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For: Oivanen M, Kuusela S, Lönnberg H. Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases. Chem Rev 1998;98:961-990. [PMID: 11848921 DOI: 10.1021/cr960425x] [Citation(s) in RCA: 358] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
301
Lermer L, Hobbs J, Perrin DM. Incorporation of 8-histaminyl-deoxyadenosine [8-(2-(4-imidazolyl)ethylamino)-2'-deoxyriboadenosine] into oligodeoxyribonucleotides by solid phase phosphoramidite coupling. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002;21:651-64. [PMID: 12502281 DOI: 10.1081/ncn-120015723] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
302
Ichikawa K, Tarnai M, Uddin MK, Nakata K, Sato S. Hydrolysis of natural and artificial phosphoesters using zinc model compound with a histidine-containing pseudopeptide. J Inorg Biochem 2002;91:437-50. [PMID: 12175936 DOI: 10.1016/s0162-0134(02)00452-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
303
Mikkola S, Mikhailov SN, Efimtseva E, Neuvonen K, Oivanen M, Beigelman L, Lönnberg H. A comparative study on the cleavage of stereoisomeric uridylyl(3',5')uridines [D,D-, D,L- and L,D-UpU] by acid, base and metal ion catalysts. ORIGINS LIFE EVOL B 2002;32:303-10. [PMID: 12458735 DOI: 10.1023/a:1020515212130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
304
Boero M, Terakura K, Tateno M. Catalytic role of metal ion in the selection of competing reaction paths: a first principles molecular dynamics study of the enzymatic reaction in ribozyme. J Am Chem Soc 2002;124:8949-57. [PMID: 12137550 DOI: 10.1021/ja017843q] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
305
Lopez X, Schaefer M, Dejaegere A, Karplus M. Theoretical evaluation of pK(a) in phosphoranes: implications for phosphate ester hydrolysis. J Am Chem Soc 2002;124:5010-8. [PMID: 11982365 DOI: 10.1021/ja011373i] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
306
Tozawa T, Tokita S, Kubo Y. An allosteric crown ether-induced activity control for the cleavage of a phosphodiester bond. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00601-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
307
Lebruska LL, Kuzmine II, Fedor MJ. Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis. CHEMISTRY & BIOLOGY 2002;9:465-73. [PMID: 11983335 DOI: 10.1016/s1074-5521(02)00130-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
308
Komiyama M, Sumaoka J, Kuzuya A, Yamamoto Y. Sequence-selective artificial ribonucleases. Methods Enzymol 2002;341:455-68. [PMID: 11582798 DOI: 10.1016/s0076-6879(01)41170-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
309
David L, Lambert D, Gendron P, Major F. Leadzyme. Methods Enzymol 2002;341:518-40. [PMID: 11582802 DOI: 10.1016/s0076-6879(01)41174-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
310
Keizer TS, De Pue LJ, Parkin S, Atwood DA. Catalytic dealkylation of phosphates with binuclear boron compounds. J Am Chem Soc 2002;124:1864-5. [PMID: 11866594 DOI: 10.1021/ja017360m] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
311
Liu C, Yu S, Li D, Liao Z, Sun X, Xu H. DNA hydrolytic cleavage by the diiron(III) complex Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2): comparison with other binuclear transition metal complexes. Inorg Chem 2002;41:913-22. [PMID: 11849094 DOI: 10.1021/ic010302h] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
312
Chambert S, Décout JL. RECENT DEVELOPMENTS IN THE SYNTHESIS, CHEMICAL MODIFICATIONS AND BIOLOGICAL APPLICATIONS OF SULFUR MODIFIED NUCLEOSIDES, NUCLEOTIDES AND OLIGONUCLEOTIDES. ORG PREP PROCED INT 2002. [DOI: 10.1080/00304940209355745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
313
Baumeister B, Matile S. Toward p-Octiphenyl β-Barrel RNases. Macromolecules 2002. [DOI: 10.1021/ma011612m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
314
Kaukinen U, Lyytikäinen S, Mikkola S, Lönnberg H. The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence. Nucleic Acids Res 2002;30:468-74. [PMID: 11788709 PMCID: PMC99829 DOI: 10.1093/nar/30.2.468] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
315
Kawahara SI, Uchimaru T. Dinucleotide Hydrolysis Promoted by Dinuclear Zn Complexes − The Effect of the Distance between Zn Ions in the Complexes on the Hydrolysis Rate. Eur J Inorg Chem 2001. [DOI: 10.1002/1099-0682(200109)2001:9<2437::aid-ejic2437>3.0.co;2-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
316
Jardine AM, Leonidas DD, Jenkins JL, Park C, Raines RT, Acharya KR, Shapiro R. Cleavage of 3',5'-pyrophosphate-linked dinucleotides by ribonuclease A and angiogenin. Biochemistry 2001;40:10262-72. [PMID: 11513604 DOI: 10.1021/bi010888j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
317
Kuzuya A, Mizoguchi R, Komiyama M. New Ribozyme-Mimics Employing Mg(II) Ion As Catalytic Center. CHEM LETT 2001. [DOI: 10.1246/cl.2001.584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
318
Putnam WC, Daniher AT, Trawick BN, Bashkin JK. Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts. Nucleic Acids Res 2001;29:2199-204. [PMID: 11353090 PMCID: PMC55460 DOI: 10.1093/nar/29.10.2199] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Revised: 01/29/2001] [Accepted: 03/10/2001] [Indexed: 11/13/2022]  Open
319
Takagi Y, Warashina M, Stec WJ, Yoshinari K, Taira K. Recent advances in the elucidation of the mechanisms of action of ribozymes. Nucleic Acids Res 2001;29:1815-34. [PMID: 11328865 PMCID: PMC37246 DOI: 10.1093/nar/29.9.1815] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
320
Kubiak RJ, Bruzik KS. Reactivities of inositol and ribonucleoside phosphodiesters toward P--O bond cleavage. J Am Chem Soc 2001;123:1760-1. [PMID: 11456778 DOI: 10.1021/ja003675a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
321
Li Y, Breaker RR. In vitro selection of kinase and ligase deoxyribozymes. Methods 2001;23:179-90. [PMID: 11181037 DOI: 10.1006/meth.2000.1119] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
322
Michaelis K, Kalesse M. Selective cleavage of unpaired uridines with a tyrosine-cyclen conjugate. Chembiochem 2001;2:79-83. [PMID: 11828431 DOI: 10.1002/1439-7633(20010105)2:1<79::aid-cbic79>3.0.co;2-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
323
Belen’kii L, Kruchkovskaya N, Gramenitskaya V. The Literature of Heterocyclic Chemistry, Part VII: 1997–1999. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)79024-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
324
Kuzuya A, Komiyama M. Sequence-Selective RNA Scission by Non-Covalent Combination of Acridine-Tethered DNA and Lanthanide(III) Ion. CHEM LETT 2000. [DOI: 10.1246/cl.2000.1378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
325
Ren R, Yang P, Zheng W, Hua Z. A simple copper(II)-L-histidine system for efficient hydrolytic cleavage of DNA. Inorg Chem 2000;39:5454-63. [PMID: 11154560 DOI: 10.1021/ic0000146] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
326
Wan R, Zhao G, Chen J, Zhao Y. Research progresses of artificial nucleic acid cleavage agents. ACTA ACUST UNITED AC 2000. [DOI: 10.1007/bf03183520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
327
Takeda N, Shibata M, Tajima N, Hirao K, Komiyama M. Kinetic and theoretical studies on the mechanism of alkaline hydrolysis of DNA. J Org Chem 2000;65:4391-6. [PMID: 10891143 DOI: 10.1021/jo000323d] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
328
Hydrolytic reactions of the phosphorodithioate analogue of uridylyl(3',5')uridine: kinetics and mechanisms for the cleavage, desulfurization, and isomerization of the internucleosidic linkage. J Org Chem 2000;65:2651-7. [PMID: 10808437 DOI: 10.1021/jo991632a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
329
Yoshinari K, Taira K. A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme. Nucleic Acids Res 2000;28:1730-42. [PMID: 10734192 PMCID: PMC102831 DOI: 10.1093/nar/28.8.1730] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
330
Elzagheid MI, Mäki E, Kaukinen U, Oivanen M, Lönnberg H. Preparation, hydrolysis and intramolecular transesterification of 3'-deoxy-3'-thioinosine 3'-S-dimethylphosphorothiolate. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000;19:827-38. [PMID: 10960039 DOI: 10.1080/15257770008035028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
331
Pogocki D, Schöneich C. Chemical stability of nucleic acid-derived drugs. J Pharm Sci 2000;89:443-56. [PMID: 10737906 DOI: 10.1002/(sici)1520-6017(200004)89:4<443::aid-jps2>3.0.co;2-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
332
Nakano S, Chadalavada DM, Bevilacqua PC. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 2000;287:1493-7. [PMID: 10688799 DOI: 10.1126/science.287.5457.1493] [Citation(s) in RCA: 299] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
333
Roussev CD, Ivanova GD, Bratovanova EK, Vassilev NG, Petkov DD. External Transesterification of Ribonucleotide Esters Naturally Catalyzed by Large Ribozymes. J Am Chem Soc 1999. [DOI: 10.1021/ja990491r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
334
Kuzuya A, Akai M, Komiyama M. Non-Covalent Combinations of Lanthanide(III) Ion and Two DNA Oligomers for Sequence-Selective RNA Scission. CHEM LETT 1999. [DOI: 10.1246/cl.1999.1035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
335
Elzagheid MI, Oivanen M, Klika KD, Jones BCNM, Cosstick R, Lönnberg H. Hydrolytic Reactions of 3′-Deoxy-3′-thioinosylyl-(3′→ >5′)-uridine; An RNA Dinucleotide Containing a 3′-S-Phosphorothiolate Linkage. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/07328319908044866] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
336
Michaelis K, Kalesse M. Selektive Spaltung der HIV-1-TAR-RNA durch ein Peptid-Cyclen-Konjugat. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990802)111:15<2382::aid-ange2382>3.0.co;2-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
337
Li Y, Breaker RR. Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group. J Am Chem Soc 1999. [DOI: 10.1021/ja990592p] [Citation(s) in RCA: 389] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
338
Sumaoka J, Kawata K, Komiyama M. Photo-Regulation of RNA Hydrolysis by the Zinc(II) Complex Carrying Azobenzene. CHEM LETT 1999. [DOI: 10.1246/cl.1999.439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
339
Li Y, Breaker RR. Phosphorylating DNA with DNA. Proc Natl Acad Sci U S A 1999;96:2746-51. [PMID: 10077582 PMCID: PMC15840 DOI: 10.1073/pnas.96.6.2746] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
340
Komiyama M, Sumaoka J. Progress towards synthetic enzymes for phosphoester hydrolysis. Curr Opin Chem Biol 1998;2:751-7. [PMID: 9914189 DOI: 10.1016/s1367-5931(98)80113-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
341
Zhou DM, Taira K. The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA. Chem Rev 1998;98:991-1026. [PMID: 11848922 DOI: 10.1021/cr9604292] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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