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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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2
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Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
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Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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3
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Abstract
Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. This makes them completely different from cellular RNAs transcribed from the genome that usually consist of unmodified ribonucleotides or just contain a few posttranscriptional modifications. The use of synthetic RNA mimics for RNA research and drug development is also in contrast with the ultimate success of protein research and therapy utilizing biologic or recombinant proteins produced and folded in living cells instead of polypeptides or proteins synthesized in vitro. Indeed, efforts have been made recently to develop RNA bioengineering technologies for cost-effective and large-scale production of biologic RNA molecules that may better capture the structures, functions, and safety profiles of natural RNAs. In this article, we provide an overview on RNA therapeutics for the treatment of human diseases via RNA interference mechanisms. By illustrating the structural differences between natural RNAs and chemo-engineered RNA mimics, we focus on discussion of a novel class of bioengineered/biologic RNA agents produced through fermentation and their potential applications to RNA research and drug development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Chao Jian
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Allan H Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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4
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DFT investigations of phosphotriesters hydrolysis in aqueous solution: a model for DNA single strand scission induced by N-nitrosoureas. J Mol Model 2012; 19:647-59. [DOI: 10.1007/s00894-012-1592-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 08/23/2012] [Indexed: 01/21/2023]
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5
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Li NS, Frederiksen JK, Piccirilli JA. Synthesis, properties, and applications of oligonucleotides containing an RNA dinucleotide phosphorothiolate linkage. Acc Chem Res 2011; 44:1257-69. [PMID: 21882874 DOI: 10.1021/ar200131t] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA represents a prominent class of biomolecules. Present in all living systems, RNA plays many essential roles in gene expression, regulation, and development. Accordingly, many biological processes depend on the accurate enzymatic processing, modification, and cleavage of RNA. Understanding the catalytic mechanisms of these enzymes therefore represents an important goal in defining living systems at the molecular level. In this context, RNA molecules bearing 3'- or 5'-S-phosphorothiolate linkages comprise what are arguably among the most incisive mechanistic probes available. They have been instrumental in showing that RNA splicing systems are metalloenzymes and in mapping the ligands that reside within RNA active sites. The resulting models have in turn verified the functional relevance of crystal structures. In other cases, phosphorothiolates have offered an experimental strategy to circumvent the classic problem of kinetic ambiguity; mechanistic enzymologists have used this tool to assign precise roles to catalytic groups as general acids or bases. These insights into macromolecular function are enabled by the synthesis of nucleic acids bearing phosphorothiolate linkages and the unique chemical properties they impart. In this Account, we review the synthesis, properties, and applications of oligonucleotides and oligodeoxynucleotides containing an RNA dinucleotide phosphorothiolate linkage. Phosphorothioate linkages are structurally very similar to phosphorothiolate linkages, as reflected in the single letter of difference in nomenclature. Phosphorothioate substitutions, in which sulfur replaces one or both nonbridging oxygens within a phosphodiester linkage, are now widely available and are used routinely in numerous biochemical and medicinal applications. Indeed, synthetic phosphorothioate linkages can be introduced readily via a sulfurization step programmed into automated solid-phase oligonucleotide synthesizers. In contrast, phosphorothiolate oligonucleotides, in which sulfur replaces a specific 3'- or 5'-bridging oxygen, have presented a more difficult synthetic challenge, requiring chemical alterations to the attached sugar moiety. Here we begin by outlining the synthetic strategies used to access these phosphorothiolate RNA analogues. The Arbuzov reaction and phosphoramidite chemistry are often brought to bear in creating either 3'- or 5'-S-phosphorothiolate dinucleotides. We then summarize the responses of the phosphorothiolate derivatives to chemical and enzymatic cleavage agents, as well as mechanistic insights their use has engendered. They demonstrate particular utility as probes of metal-ion-dependent phosphotransesterification, general acid-base-catalyzed phosphotransesterification, and rate-limiting chemistry. The 3'- and 5'-S-phosphorothiolates have proven invaluable in elucidating the mechanisms of enzymatic and nonenzymatic phosphoryl transfer reactions. Considering that RNA cleavage represents a fundamental step in the maturation, degradation, and regulation of this important macromolecule, the significant synthetic challenges that remain offer rich research opportunities.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - John K. Frederiksen
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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6
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Wang J, Zhou J, Donaldson GP, Nakayama S, Yan L, Lam YF, Lee VT, Sintim HO. Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins. J Am Chem Soc 2011; 133:9320-30. [PMID: 21612220 DOI: 10.1021/ja1112029] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The cyclic dinucleotide c-di-GMP is a master regulator of bacterial virulence and biofilm formation. The activations of c-di-GMP metabolism proteins, diguanylate cyclases (DGCs) and phosophodiesterases (PDEs), usually lead to diametrically opposite phenotypes in bacteria. Analogues of c-di-GMP, which can selectively modulate the activities of c-di-GMP processing proteins, will be useful chemical tools for studying and altering bacterial behavior. Herein we report that a conservative modification of one of the phosphate groups in c-di-GMP with a bridging sulfur in the phosphodiester linkage affords an analogue called endo-S-c-di-GMP. Computational, NMR (including DOSY), and CD experiments all reveal that, unlike c-di-GMP, endo-S-c-di-GMP does not readily form higher aggregates. The lower propensity of endo-S-c-di-GMP to form aggregates (as compared to that of c-di-GMP) is probably due to a higher activation barrier to convert from the "open" conformer (where the two guanines are on opposite faces) to the "closed" conformer (where the two guanines are on the same face). Consequently, endo-S-c-di-GMP has selectivity for proteins that bind monomeric but not dimeric c-di-GMP, which form from the "closed" conformer. For example, endo-S-c-di-GMP can inhibit the hydrolysis of c-di-GMP by RocR (a PDE enzyme that binds monomeric c-di-GMP) but did not bind to Alg44 (a PilZ protein) or regulate WspR (a DGC enzyme that has been shown to bind to dimeric c-di-GMP). This work demonstrates that selective binding to different classes of c-di-GMP binding proteins could be achieved by altering analogue conformer populations (conformational steering). We provide important design principles for the preparation of selective PDE inhibitors and reveal the role played by the c-di-GMP backbone in c-di-GMP polymorphism and binding to processing proteins.
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Affiliation(s)
- Jingxin Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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7
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Li NS, Frederiksen JK, Koo SC, Lu J, Wilson TJ, Lilley DMJ, Piccirilli JA. A general and efficient approach for the construction of RNA oligonucleotides containing a 5'-phosphorothiolate linkage. Nucleic Acids Res 2010; 39:e31. [PMID: 21148150 PMCID: PMC3061073 DOI: 10.1093/nar/gkq1265] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Oligoribonucleotides containing a 5′-phosphorothiolate linkage have provided effective tools to study the mechanisms of RNA catalysis, allowing resolution of kinetic ambiguity associated with mechanistic dissection and providing a strategy to establish linkage between catalysis and specific functional groups. However, challenges associated with their synthesis have limited wider application of these modified nucleic acids. Here, we describe a general semisynthetic strategy to obtain these oligoribonucleotides reliably and relatively efficiently. The approach begins with the chemical synthesis of an RNA dinucleotide containing the 5′-phosphorothiolate linkage, with the adjacent 2′-hydroxyl group protected as the photolabile 2′-O-o-nitrobenzyl or 2′-O-α-methyl-o-nitrobenzyl derivative. Enzymatic ligation of the 2′-protected dinucleotide to transcribed or chemically synthesized 5′ and 3′ flanking RNAs yields the full-length oligoribonucleotide. The photolabile protecting group increases the chemical stability of these highly activated oligoribonucleotides during synthesis and long-term storage but is easily removed with UV irradiation under neutral conditions, allowing immediate use of the modified RNA in biochemical experiments.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street, Room W406, Chicago, IL 60637, USA.
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8
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Watts JK, Katolik A, Viladoms J, Damha MJ. Studies on the hydrolytic stability of 2'-fluoroarabinonucleic acid (2'F-ANA). Org Biomol Chem 2009; 7:1904-10. [PMID: 19590787 DOI: 10.1039/b900443b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of 2'-deoxy-2'-fluoroarabinonucleic acid (2'F-ANA) to hydrolysis under acidic and basic conditions was compared to that of DNA, RNA and 2'F-RNA. In enzyme-free simulated gastric fluid (pH approximately 1.2), 2'F-ANA was found to have dramatically increased stability (virtually no cleavage observed after 2 days) with respect to both DNA (t(1/2) approximately 2 min) and RNA (t(1/2) approximately 3 h (PO) or 3 days (PS)). These results were observed for both phosphodiester and phosphorothioate backbones and with multiple mixed-base sequences. Under basic conditions, 2'F-ANA also showed good stability. In 1 M NaOH at 65 degrees C, 2'F-ANA had a t(1/2) of approximately 20 h, while RNA was entirely degraded in a few minutes. Furthermore, the nuclease cleavage of phosphorothioate 2'F-ANA and DNA by snake venom phosphodiesterase was studied in detail. One diastereomer of the PS-2'F-ANA linkage was found to be much more vulnerable to enzymatic cleavage than the other, which is parallel to the properties observed for PS-DNA. Additional studies of 2'F-ANA-containing oligonucleotides are warranted based on the excellent stability properties described here.
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Affiliation(s)
- Jonathan K Watts
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 2K6
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9
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Bruice TC. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 2007; 106:3119-39. [PMID: 16895321 DOI: 10.1021/cr050283j] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas C Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA.
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10
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Jahn-Hofmann K, Engels J. Efficient Solid Phase Synthesis of Cleavable Oligodeoxynucleotides Based on a Novel Strategy for the Synthesis of 5?-S-(4,4?-Dimethoxytrityl)-2?-deoxy-5?-thionucleoside Phosphoramidites. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490252] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Noodleman L, Lovell T, Han WG, Li J, Himo F. Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 2004; 104:459-508. [PMID: 14871132 DOI: 10.1021/cr020625a] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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12
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Torres RA, Himo F, Bruice TC, Noodleman L, Lovell T. Theoretical examination of Mg(2+)-mediated hydrolysis of a phosphodiester linkage as proposed for the hammerhead ribozyme. J Am Chem Soc 2003; 125:9861-7. [PMID: 12904054 DOI: 10.1021/ja021451h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hammerhead ribozyme is an RNA molecule capable of self-cleavage at a unique site within its sequence. Hydrolysis of this phosphodiester linkage has been proposed to occur via an in-line attack geometry for nucleophilic displacement by the 2'-hydroxyl on the adjoining phosphorus to generate a 2',3'-cyclic phosphate ester with elimination of the 5'-hydroxyl group, requiring a divalent metal ion under physiological conditions. The proposed S(N)2(P) reaction mechanism was investigated using density functional theory calculations incorporating the hybrid functional B3LYP to study this metal ion-dependent reaction with a tetraaquo magnesium (II)-bound hydroxide ion. For the Mg(2+)-catalyzed reaction, the gas-phase geometry optimized calculations predict two transition states with a kinetically insignificant, yet clearly defined, pentacoordinate intermediate. The first transition state located for the reaction is characterized by internal nucleophilic attack coupled to proton transfer. The second transition state, the rate-determining step, involves breaking of the exocyclic P-O bond where a metal-ligated water molecule assists in the departure of the leaving group. These calculations demonstrate that the reaction mechanism incorporating a single metal ion, serving as a Lewis acid, functions as a general base and can afford the necessary stabilization to the leaving group by orienting a water molecule for catalysis.
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Affiliation(s)
- Rhonda A Torres
- Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, California 92037, USA
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13
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Abstract
The speed at which RNA molecules decompose is a critical determinant of many biological processes, including those directly involved in the storage and expression of genetic information. One mechanism for RNA cleavage involves internal phosphoester transfer, wherein the 2'-oxygen atom carries out an SN2-like nucleophilic attack on the adjacent phosphorus center (transesterification). In this article, we discuss fundamental principles of RNA transesterification and define a conceptual framework that can be used to assess the catalytic power of enzymes that cleave RNA. We deduce that certain ribozymes and deoxyribozymes, like their protein enzyme counterparts, can bring about enormous rate enhancements.
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Affiliation(s)
- Gail Mitchell Emilsson
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
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14
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Abstract
Nucleic acid microarrays are a growing technology in which high densities of known sequences are attached to a substrate in known locations (addressed). Hybridization of complementary sequences leads to a detectable signal such as an electrical impulse or fluorescence. This combination of sequence addressing, hybridization, and detection increases the efficiency of a variety of genomic disciplines including those that profile genetic expression, search for single nucleotide polymorphisms (SNPs), or diagnose infectious diseases by sequencing portions of microbial or viral genomes. Incorporation of reporter molecules into nucleic acids is essential for the sensitive detection of minute amounts of nucleic acids on most types of microarrays. Furthermore, polynucleic acid size reduction increases hybridization because of increased diffusion rates and decreased competing secondary structure of the target nucleic acids. Typically, these reactions would be performed as two separate processes. An improvement to past techniques, termed labeling-during-cleavage (LDC), is presented in which DNA or RNA is alkylated with fluorescent tags and fragmented in the same reaction mixture. In model studies with 26 nucleotide-long RNA and DNA oligomers using ultraviolet/visible and fluorescence spectroscopies as well as high-pressure liquid chromatography and mass spectrometry, addition of both alkylating agents (5-(bromomethyl)fluorescein, 5- or 6-iodoacetamidofluorescein) and select metal ions (of 21 tested) to nucleic acids in aqueous solutions was critical for significant increases in both labeling and fragmentation, with >or=100-fold increases in alkylation possible relative to metal ion-free reactions. Lanthanide series metal ions, Pb(2+), and Zn(2+) were the most reactive ions in terms of catalyzing alkylation and fragmentation. While oligonucleotides were particularly susceptible to fragmentation at sites containing phosphorothioate moieties, labeling and cleavage reactions occurred even without incorporation of phosphorothioate moieties into the RNA and DNA target molecules. In fact, LDC conditions were found in which RNA could be fragmented into its component monomers, allowing simultaneous sequencing from both the 5'- and the 3'-termini by mass spectrometry. The results can be explained by alkylation of the (thio)phosphodiester linkages to form less hydrolytically stable (thio)phosphotriesters, which then decompose into 2',3'-cyclic phosphate (or 2'-phosphate) and 5'-hydroxyl terminal products. Analysis of fragmentation and alkylation products of Mycobacterium tuberculosis (Mtb) ribosomal RNA (rRNA) transcripts by polyacrylamide gel electrophoresis was consistent with the model studies. Building upon these results, I found that products from Mtb rRNA amplification products were processed with fluorescent reporters and metal ions in a single reaction milieu for analysis on an Affymetrix GeneChip. Mild conditions were discovered which balanced the need for aggressive alkylation and the need for controlled fragmentation, advantageously yielding GeneChip results with greater than 98% of the nucleotides reported correctly relative to reference sequences, results sufficient for accurately identifying Mtb from other Mycobacterium species. Thus, LDC is a new, straightforward, and rapid aqueous chemistry that is based on metal ion-catalyzed alkylation and alkylation-catalyzed fragmentation of nucleic acids for analysis on microarrays or other hybridization assays and that, possibly, has utility in similar processing of other appropriately functionalized biomolecules.
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Affiliation(s)
- Kenneth A Browne
- Gen-Probe Incorporated, 10210 Genetic Center Drive, San Diego, California 92121, USA.
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15
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Nunes-Düby SE, Radman-Livaja M, Kuimelis RG, Pearline RV, McLaughlin LW, Landy A. Gamma integrase complementation at the level of DNA binding and complex formation. J Bacteriol 2002; 184:1385-94. [PMID: 11844768 PMCID: PMC134844 DOI: 10.1128/jb.184.5.1385-1394.2002] [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] [Received: 08/20/2001] [Accepted: 11/02/2001] [Indexed: 11/20/2022] Open
Abstract
Site-specific recombinases of the gamma Int family carry out two single-strand exchanges by binding as head-to-head dimers on inverted core-type DNA sites. Each protomer may cleave its own site as a monomer in cis (as for Cre recombinase), or it may recruit the tyrosine from its partner in trans to form a composite active site (as for Flp recombinase). The crystal structure of the gamma Int catalytic domain is compatible with both cleavage mechanisms, but two previous biochemical studies on gamma integrase (Int) generated data that were not in agreement. Support for cis and trans cleavage came from assays with bispecific DNA substrates for gamma and HK022 Ints and from functional complementation between recombination-deficient mutants, respectively. The data presented here do not provide new evidence for cis cleavage, but they strongly suggest that the previously described complementation results cannot be used in support of a trans-cleavage mechanism. We show here that IntR212Q retains some residual catalytic function but is impaired in binding to core-type DNA on linear substrates and in forming higher-order attL intasome structures. The binding-proficient mutant IntY342F can stabilize IntR212Q binding to core-type DNA through protein-protein interactions. Similarly, the formation of higher-order Int complexes with arm- and core-type DNA is boosted with both mutants present. This complementation precedes cleavage and thus precludes any conclusions about the mechanism of catalysis. Cross-core stimulation of wild-type HK022-Int cleavage on its cognate site (in cis) by mutant gamma Ints on bispecific core DNA suicide substrates is shown to be independent of the catalytic tyrosine but appears to be proportional to the respective core-binding affinities of the gamma Int mutants.
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Affiliation(s)
- Simone E Nunes-Düby
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
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16
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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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17
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Metelev VG, Borisova OA, Volkov EM, Oretskaya TS, Dolinnaya NG. New chemically reactive dsDNAs containing single internucleotide monophosphoryldithio links: reactivity of 5'-mercapto-oligodeoxyribonucleotides. Nucleic Acids Res 2001; 29:4062-9. [PMID: 11574689 PMCID: PMC60246 DOI: 10.1093/nar/29.19.4062] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel modified DNA duplexes with single bridging 5'-SS-monophosphoryldithio links [-OP(=O)-O(-)-SS-CH(2)-] were synthesized by autoligation of an oligonucleotide 3'-phosphorothioate and a 5'-mercapto-oligonucleotide previously converted to a 2-pyridyldisulfide adduct. Monophosphoryldisulfide link formation is not a stringent template-dependent process under the conditions used and does not require strong binding of the reactive oligomers to the complementary strand. The modified internucleotide linkage, resembling the natural phosphodiester bond in size and charge density, is stable in water, easily undergoes thiol-disulfide exchange and can be specifically cleaved by the action of reducing reagents. DNA molecules containing an internal -OP(=O)-O(-)-SS-CH(2)- bridge are stable to spontaneous exchange of disulfide-linked fragments (recombination) even in the single-stranded state and are promising reagents for autocrosslinking with cysteine-containing proteins. The chemical and supramolecular properties of oligonucleotides with 5'-sulfhydryl groups were further characterized. We have shown that under the conditions of chemical ligation the 5'-SH group of the oligonucleotide has a higher reactivity towards N-hydroxybenzotriazole-activated phosphate in an adjacent oligonucleotide than does the OH group. This autoligation, unlike disulfide bond formation, proceeds only in the presence of template oligonucleotide, necessary to provide the activated phosphate in close proximity to the SH-, OH- or phosphate function.
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Affiliation(s)
- V G Metelev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia
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18
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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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Bashkin JK. Hydrolysis of phosphates, esters and related substrates by models of biological catalysts. Curr Opin Chem Biol 1999; 3:752-8. [PMID: 10600728 DOI: 10.1016/s1367-5931(99)00036-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Why study hydrolases, and why model them? First, hydrolases themselves are of fundamental importance and utility. Examples of their utility in organic synthesis include kinetic resolutions of optical isomers. Restriction endonucleases (DNA hydrolases) are key tools for biotechnology and are vital biological catalysts. Peptidases are necessary for protein digestion and can be harnessed to perform the reverse reaction (peptide synthesis). Thus, for these and many other reasons, hydrolases receive the attention of fundamental and applied research. Models of hydrolases can contribute to our understanding of reaction mechanisms and may also supplant the enzymes as useful catalysts under some conditions. Altering or even increasing the specificity of natural catalysts are also goals of these model studies.
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Affiliation(s)
- J K Bashkin
- Monsanto Company R3A, St Louis, MO 63167, USA. james.k.
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21
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Xu Y, Kool ET. Chemical and enzymatic properties of bridging 5'-S-phosphorothioester linkages in DNA. Nucleic Acids Res 1998; 26:3159-64. [PMID: 9628913 PMCID: PMC147688 DOI: 10.1093/nar/26.13.3159] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe physicochemical and enzymatic properties of 5' bridging phosphorothioester linkages at specific sites in DNA oligonucleotides. The susceptibility to hydrolysis at various pH values is examined and no measurable hydrolysis is observed at pH 5-9 after 4 days at 25 degrees C. The abilities of three 3'- and 5'-exonuclease enzymes to hydrolyze the DNA past this linkage are examined and it is found that the linkage causes significant pauses at the sulfur linkage for T4 DNA polymerase and calf spleen phosphodiesterase, but not for snake venom phosphodiesterase. Restriction endonuclease (Nsi I) cleavage is also attempted at a 5'-thioester junction and strong resistance to cleavage is observed. Also tested is the ability of polymerase enzymes to utilize templates containing single 5'-S-thioester linkages; both Klenow DNA polymerase and T7 RNA polymerase are found to synthesize complementary strands successfully without any apparent pause at the sulfur linkage. Finally, the thermal stabilities of duplexes containing such linkages are measured; results show that T m values are lowered by a small amount (2 degrees C) when one or two thioester linkages are present in an otherwise unmodified duplex. The chemical stability and surprisingly small perturbation by the 5' bridging sulfur make it a good candidate as a physical and mechanistic probe for specific protein or metal interactions involving this position in DNA.
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Affiliation(s)
- Y Xu
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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22
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Trawick BN, Daniher AT, Bashkin JK. Inorganic Mimics of Ribonucleases and Ribozymes: From Random Cleavage to Sequence-Specific Chemistry to Catalytic Antisense Drugs. Chem Rev 1998; 98:939-960. [PMID: 11848920 DOI: 10.1021/cr960422k] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bobby N. Trawick
- Department of Chemistry, Washington University, St. Louis, Missouri 63130
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Affiliation(s)
- Robert G. Kuimelis
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
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24
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikko Oivanen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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25
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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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26
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Ora M, Peltomäki M, Oivanen M, Lönnberg H. Metal-Ion-Promoted Cleavage, Isomerization, and Desulfurization of the Diastereomeric Phosphoromonothioate Analogues of Uridylyl(3‘,5‘)uridine. J Org Chem 1998. [DOI: 10.1021/jo972112n] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mikko Ora
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Markku Peltomäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Oivanen
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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Curley JF, Joyce CM, Piccirilli JA. Functional Evidence That the 3‘-5‘ Exonuclease Domain ofEscherichia coliDNA Polymerase I Employs a Divalent Metal Ion in Leaving Group Stabilization. J Am Chem Soc 1997. [DOI: 10.1021/ja972014j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Burlina F, Favre A, Fourrey JL. Chemical engineering of RNase resistant and catalytically active hammerhead ribozymes. Bioorg Med Chem 1997; 5:1999-2010. [PMID: 9416417 DOI: 10.1016/s0968-0896(97)00144-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- F Burlina
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
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29
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Matulic-Adamic J, Haeberli P, DiRenzo AB, Mokler VR, Maloney L, Beigelman L, Usman N, Wincott FE. Synthesis and Incorporation of 5″-Amino- and 5′-Mercapto-5′-Deoxy-2′-O-Methyl Nucleosides Into Hammerhead Ribozymes. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Weinstein LB, Jones BC, Cosstick R, Cech TR. A second catalytic metal ion in group I ribozyme. Nature 1997; 388:805-8. [PMID: 9285596 DOI: 10.1038/42076] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although only a subset of protein enzymes depend on the presence of a metal ion for their catalytic function, all naturally occurring RNA enzymes require metal ions to stabilize their structure and for catalytic competence. In the self-splicing group I intron from Tetrahymena thermophila, several divalent metals can serve structural roles, but only Mg2+ and Mn2+ promote splice-site cleavage and exon ligation. A study of a ribozyme reaction analogous to 5'-splice-site cleavage by guanosine uncovered the first metal ion with a definitive role in catalysis. Substitution of the 3'-oxygen of the leaving group with sulphur resulted in a metal-specificity switch, indicating an interaction between the leaving group and the metal ion. Here we use 3'-(thioinosylyl)-(3'-->5')-uridine, IspU, as a substrate in a reaction that emulates exon ligation. Activity requires the addition of a thiophilic metal ion (Cd2+ or Mn2+), providing evidence for stabilization of the leaving group by a metal ion in that step of splicing. Based on the principle of microscopic reversibility, this metal ion activates the nucleophilic 3'-hydroxyl of guanosine in the first step of splicing, supporting the model of a two-metal-ion active site.
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Affiliation(s)
- L B Weinstein
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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31
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Kuimelis RG, McLaughlin LW. Application of a 5'-bridging phosphorothioate to probe divalent metal and hammerhead ribozyme mediated RNA cleavage. Bioorg Med Chem 1997; 5:1051-61. [PMID: 9222498 DOI: 10.1016/s0968-0896(97)00041-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This paper describes the preparation and application of a chimeric DNA/RNA oligonucleotide that contains a single 5'-bridging phosphorothioate linkage adjacent to a ribonucleotide and embedded in an otherwise all-DNA sequence. The influence of pH, divalent metal cation, hybridization, and secondary structure on the susceptibility of the thio linkage towards transesterification is investigated in an effort to better understand the metal-phosphorothioate interactions and the basis for catalysis. In addition to the chemical cleavage, we have examined the hammerhead ribozyme mediated cleavage of the 5'-bridging phosphorothioate linkage specifically to test the hypothesis that the ribozyme employs a second metal cofactor, which functions as a Lewis acid, to catalyze transesterification. The results of our kinetics experiments do not support this double-metal model.
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Affiliation(s)
- R G Kuimelis
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02167, USA
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Sigel RKO, Song B, Sigel H. Stabilities and Structures of Metal Ion Complexes of Adenosine 5‘-O-Thiomonophosphate (AMPS2-) in Comparison with Those of Its Parent Nucleotide (AMP2-) in Aqueous Solution. J Am Chem Soc 1997. [DOI: 10.1021/ja962970l] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roland K. O. Sigel
- Contribution from the Institute of Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Bin Song
- Contribution from the Institute of Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
| | - Helmut Sigel
- Contribution from the Institute of Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
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Weinstein LB, Earnshaw DJ, Cosstick R, Cech TR. Synthesis and Characterization of an RNA Dinucleotide Containing a 3‘-S-Phosphorothiolate Linkage. J Am Chem Soc 1996. [DOI: 10.1021/ja9616903] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lara B. Weinstein
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - David J. Earnshaw
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Richard Cosstick
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Thomas R. Cech
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
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