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Maruyama H, Oikawa R, Hayakawa M, Takamori S, Kimura Y, Abe N, Tsuji G, Matsuda A, Shuto S, Ito Y, Abe H. Chemical ligation of oligonucleotides using an electrophilic phosphorothioester. Nucleic Acids Res 2017; 45:7042-7048. [PMID: 28520986 PMCID: PMC5499596 DOI: 10.1093/nar/gkx459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 05/11/2017] [Indexed: 11/14/2022] Open
Abstract
We developed a new approach for chemical ligation of oligonucleotides using the electrophilic phosphorothioester (EPT) group. A nucleophilic phosphorothioate group on oligonucleotides was converted into the EPT group by treatment with Sanger's reagent (1-fluoro-2,4-dinitrobenzene). EPT oligonucleotides can be isolated, stored frozen, and used for the ligation reaction. The reaction of the EPT oligonucleotide and an amino-modified oligonucleotide took place without any extra reagents at pH 7.0–8.0 at room temperature, and resulted in a ligation product with a phosphoramidate bond with a 39–85% yield. This method has potential uses in biotechnology and chemical biology.
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Affiliation(s)
- Hideto Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Ryota Oikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Mayu Hayakawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Shono Takamori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Genichiro Tsuji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan.,Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198, Japan
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van Schie SNS, Sengupta RN, Herschlag D. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes. PLoS One 2016; 11:e0160457. [PMID: 27501145 PMCID: PMC4976970 DOI: 10.1371/journal.pone.0160457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 07/19/2016] [Indexed: 11/18/2022] Open
Abstract
Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes.
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Affiliation(s)
- Sabine N. S. van Schie
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
- Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, the Netherlands
| | - Raghuvir N. Sengupta
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, 94305, United States of America
- Departments of Chemical Engineering and Chemistry, Stanford University, Stanford, California, 94305, United States of America
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California, 94305, United States of America
- * E-mail:
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Sengupta RN, Van Schie SNS, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. RNA (NEW YORK, N.Y.) 2016; 22:32-48. [PMID: 26567314 PMCID: PMC4691833 DOI: 10.1261/rna.053710.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function.
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Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Sabine N S Van Schie
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA Leiden Institute of Chemistry, Leiden University, Leiden, 2333 CC, The Netherlands
| | - George Giambaşu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph D Yesselman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Darrin York
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA Department of Chemical Engineering, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA Department of Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, USA
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Rothenstein D, Claasen B, Omiecienski B, Lammel P, Bill J. Isolation of ZnO-Binding 12-mer Peptides and Determination of Their Binding Epitopes by NMR Spectroscopy. J Am Chem Soc 2012; 134:12547-56. [DOI: 10.1021/ja302211w] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dirk Rothenstein
- Institute
for Materials Science and §Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute
for Materials Science and §Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Beatrice Omiecienski
- Institute
for Materials Science and §Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Patricia Lammel
- Institute
for Materials Science and §Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Joachim Bill
- Institute
for Materials Science and §Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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Dai Q, Sengupta R, Deb SK, Piccirilli JA. Synthesis of 2′- N-Methylamino-2′-deoxyguanosine and 2′- N, N-Dimethylamino-2′-deoxyguanosine and Their Incorporation into RNA by Phosphoramidite Chemistry. J Org Chem 2011; 76:8718-25. [DOI: 10.1021/jo201364x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qing Dai
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Raghuvir Sengupta
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Shirshendu K. Deb
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department of Biochemistry & Molecular Biology and ‡Department of Chemistry, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, United States
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Bookser BC, Raffaele NB, Reddy KR, Fan K, Huang W, Erion MD. Synthesis of 3'-amino-3'-deoxyguanosine and 3'-amino-3'-deoxyxyloguanosine monophosphate HepDirect prodrugs from guanosine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:969-86. [PMID: 20183565 DOI: 10.1080/15257770903307151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The synthesis of 3'-amino-3'-deoxyguanosine and 3'-amino-3'-deoxyxyloguanosine monophosphate HepDirect prodrugs from guanosine is reported. Initial incorporation of N,N-dibenzylformamidino protection of the C2-amino of guanosine masked the reactivity of that group and simplified purification of subsequent analogues. The first key intermediate, 9-(2,5-bis-O-tert-butyldimethylsilyl-beta-D-ribofuranosyl)-2-N-(N,N-dibenzylformamidino)guanine (3a), was prepared in 60% yield after recycling of the undesired 3',5'-bis-O-protected byproduct (4a) by simple equilibration in methanol to a mixture of the two bis-O-protected compounds. Thus, protected, the 3'-position was manipulated to form the 3'-deoxyribo- or 3'-deoxyxylo-3'-azido derivatives (9 or 16, respectively). Further selective manipulations provided the cis-5'-monophosphate (3-chlorophenyl)-1,3-propanyl diester prodrugs (HepDirect prodrugs), 15 and 21. These HepDirect prodrugs were demonstrated to activate to their respective NTPs in rat hepatocytes.
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Abstract
The 2'-hydroxyl group plays an integral role in RNA structure and catalysis. This ubiquitous component of the RNA backbone can participate in multiple interactions essential for RNA function, such as hydrogen bonding and metal ion coordination, but the multifunctional nature of the 2'-hydroxyl renders identification of these interactions a significant challenge. By virtue of their versatile physicochemical properties, such as distinct metal coordination preferences, hydrogen bonding properties, and ability to be protonated, 2'-amino-2'-deoxyribonucleotides can serve as tools for probing local interactions involving 2'-hydroxyl groups within RNA. The 2'-amino group can also serve as a chemoselective site for covalent modification, permitting the introduction of probes for investigation of RNA structure and dynamics. In this chapter, we describe the use of 2'-aminonucleotides for investigation of local interactions within RNA, focusing on interactions involving 2'-hydroxyl groups required for RNA structure, function, and catalysis.
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Osborne EM, Ward WL, Ruehle MZ, DeRose VJ. The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme. Biochemistry 2009; 48:10654-64. [PMID: 19778032 PMCID: PMC2901799 DOI: 10.1021/bi900614v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Potential metal interactions with the cleavage site of a minimal hammerhead ribozyme (mHHRz) were probed using (31)P NMR-detected Cd(2+) titration studies of HHRz constructs containing a phosphorothioate (PS) modification at the cleavage site. The mHHRz nucleophile position was replaced by either a 2'-F or a 2'-NH(2) in order to block cleavage activity during the study. The 2'-F/PS cleavage site mHHRz construct, in which the 2'-F should closely imitate the atom size and electronegativity of a 2'-OH, demonstrates low levels of metal ion association (<1 ppm (31)P chemical shift changes). This observation indicates that having an atom size and electrostatic properties that are similar to the 2'-OH are not the governing factors in allowing metal interactions with the scissile phosphate of the mHHRz. With a 2'-NH(2) substitution, a large upfield change in (31)P NMR chemical shift of the phosphorothioate peak (Delta approximately 3 ppm with 6 equiv of added Cd(2+)) indicates observable Cd(2+) interactions with the substituted site. Since a 2'-NH(2), but not a 2'-F, can serve as a metal ligand, these data suggest that a metal ion interaction with the HHRz cleavage site may include both the scissile phosphate and the 2' nucleophile. Control samples in which the 2'-NH(2)/PS unit is placed either next to the mHHRz cleavage site (at U16.1), in a duplex, or in a (am)U(PS)U dinucleotide show much weaker interactions with Cd(2+). Results with these control samples indicate that simply the presence of a 2'-NH(2)/PS unit does not create a strong metal binding site, reinforcing the possibility that the 2'-NH(2)-moderated Cd-PS interaction is specific to the mHHRz cleavage site. Upfield chemical shifts of both (31)P and H-2' (1)H resonances in (am)U(PS)U are observed with addition of Cd(2+), consistent with the predicted metal coordination to both 2'-NH(2) and phosphorothioate ligands. These data suggest that metal ion association with the HHRz cleavage site may include an interaction with the 2'-OH nucleophile.
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Affiliation(s)
| | | | - Max Z. Ruehle
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253
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