMed]
  • Hall J, Hüsken D, Pieles U, Moser HE, Häner R. Efficient sequence-specific cleavage of RNA using novel europium complexes conjugated to oligonucleotides. Chem Biol. 1994 Nov;1(3):185–190. [PubMed]
  • Butzow JJ, Eichhorn GL. Interaction of metal ions with nucleic acids and related compounds. XVII. On the mechanism of degradation of polyribonucleotides and oligoribonucleotides by zinc(II) ions. Biochemistry. 1971 May 25;10(11):2019–2027. [PubMed]
  • Hüsken D, Goodall G, Blommers MJ, Jahnke W, Hall J, Häner R, Moser HE. Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis. Biochemistry. 1996 Dec 24;35(51):16591–16600. [PubMed]
  • Hegg Eric L, Deal Kim A, Kiessling Laura L, Burstyn Judith N. Hydrolysis of Double-Stranded and Single-Stranded RNA in Hairpin Structures by the Copper(II) Macrocycle Cu([9]aneN(3))Cl(2). Inorg Chem. 1997 Apr 9;36(8):1715–1718. [PubMed]
  • Pan T, Uhlenbeck OC. A small metalloribozyme with a two-step mechanism. Nature. 1992 Aug 13;358(6387):560–563. [PubMed]
  • Usher DA, McHale AH. Hydrolytic stability of helical RNA: a selective advantage for the natural 3',5'-bond. Proc Natl Acad Sci U S A. 1976 Apr;73(4):1149–1153. [PMC free article] [PubMed]
  • Portmann S, Grimm S, Workman C, Usman N, Egli M. Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem Biol. 1996 Mar;3(3):173–184. [PubMed]
  • Zaug AJ, Cech TR. The intervening sequence RNA of Tetrahymena is an enzyme. Science. 1986 Jan 31;231(4737):470–475. [PubMed]
  • Popenda M, Biala E, Milecki J, Adamiak RW. Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions. Nucleic Acids Res. 1997 Nov 15;25(22):4589–4598. [PMC free article] [PubMed]
  • Tuerk C, Gauss P, Thermes C, Groebe DR, Gayle M, Guild N, Stormo G, d'Aubenton-Carafa Y, Uhlenbeck OC, Tinoco I, Jr, et al. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1364–1368. [PMC free article] [PubMed]
  • Woese CR, Winker S, Gutell RR. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". Proc Natl Acad Sci U S A. 1990 Nov;87(21):8467–8471. [PMC free article] [PubMed]
  • Heus HA, Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 1991 Jul 12;253(5016):191–194. [PubMed]
  • SantaLucia J, Jr, Kierzek R, Turner DH. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science. 1992 Apr 10;256(5054):217–219. [PubMed]
  • Sich C, Ohlenschläger O, Ramachandran R, Görlach M, Brown LR. Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry. Biochemistry. 1997 Nov 18;36(46):13989–14002. [PubMed]
  • Cummins LL, Owens SR, Risen LM, Lesnik EA, Freier SM, McGee D, Guinosso CJ, Cook PD. Characterization of fully 2'-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res. 1995 Jun 11;23(11):2019–2024. [PMC free article] [PubMed]
  • Ciesiołka J, Michałowski D, Wrzesinski J, Krajewski J, Krzyzosiak WJ. Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs. J Mol Biol. 1998 Jan 16;275(2):211–220. [PubMed]

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


Save items

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...