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Rydzik AM, Balk R, Koegler M, Steinle T, Riether D, Gottschling D. Access to 1'-Amino Carbocyclic Phosphoramidite to Enable Postsynthetic Functionalization of Oligonucleotides. Org Lett 2021; 23:6735-6739. [PMID: 34424724 DOI: 10.1021/acs.orglett.1c02302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report a synthesis of a carbocyclic, abasic RNA phosphoramidite decorated with an amino functionality. The building block was efficiently incorporated into an RNA oligonucleotide in a site-specific manner, followed by deprotection to a free amino group. The amino moiety could be further derivatized as exemplified with fluorescein N-hydroxysuccinimide ester. Hence, this convertible building block may provide access to a variety of RNA oligonucleotides via postsynthetic amino group functionalization. In particular, providing a vector toward nucleobase replacements.
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Affiliation(s)
- Anna M Rydzik
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Regina Balk
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | | | - Tobias Steinle
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
| | - Dirk Gottschling
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88400 Biberach an der Riss, Germany
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2
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Wilson T, Liu Y, Li NS, Dai Q, Piccirilli JA, Lilley DMJ. Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes. J Am Chem Soc 2019; 141:7865-7875. [PMID: 31017785 PMCID: PMC6523996 DOI: 10.1021/jacs.9b02141] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Indexed: 01/10/2023]
Abstract
Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical. We have determined a new crystal structure of the pistol ribozyme and have shown that G40 acts as general base in the cleavage reaction. The conformation in the active site ensures an in-line attack of the O2' nucleophile, and the conformation at the scissile phosphate and the position of the general base are closely similar to those in the hammerhead ribozyme. However, the two ribozymes differ in the nature of the general acid. 2'-Amino substitution experiments indicate that the general acid of the hammerhead ribozyme is the O2' of G8, while that of the pistol ribozyme is a hydrated metal ion. The two ribozymes are related but mechanistically distinct.
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Affiliation(s)
- Timothy
J. Wilson
- Cancer
Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
| | - Yijin Liu
- Cancer
Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
| | - Nan-Sheng Li
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - David M. J. Lilley
- Cancer
Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
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3
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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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4
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Forconi M, Porecha RH, Piccirilli JA, Herschlag D. Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme. J Am Chem Soc 2011; 133:7791-800. [PMID: 21539364 PMCID: PMC3119543 DOI: 10.1021/ja111316y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein enzymes establish intricate networks of interactions to bind and position substrates and catalytic groups within active sites, enabling stabilization of the chemical transition state. Crystal structures of several RNA enzymes also suggest extensive interaction networks, despite RNA's structural limitations, but there is little information on the functional and the energetic properties of these inferred networks. We used double mutant cycles and presteady-state kinetic analyses to probe the putative interaction between the exocyclic amino group of the guanosine nucleophile and the N7 atom of residue G264 of the Tetrahymena group I ribozyme. As expected, the results supported the presence of this interaction, but remarkably, the energetic penalty for introducing a CH group at the 7-position of residue G264 accumulates as the reaction proceeds toward the chemical transition state to a total of 6.2 kcal/mol. Functional tests of neighboring interactions revealed that the presence of the CH group compromises multiple contacts within the interaction network that encompass the reactive elements, apparently forcing the nucleophile to bind and attack from an altered, suboptimal orientation. The energetic consequences of this indirect disruption of neighboring interactions as the reaction proceeds demonstrate that linkage between binding interactions and catalysis hinges critically on the precise structural integrity of a network of interacting groups.
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Affiliation(s)
- Marcello Forconi
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Rishi H. Porecha
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, USA
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5
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Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010; 11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Falk Wachowius
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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6
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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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Hougland JL, Sengupta RN, Dai Q, Deb SK, Piccirilli JA. The 2'-hydroxyl group of the guanosine nucleophile donates a functionally important hydrogen bond in the tetrahymena ribozyme reaction. Biochemistry 2008; 47:7684-94. [PMID: 18572927 DOI: 10.1021/bi8000648] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the first step of self-splicing, group I introns utilize an exogenous guanosine nucleophile to attack the 5'-splice site. Removal of the 2'-hydroxyl of this guanosine results in a 10 (6)-fold loss in activity, indicating that this functional group plays a critical role in catalysis. Biochemical and structural data have shown that this hydroxyl group provides a ligand for one of the catalytic metal ions at the active site. However, whether this hydroxyl group also engages in hydrogen-bonding interactions remains unclear, as attempts to elaborate its function further usually disrupt the interactions with the catalytic metal ion. To address the possibility that this 2'-hydroxyl contributes to catalysis by donating a hydrogen bond, we have used an atomic mutation cycle to probe the functional importance of the guanosine 2'-hydroxyl hydrogen atom. This analysis indicates that, beyond its role as a ligand for a catalytic metal ion, the guanosine 2'-hydroxyl group donates a hydrogen bond in both the ground state and the transition state, thereby contributing to cofactor recognition and catalysis by the intron. Our findings continue an emerging theme in group I intron catalysis: the oxygen atoms at the reaction center form multidentate interactions that function as a cooperative network. The ability to delineate such networks represents a key step in dissecting the complex relationship between RNA structure and catalysis.
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Affiliation(s)
- James L Hougland
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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Forconi M, Lee J, Lee JK, Piccirilli JA, Herschlag D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry 2008; 47:6883-94. [PMID: 18517225 DOI: 10.1021/bi800519a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many enzymes use metal ions within their active sites to achieve enormous rate acceleration. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). The three-dimensional arrangement determined by X-ray crystallography provides a powerful starting point for identifying ground state interactions, but only functional studies can establish and interrogate transition state interactions. The Tetrahymena group I ribozyme is a paradigm for the study of RNA catalysis, and previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified catalytic metal ions making five contacts with the substrate atoms. Here, we have combined atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to establish transition state ligands on the ribozyme for one of the catalytic metal ions, referred to as M A. We identified the pro-S P oxygen atoms at nucleotides C208, A304, and A306 as ground state ligands for M A, verifying interactions suggested by the Azoarcus crystal structures. We further established that these interactions are present in the chemical transition state, a conclusion that requires functional studies, such as those carried out herein. Elucidating these active site connections is a crucial step toward an in-depth understanding of how specific structural features of the group I intron lead to catalysis.
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Affiliation(s)
- Marcello Forconi
- Department of Biochemistry and Chemistry, Stanford University, Stanford, California 94305, USA
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Porphyrin conjugated to DNA by a 2'-amido-2'-deoxyuridine linkage. Bioorg Med Chem Lett 2007; 18:850-5. [PMID: 18054487 DOI: 10.1016/j.bmcl.2007.11.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Revised: 11/06/2007] [Accepted: 11/08/2007] [Indexed: 11/21/2022]
Abstract
A porphyrin that contains a single carboxylic acid group was synthesized and coupled to 2'-amino-2'-deoxyuridine. The resultant product contained a free 3' hydroxyl group and a 4,4'-dimethoxytrityl (DMT) protecting group on the 5' hydroxyl of the uridine, making it suitable for use in oligonucleotide synthesis. The 3' H-phosphonate derivative of this molecule was synthesized and used to form a conjugate with a 19 nucleotide sequence of DNA (5'-CCTCCAGTGGAAATCAAGG-3'). This was carried out with the DNA attached at the 3' end to a control pore glass (CPG) substrate, allowing for rapid purification. After removal of the DMT group, an additional three nucleotides were added, leaving the porphyrin as an internal modification. This is the first report of porphyrin attached internally to an oligonucleotide using a hydrogen-bonding nucleoside analog. This allows oligonucleotides to be used as a scaffold for precise positioning of multiple porphyrins within biomimetic arrays.
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Dai Q, Lea CR, Lu J, Piccirilli JA. Syntheses of (2')3'-15N-amino-(2')3'-deoxyguanosine and determination of their pKa values by 15N NMR spectroscopy. Org Lett 2007; 9:3057-60. [PMID: 17629287 DOI: 10.1021/ol071129h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
2'-Amino-2'-deoxyguanosine and 3'-amino-3'-deoxyguanosine are valuable probes for investigating the metal ion interactions at the active site of the group I ribozyme. However, these experiments require a thorough understanding of the protonation state of the amino group at a specific pH. Here, we describe the first syntheses of 2'-15N-amino-2'-deoxyadenosine, 2'-15N-amino-2'-deoxyguanosine, and 3'-15N-amino-3'-deoxyguanosine. The 15N-enriched nucleus allows convenient and accurate determination of the amine pKa by 15N NMR.
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Affiliation(s)
- Qing Dai
- Department of Biochemistry & Molecular Biology, The University of Chicago, 929 East 57th Street, MC 1028, Chicago, Illinois 60637, USA
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