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.

[1]  H. Heus,et al.  Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. , 1991, Science.

[2]  J. Morrow,et al.  Catalytic transesterification and hydrolysis of RNA by zinc(II) complexes , 1991 .

[3]  O. Uhlenbeck,et al.  Properties of an in vitro selected Pb2+ cleavage motif. , 1994, Biochemistry.

[4]  L. Kiessling,et al.  Hydrolysis of Double-Stranded and Single-Stranded RNA in Hairpin Structures by the Copper(II) Macrocycle Cu([9]aneN(3))Cl(2). , 1997, Inorganic chemistry.

[5]  J R Morrow.  Hydrolytic cleavage of RNA catalyzed by metal ion complexes. , 1996, Metal ions in biological systems.

[6]  J. Bashkin,et al.  Sequence-Specific Cleavage of HIV mRNA by a Ribozyme Mimic , 1994 .

[7]  W. Jahnke,et al.  Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis. , 1996, Biochemistry.

[8]  W. Krzyzosiak,et al.  Identification of the magnesium, europium and lead binding sites in E. coli and lupine tRNAPhe by specific metal ion‐induced cleavages , 1989, FEBS letters.

[9]  C R Woese,et al.  Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[10]  C. Sich,et al.  Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry. , 1997, Biochemistry.

[11]  J. Wilkie,et al.  Metal ions in the mechanism of enzyme-catalysed phosphate monoester hydrolyses , 1997 .

[12]  J. Hall,et al.  Efficient sequence-specific cleavage of RNA using novel europium complexes conjugated to oligonucleotides. , 1994, Chemistry & biology.

[13]  W. Krzyzosiak,et al.  Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages. , 1989, European journal of biochemistry.

[14]  G. Stormo,et al.  CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[15]  T. Cech,et al.  Biological catalysis by RNA. , 1986, Annual review of biochemistry.

[16]  J. Ebel,et al.  Characterization of the lead(II)-induced cleavages in tRNAs in solution and effect of the Y-base removal in yeast tRNAPhe. , 1988, Biochemistry.

[17]  P. D. Cook,et al.  Characterization of fully 2'-modified oligoribonucleotide hetero- and homoduplex hybridization and nuclease sensitivity. , 1995, Nucleic acids research.

[18]  W. Krzyzosiak,et al.  Cleavages induced by different metal ions in yeast tRNA(Phe) U59C60 mutants. , 1996, Biochemistry.

[19]  H. Lönnberg,et al.  Metal ions that promote the hydrolysis of nucleoside phosphoesters do not enhance intramolecular phosphate migration , 1993 .

[20]  R. Adamiak,et al.  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. , 1997, Nucleic acids research.

[21]  G. Keith,et al.  Specific cleavages of pure tRNAs by plumbous ions. , 1976, Biochimica et biophysica acta.

[22]  K. Burger.  Biocoordination chemistry : coordination equilibria in biologically active systems , 1990 .

[23]  William N. Lipscomb,et al.  Recent Advances in Zinc Enzymology. , 1996, Chemical reviews.

[24]  V. Erdmann,et al.  Lead-ion-induced cleavage of RNase P RNA. , 1994, European journal of biochemistry.

[25]  G. Charles Dismukes,et al.  Manganese Enzymes with Binuclear Active Sites. , 1996, Chemical reviews.

[26]  F. Westheimer.  Pseudo-rotation in the hydrolysis of phosphate esters , 1968 .

[27]  J. Bashkin,et al.  The Role of Metals in the Hydrolytic Cleavage of DNA and RNA , 1994 .

[28]  W. Krzyzosiak,et al.  Specific RNA cleavages induced by manganese ions , 1995, FEBS letters.

[29]  D. A. Usher,et al.  Hydrolytic stability of helical RNA: a selective advantage for the natural 3',5'-bond. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[30]  N. Usman,et al.  Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. , 1996, Chemistry & biology.

[31]  H. Lönnberg,et al.  Zn2+ -Promoted Hydrolysis of 3′,5′-Dinucleoside Monophosphates and Polyribonucleotides. The Effect of Nearest Neighbours on the Cleavage of Phosphodiester Bonds , 1996 .

[32]  J. Hall,et al.  Towards artificial ribonucleases: the sequence-specific cleavage of RNA in a duplex. , 1996, Nucleic acids research.

[33]  Aaron Klug,et al.  Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA. , 1985 .

[34]  W. Krzyzosiak,et al.  Patterns of cleavages induced by lead ions in defined RNA secondary structure motifs. , 1998, Journal of molecular biology.

[35]  D. Turner,et al.  Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. , 1992, Science.

[36]  J. Sessler,et al.  SITE-SPECIFIC HYDROLYSIS OF RNA BY EUROPIUM(III) TEXAPHYRIN CONJUGATED TO A SYNTHETIC OLIGODEOXYRIBONUCLEOTIDE , 1994 .

[37]  Tao Pan,et al.  A small metalloribozyme with a two-step mechanism , 1992, Nature.

[38]  A. Pyle,et al.  Ribozymes: a distinct class of metalloenzymes. , 1993, Science.

[39]  T. Cech,et al.  The intervening sequence RNA of Tetrahymena is an enzyme. , 1986, Science.

[40]  W. Lipscomb,et al.  Two‐Metal Ion Catalysis in Enzymatic Acyl‐ and Phosphoryl‐Transfer Reactions , 1996 .

[41]  O. Uhlenbeck,et al.  Lead-catalyzed cleavage of yeast tRNAPhe mutants. , 1990, Biochemistry.

[42]  V. Erdmann,et al.  Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis. , 1992, European journal of biochemistry.

[43]  A. Azhayev,et al.  Imidazole Tethered Oligodeoxyribonucleotides: Synthesis and RNA Cleaving Activity , 1995 .

[44]  V. Erdmann,et al.  Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA--ribosomal-protein complexes by means of Pb(II)-induced hydrolysis. , 1992, European journal of biochemistry.

[45]  E. Hegg,et al.  COPPER(II) MACROCYCLES CLEAVE SINGLE-STRANDED AND DOUBLE-STRANDED DNA UNDER BOTH AEROBIC AND ANAEROBIC CONDITIONS , 1996 .

[46]  H. Lönnberg,et al.  Effect of metal ions on the hydrolytic reactions of nucleosides and their phosphoesters. , 1996, Metal ions in biological systems.

[47]  J. Morrow,et al.  Trivalent lanthanide ions do not cleave RNA in DNA-RNA hybrids , 1993 .

[48]  A. Klug,et al.  Pb(II)-catalysed cleavage of the sugar–phosphate backbone of yeast tRNAPhe—implications for lead toxicity and self-splicing RNA , 1983, Nature.

[49]  T. Klabunde,et al.  The Dimetal Center in purple acid phosphatases , 1997 .