301
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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]
Abstract
The 3'phosphoramidite of 8-histaminyl deoxyadenosine has been prepared and successfully incorporated into a short oligodeoxyribonucleotide. The synthetic methodology leading to this preparation is given and the implications for developing new DNAzymes as well as probing unusual nucleic acid structures are discussed.
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Affiliation(s)
- Leonard Lermer
- Department of Chemistry, 2036 Main Mall, 6174 University Blvd, University of British Columbia, Vancouver, B. C., V6T-1Z1 Canada
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302
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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]
Abstract
Zinc(II) complex with histidine-containing pseudopeptide derived from N,N'-bis(benzylhistidyl) diethylenetriamine L was examined as catalyst for the hydrolysis of bis(p-nitrophenyl) phosphate (BNPP), p-nitrophenyl phosphate (NPP), adenylyl-(3'-5')adenosine (ApA), thymidylyl-(3'-5') thymidine (TpT) and PBR 322 supercoiled DNA. The stepwise protonation constants of the ligand, stability constants for its zinc(II) complex LZn have been determined potentiometrically in aqueous solution. LZn efficiently hydrolyzed BNPP and NPP and their pseudo-first-order rate constants k(obs) are 1.1 x 10(-5) s(-1) and 2.1 x 10(-5) s(-1), respectively. Bell-shaped pH-k(obs) profile was seen in BNPP hydrolysis around pH 7. Kinetic parameters were obtained from temperature dependence of hydrolysis rate constants where entropy of activation showed considerably high negative value. ApA and TpT as RNA-type and DNA-type dinucleotides were slowly hydrolyzed by LZn. On the basis of the kinetic evidence of bell-shaped pH-k(obs) profile and species distribution curve, we propose a mechanism for LZn-promoted hydrolysis of BNPP as well as ApA where cooperative achieve of zinc-hydroxo and zinc-aqua complex species may be responsible for enzymatic activity. The agarose gel electrophoresis and AFM demonstrated that LZn performed good activity on the selective cleavage of pBR322 supercoiled DNA at pH 7.0 providing evidence for its probable applicability.
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Affiliation(s)
- Kazuhiko Ichikawa
- Division of Material Science, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan.
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303
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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]
Abstract
Stereoisomeric uridylyl(3',5')uridines D,L-UpU and L,D-UpU were synthesised. Their cleavage was followed in the presence of acid, base and metal ion catalysts to study whether the stereochemistry affects the inherent reactivity of the internucleosidic phosphodiester bond, and whether the low molecular weight catalysts can distinguish between the substrates. The rate constants obtained were compared to those of D,D-UpU. The comparison shows that the stability of the phosphodiester bond does not depend on the stereochemistry of the sugar rings. In contrast slight reactivity differences are observed in the presence of metal ion catalysts, which suggests that selective cleavage of stereoisomeric substrates even by small molecular weight chemical catalysts may be possible.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, Finland.
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304
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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]
Abstract
By using finite temperature first principles molecular dynamics, the mechanism of the enzymatic reaction of ribozyme was investigated for both the anionic and the radical charge states of the modeled RNA fragment. In the case of the anionic system, a pseudorotation and the subsequent 3' --> 2' migration occur in a vacuum, rather than the self-cleavage of the phosphodiester. On the other hand, when either a divalent metal ion (Mg(2+)) catalyst or the continuous hydrogen bond network of the solvent is present, the reaction path of the anionic species changes dramatically, going toward the transesterification channel. In a radical system, the transesterification can occur without a metal catalyst, as a consequence of the displacement of a hole (empty electronic state) along the reaction path. Thus, the present analysis suggests that a metal ion might be essential not only in lowering the activation barrier but also in selecting the reaction path among those corresponding to possible different charge states of the intermediate structure in vivo. Furthermore, simulation of the anionic species in solution shows that, in the absence of a metal catalyst, water molecules cooperate with the proton transfer via a proton wire mechanism and the hydrogen bond network plays a crucial role in preventing pseudorotations. On the other hand, when a metal cation is present in the vicinity of the site where the nucleophilic attack occurs, the hydrogen bond network is interrupted and detachment of the proton, enhanced by the catalyst, does not give rise to any proton-transfer process.
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Affiliation(s)
- Mauro Boero
- Angstrom Technology Partnership, Joint Research Center for Atom Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-0046, Japan.
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305
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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]
Abstract
Knowledge of the pK(a) of phosphoranes is important for the interpretation of phosphate ester hydrolysis. Calculated pK(a)'s of the model phosphorane, ethylene phosphorane, are reported. The method of calculation is based on the use of dimethyl phosphate as a reference state for evaluating relative pK(a) values, and on the optimization of the oxygen and acidic hydrogen van der Waals radii to give reasonable pK(1)(a), pK(2)(a), and pK(3)(a) for phosphoric acid in solution. Density functional theory is employed to calculate the gas-phase protonation energies, and continuum dielectric methods are used to determine the solvation corrections. The calculated pK(1)(a) and p(2)(a) for the model phosphorane are 7.9 and 14.3, respectively. These values are within the range of proposed experimental values, 6.5-11.0 for pK(1)(a), and 11.3-15.0 for pK(2)(a). The mechanistic implications of the calculated pK(a)'s are discussed.
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Affiliation(s)
- Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Spain
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306
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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]
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307
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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]
Abstract
The hairpin ribozyme catalyzes a reversible phosphodiester cleavage reaction. We examined the roles of conserved nucleobases in catalysis using an abasic ribozyme rescue strategy. Loss of the active site G8 nucleobase reduced the cleavage rate constant by 350-fold while loss of A9 and A10 nucleobases reduced activity less than 10-fold. Certain heterocyclic amines restored partial activity when provided in solution to the variant lacking G8. Heterocyclic amines that were capable of rescue shared the exocyclic amine and cyclic amide in common with the Watson-Crick hydrogen bonding face of guanine. In contrast to the shallow pH dependence of unmodified ribozyme activity, rescue activity increased sharply with decreasing pH. These results support a novel model for RNA catalysis in which a cationic nucleobase contributes electrostatic stabilization to negative charge developing in the transition state.
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Affiliation(s)
- Lori L Lebruska
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB35, La Jolla, CA 92037, USA
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308
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Affiliation(s)
- M Komiyama
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
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309
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Affiliation(s)
- L David
- Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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310
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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]
Abstract
The Salen(tBu) ligand and its derivatives were used to prepare binuclear boron complexes. These compounds have the formula, L(BBr2)2 (L = Salpen(tBu) and Salben(tBu)). These are formed from the reaction of the corresponding L[B(OMe)2]2 with BBr3. They represent a new type of binuclear boron compound. These compounds are active towards the dealkylation of many phosphates. They are also catalytically active with a stoichiometric amount of BBr3 to trimethylphosphate.
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Affiliation(s)
- Timothy S Keizer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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311
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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]
Abstract
The binuclear structure of Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) (DTPB = 1,1,4,7,7-penta (2'-benzimidazol-2-ylmethyl)-triazaheptane, Ac = acetate) was characterized by UV-visible absorption and infrared spectra and NMR and ESR. The binding interaction of DNA with the diiron complex was examined spectroscopically. Supercoiled and linear DNA hydrolytic cleavage by the diiron complex is supported by the evidence from anaerobic reactions, free radical quenching, high performance liquid chromatography experiments, and enzymatic manipulation such as T4 ligase ligation, 5'-(32)P end-labeling, and footprinting analysis. The estimation of rate for the supercoiled DNA double strand cleavage shows one of the largest known rate enhancement factors, approximately 10(10) against DNA. Moreover, the DNA hydrolysis chemistry needs no coreactant such as hydrogen peroxide. The poor sequence-specific DNA cleavage indicated by the restriction analysis of the pBR322 DNA linearized by the diiron complex might be due to the diiron complex bound to DNA by a coordination of its two ferric ions to the DNA phosphate oxygens, as suggested by spectral characterizations. The hydrolysis chemistry for a variety of binuclear metal complexes including Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) is compared. It is established that the dominant factors for the DNA hydrolysis activities of the binuclear metal complexes are the mu-oxo bridge, labile and anionic ligands, and open coordination site(s). Concerning the hydrolytic mechanisms, the diiron complex Fe(2)(DTPB)(mu-O)(mu-Ac)Cl(BF(4))(2) might share many points in common with the native purple acid phosphatases.
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Affiliation(s)
- Changlin Liu
- Department of Chemistry, Huazhong University of Science and Technology, Wuhan 430074, China.
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312
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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]
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313
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Affiliation(s)
- Bodo Baumeister
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva 4, Switzerland
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314
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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
Abstract
The cleavage of short chimeric oligonucleotides containing only one reactive ribonucleoside unit, all other nucleosides being 2'-O-methylated, has been studied at pH 8.5 and 35 degrees C. Among the 20 different sequences that did not exhibit any tendency to form a defined secondary structure, the scissile 5'-UpA-3' and 5'-CpA-3' phosphodiester bonds experienced >100- and up to 35-fold reactivity differences, respectively. Compared with dinucleoside monophosphates, both rate accelerations and retardations of more than one order of magnitude were observed. Even a change of a single base several nucleosides away from the scissile bond markedly affected the reaction rate. Duplex formation at the 3'- and/or 5'-side of the scissile bond was also studied and observed to be strongly rate retarding. The origin of the high sensitivity of phosphodiester bonds to the molecular environment is discussed.
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Affiliation(s)
- Ulla Kaukinen
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland
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315
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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]
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316
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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]
Abstract
Recently, 3',5'-pyrophosphate-linked 2'-deoxyribodinucleotides were shown to be >100-fold more effective inhibitors of RNase A superfamily enzymes than were the corresponding monophosphate-linked (i.e., standard) dinucleotides. Here, we have investigated two ribo analogues of these compounds, cytidine 3'-pyrophosphate (P'-->5') adenosine (CppA) and uridine 3'-pyrophosphate (P'-->5') adenosine (UppA), as potential substrates for RNase A and angiogenin. CppA and UppA are cleaved efficiently by RNase A, yielding as products 5'-AMP and cytidine or uridine cyclic 2',3'-phosphate. The k(cat)/K(m) values are only 4-fold smaller than for the standard dinucleotides CpA and UpA, and the K(m) values (10-16 microM) are lower than those reported for any earlier small substrates (e.g., 500-700 microM for CpA and UpA). The k(cat)/K(m) value for CppA with angiogenin is also only severalfold smaller than for CpA, but the effect of lengthening the internucleotide linkage on K(m) is more modest. Ribonucleotide 3',5'-pyrophosphate linkages were proposed previously to exist in nature as chemically labile intermediates in the pathway for the generation of cyclic 2',3'-phosphate termini in various RNAs. We demonstrate that in fact they are relatively stable (t(1/2) > 15 days for uncatalyzed degradation of UppA at pH 6 and 25 degrees C) and that cleavage in vivo is most likely enzymatic. Replacements of the RNase A catalytic residues His12 and His119 by alanine reduce activity toward UppA by approximately 10(5)-and 10(3.3)-fold, respectively. Thus, both residues play important roles. His12 probably acts as a base catalyst in cleavage of UppA (as with RNA). However, the major function of His119 in RNA cleavage, protonation of the 5'-O leaving group, is not required for UppA cleavage because the pK(a) of the leaving group is much lower than that for RNA substrates. A crystal structure of the complex of RNase A with 2'-deoxyuridine 3'-pyrophosphate (P'-->5') adenosine (dUppA), determined at 1.7 A resolution, together with models of the UppA complex based on this structure suggest that His119 contributes to UppA cleavage through a hydrogen bond with a nonbridging oxygen atom in the pyrophosphate and through pi-pi stacking with the six-membered ring of adenine.
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Affiliation(s)
- A M Jardine
- Center for Biochemical and Biophysical Sciences and Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
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317
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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]
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318
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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
Abstract
Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phenanthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents.
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Affiliation(s)
- W C Putnam
- Department of Chemistry, Washington University, St Louis, MO 63130-4899, USA
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319
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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
Abstract
The cleavage of RNA can be accelerated by a number of factors. These factors include an acidic group (Lewis acid) or a basic group that aids in the deprotonation of the attacking nucleophile, in effect enhancing the nucleophilicity of the nucleophile; an acidic group that can neutralize and stabilize the leaving group; and any environment that can stabilize the pentavalent species that is either a transition state or a short-lived intermediate. The catalytic properties of ribozymes are due to factors that are derived from the complicated and specific structure of the ribozyme-substrate complex. It was postulated initially that nature had adopted a rather narrowly defined mechanism for the cleavage of RNA. However, recent findings have clearly demonstrated the diversity of the mechanisms of ribozyme-catalyzed reactions. Such mechanisms include the metal-independent cleavage that occurs in reactions catalyzed by hairpin ribozymes and the general double-metal-ion mechanism of catalysis in reactions catalyzed by the Tetrahymena group I ribozyme. Furthermore, the architecture of the complex between the substrate and the hepatitis delta virus ribozyme allows perturbation of the pK(a) of ring nitrogens of cytosine and adenine. The resultant perturbed ring nitrogens appear to be directly involved in acid/base catalysis. Moreover, while high concentrations of monovalent metal ions or polyamines can facilitate cleavage by hammerhead ribozymes, divalent metal ions are the most effective acid/base catalysts under physiological conditions.
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Affiliation(s)
- Y Takagi
- Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Science City 305-8562, Japan
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320
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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]
Affiliation(s)
- R J Kubiak
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois 60612, USA
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321
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Abstract
Exploration of the limits of biocatalysis has led to the discovery that DNA has significant potential for enzymatic function. This makes possible the construction of DNA enzymes or "deoxyribozymes" for catalyzing various chemical reactions that could be used to address fundamental questions in biocatalysis or that could find unique applications in biotechnology. Of significant interest are self-modification reactions, given the fundamental role that DNA serves in modern living systems. Recently, in vitro selection strategies have been used to isolate prototypical ATP-dependent deoxyribozymes from random-sequence populations of DNA that catalyze DNA phosphorylation and others that catalyze DNA adenylation. In nature, protein enzymes such as T4 DNA kinase and T4 DNA ligase catalyze identical chemical reactions. These findings suggest that DNA constructs could be engineered to efficiently catalyze other self-modifying reactions, including ATP-dependent DNA ligation. This article provides a detailed overview of the methods used to isolate deoxyribozymes that promote ATP-dependent DNA ligation.
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Affiliation(s)
- Y Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520-8103, USA
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322
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Affiliation(s)
- K Michaelis
- Institut für Organische Chemie der Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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323
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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]
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324
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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]
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325
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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]
Abstract
Copper(II)-L-histidine complexes effectively promote the cleavage of plasmid DNA and dideoxynucleotide dApdA at physiological pH and temperature. Studies of the mechanism of plasmid DNA cleavage by added radical scavengers, using rigorously anaerobic experiments, analyses for malondialdehyde-like products, religation assays, and HPLC analyses, indicate that DNA cleavage mediated by Cu(L-His) occurs via a hydrolytic path. The hydrolytic cleavage rate constants at 37 degrees C are estimated to be 0.76 h-1 for the decrease of form I and 0.25 h-1 for the increase of form III. The phosphoimager picture reveals that Cu(L-His) cleaves DNA with a certain sequence specificity (preferentially at 5'-GT-3'). The dinucleotide hydrolysis shows, with [Cu(L-His)] = 0.8 mM, rate enhancement factors of > 10(8). Interestingly, histidine-metal ion interactions (with Cu(II), Ni(II), Zn(II), etc.) have been used for various applications, e.g., protein purification, cross-linking, and targeting proteins to lipid bilayers. Our findings may provide the basis for developing new applications and new ways to design more effective and useful catalysts for DNA cleavage. Cu(L-His) is one of only a few well-defined metal complexes demonstrated to hydrolytically cleave dideoxynucleotides and DNA.
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Affiliation(s)
- R Ren
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, People's Republic of China
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326
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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]
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327
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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]
Abstract
The reaction mechanism of alkaline hydrolysis of DNA has been investigated by kinetic analysis and density-functional-theory calculation. The rates of hydrolysis of thymidine 3'-monophosphate esters (including thymidylyl(3'-5')thymidine (Tp-OT)) monotonically decrease as the leaving groups get poorer. According to the theoretical calculation in which the solvent effects are incorporated, no intermediate is formed in the course of the reaction. In the alkaline hydrolysis of the activated Tp-OT analogues having good leaving groups, the 3',5'-cyclic monophosphate of thymidine is concurrently formed through the intramolecular attack by the 5'-alkoxide ion. In the hydrolysis of the native dinucleotide, however, this side reaction does not occur, since the transition state leading to the departure of its poor leaving group cannot be formed due to conformational restraint. These arguments are supported by the theoretical analysis on the hydrolysis of both dimethyl phosphate and its O(bridging)-->S substituted analogue.
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Affiliation(s)
- N Takeda
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Japan
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328
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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]
Abstract
The hydrolytic reactions of the phosphorodithioate analogue of uridylyl(3',5')uridine [3',5'-Up(s)2U] were followed by HPLC over a wide pH range at 363.2 K. Under acidic and neutral conditions, three reactions compete: (i) desulfurization to a mixture of the (Rp)- and (Sp)-diastereomers of the corresponding 3',5'- and 2',5'-phosphoromonothioates [3',5'- and 2',5'-Up(s)U], which are subsequently desulfurized to a mixture of uridylyl(3',5')- and -(2',5')uridine [3',5'- and 2',5'-UpU], (ii) isomerization to 2',5'-Up(s)2U, and (iii) cleavage to uridine, in all likelihood via a 2',3'-cyclic phosphorodithioate (2',3'-cUMPS2). Under alkaline conditions (pH > 8), only a hydroxide ion catalyzed hydrolysis to uridine via 2',3'-cUMPS2 takes place. At pH 3-7, all three reactions are pH-independent, the desulfurization being approximately 1 order of magnitude faster than the cleavage and isomerization. At pH < 3, all the reactions are hydronium ion catalyzed. On going to very acidic solutions, the cleavage gradually takes over the desulfurization and isomerization. Accordingly, the cleavage overwhelmingly predominates at pH < 0. The overall hydrolytic stability of 3',5'-Up(s)2U is comparable to that of (Sp)- and (Rp)-3',5'-Up(s)U (and to that of 3',5'-UpU, except at pH < 2). The rate of the hydroxide ion catalyzed hydrolysis of 3',5'-Up(s)2U is 37% and 53% of that of (Sp)- and (Rp)-3',5'-Up(s)U, respectively. The reactions, however, differ with the respect of the product accumulation. While the phosphoromonothioates produce a mixture of 2'- and 3'-thiophosphates as stable products, 3',5'-Up(s)2U is hydrolyzed to uridine without accumulation of the corresponding dithiophosphates. At pH < 3, where the hydrolysis is hydronium ion catalyzed, the kinetic thio-effect of the second thio substitution is small: under very acidic conditions (Ho -0.69), (Sp)-3',5'-Up(s)U reacts 1.6 times as fast as 3',5'-Up(s)2U, but the reactivity difference decreases on going to less acidic solutions. In summary, the hydrolytic stability of 3',5'-Up(s)2U closely resembles that of the corresponding phosphoromonothioate. While replacing one of the nonbridging phosphate oxygens of 3',5'-UpU with sulfur stabilizes the phosphodiester bond under acidic conditions by more than 1 order of magnitude, the replacement of the remaining nonbridging oxygen has only a minor influence on the overall hydrolytic stability.
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329
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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
Abstract
We synthesized three types of 11mer substrate, namely the natural substrate S11O and the thio-substituted substrates S11 S pS and S11 R pS, in which the respective pro-S p and pro-R p oxygen atoms were replaced by sulfur, and subjected them to detailed kinetic analysis in the cleavage reaction catalyzed by a hammerhead ribozyme. In agreement with previous findings, in the presence of Mg(2+)or Ca(2+)ions the rate of ribozyme-catalyzed cleavage of S11 S pS was as high as that of S11O, whereas the corresponding rate for S11 R pS was nearly four orders of magnitude lower than that for either S11O or S11 S pS. However, the rate of the ribozyme-catalyzed reaction with each of the three substrates was enhanced by Cd(2+)ions. Such results have generally been taken as evidence that supports the direct interaction of the sulfur atom at the R p position of the cleavage site with the added Cd(2+)ion. However, our present analysis demonstrates that (i) the added Cd(2+)ion binds at the P9 site; (ii) the bound Cd(2+)ion at the P9 site replaces two Mg(2+)or two Ca(2+)ions, an observation that suggests a different mode of interaction with the added Cd(2+)ion; and, most importantly and in contrast to the conclusion reached by other investigators, (iii) the Cd(2+)ion does not interact with the sulfur atom at the R p position of the scissile phosphate either in the ground state or in the transition state.
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Affiliation(s)
- K Yoshinari
- National Institute for Advanced Interdisciplinary Research, Tsukuba Science City 305-8562, Japan
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330
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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]
Abstract
The hydrolytic reactions of the dimethyl ester of 3'-deoxy-3'-thioinosine 3'-S-phosphorothiolate have been followed over a wide aciditiy range by HPLC. At pH > 3, only hydroxide ion catalyzed isomerization to the 2'-dimethylphosphate takes place, whereas under more acidic conditions hydrolysis to the 2'-monomethylphosphate and 3'-S-monomethylphosphorothiolate competes. The latter is the only product accumulating in very acidic solutions (1 M hydrochloric acid). Mechanisms of the reactions are discussed.
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Affiliation(s)
- M I Elzagheid
- Department of Chemistry, University of Turku, Finland
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331
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Abstract
Nucleic acid-derived drugs exhibit both chemical and physical instability. This mini-review focuses on the prevalent hydrolytic and oxidative pathways of chemical degradation as they are affected by various endogenous (primary structure, chemical modifications in bases, sugars and phosphate residues) and exogenous (pH, buffer concentration, metal cation presence, oxygen presence) factors.
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Affiliation(s)
- D Pogocki
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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332
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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]
Abstract
Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.
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Affiliation(s)
- S Nakano
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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333
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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]
Affiliation(s)
- Christo D. Roussev
- Contribution from the Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Gabriela D. Ivanova
- Contribution from the Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Emilia K. Bratovanova
- Contribution from the Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nikolay G. Vassilev
- Contribution from the Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Dimiter D. Petkov
- Contribution from the Laboratory of BioCatalysis, Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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334
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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]
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335
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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]
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336
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337
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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]
Affiliation(s)
- Yingfu Li
- Contribution from the Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520-8103
| | - Ronald R. Breaker
- Contribution from the Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520-8103
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338
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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]
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339
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Abstract
Nearly 50 individual DNAs with polynucleotide kinase-like activity were isolated from a random-sequence pool by using in vitro selection. Each self-phosphorylating deoxyribozyme makes use of one or more of the eight standard NTPs or dNTPs as a source of activated phosphate. Although most prototypic deoxyribozymes poorly differentiate between the ribose and deoxyribose moieties, further optimization by in vitro selection produced variants that display up to 100-fold discrimination between related NTP and dNTP substrates. An optimized ATP-dependent deoxyribozyme uses ATP >40,000-fold more efficiently than CTP, GTP, or UTP. This enzyme operates with a rate enhancement of nearly one billion-fold over the uncatalyzed rate of ATP hydrolysis. A bimolecular version of the ATP-dependent deoxyribozyme was further engineered to phosphorylate specific target DNAs with multiple turnover. The substrate-recognition patterns and rate enhancements intrinsic to these DNAs are characteristic of naturally occurring RNA and protein enzymes, supporting the hypothesis that DNA has sufficient catalytic potential to function as an enzyme in biological systems.
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Affiliation(s)
- Y Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
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340
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Abstract
Synthesis of artificial enzymes for catalyzing phosphoester hydrolysis has been attracting interest for a long time. The remarkable discovery that lanthanide ions catalyze the hydrolysis of DNA and RNA spurred the trend. Currently, progress is being made, mainly in the preparation of homogeneous catalysts, the promotion of catalytic activity by using acid/base cooperation within catalysts, the detailed understanding of the reaction mechanisms involved, and the design of artificial enzymes expressing high specificity and catalytic turn-over.
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Affiliation(s)
- M Komiyama
- Department of Chemistry and Biotechnology Graduate School of Engineering University of Tokyo Hongo Tokyo 113-8656 Japan.
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341
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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]
Affiliation(s)
- De-Min Zhou
- Institute of Applied Biochemistry, University of Tsukuba, Tennoudai 1-1-1, Tsukuba Science City 305-8572, Japan, National Institute for Advanced Interdisciplinary Research, 1-1-4 Higashi, Tsukuba Science City 305-8562, Japan, and National Institute of Bioscience & Human Technology, 1-1 Higashi, Tsukuba Science City 305-8566, Japan
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