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Lu G, Shivalila C, Monian P, Yu H, Harding I, Briem S, Byrne M, Faraone A, Friend S, Huth O, Iwamoto N, Kawamoto T, Kumarasamy J, Lamattina A, Longo K, McCarthy L, McGlynn A, Molski A, Pan Q, Pu T, Purcell-Estabrook E, Rossi J, Standley S, Thomas C, Walen A, Yang H, Kandasamy P, Vargeese C. Rational design of base, sugar and backbone modifications improves ADAR-mediated RNA editing. Nucleic Acids Res 2024; 52:10068-10084. [PMID: 39149897 PMCID: PMC11417349 DOI: 10.1093/nar/gkae681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
AIMers are short, chemically modified oligonucleotides that induce A-to-I RNA editing through interaction with endogenous adenosine deaminases acting on RNA (ADAR) enzymes. Here, we describe the development of new AIMer designs with base, sugar and backbone modifications that improve RNA editing efficiency over our previous design. AIMers incorporating a novel pattern of backbone and 2' sugar modifications support enhanced editing efficiency across multiple sequences. Further efficiency gains were achieved through incorporation of an N-3-uridine (N3U), in place of cytidine (C), in the 'orphan base' position opposite the edit site. Molecular modeling suggests that N3U might enhance ADAR catalytic activity by stabilizing the AIMer-ADAR interaction and potentially reducing the energy required to flip the target base into the active site. Supporting this hypothesis, AIMers containing N3U consistently enhanced RNA editing over those containing C across multiple target sequences and multiple nearest neighbor sequence combinations. AIMers combining N3U and the novel pattern of 2' sugar chemistry and backbone modifications improved RNA editing both in vitro and in vivo. We provide detailed N3U synthesis methods and, for the first time, explore the impact of N3U and its analogs on ADAR-mediated RNA editing efficiency and targetable sequence space.
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Affiliation(s)
| | | | | | - Hui Yu
- Wave Life Sciences, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tom Pu
- Wave Life Sciences, Cambridge, MA, USA
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Yamamoto S, Park S, Sugiyama H. Development of a visible nanothermometer with a highly emissive 2′-O-methylated guanosine analogue. RSC Adv 2015. [DOI: 10.1039/c5ra24756j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have synthesized a fluorescent base analogue, 2-aminothieno[3,4-d]pyrimidine based G-mimic deoxyribonucleoside, 2′-OMe-thG, and investigated its photophysical properties and DNA incorporation.
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Affiliation(s)
- Seigi Yamamoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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Martínez-Montero S, Fernández S, Rodríguez-Pérez T, Sanghvi YS, Wen K, Gotor V, Ferrero M. Improved Synthesis and Isolation of 2′-O-Methyladenosine: Effective and Scalable Enzymatic Separation of 2′/3′-O-Methyladenosine Regioisomers. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900348] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Roy SK, Tang JY. Efficient Large Scale Synthesis of 2‘-O-Alkyl Pyrimidine Ribonucleosides. Org Process Res Dev 2000. [DOI: 10.1021/op990100t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saroj K. Roy
- Hybridon Inc., 155 Fortune Boulevard, Milford, Massachusetts 01757
| | - Jin-yan Tang
- Hybridon Inc., 155 Fortune Boulevard, Milford, Massachusetts 01757
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Krivonogov VP, Tolstikov GA, Murinov YI, Zarudii FS, Lazareva DN, Ismagilova AF, Volkova SS, Sakhautdinova GM, Spirikhin LV, Abdrakhmanov IB, Krivonogova II. Synthesis and immunotropic activity of derivatives of pyrimidines. Pharm Chem J 1993. [DOI: 10.1007/bf00781072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Tolstikov GA, Baltina LA, Khalilov LM, Spirikhin LV, Sultanmuratova VR, Murinov YI. Synthesis of 5-hydroxy-6-methyluracil 3-?-D-ribofuranoside. Chem Heterocycl Compd (N Y) 1991. [DOI: 10.1007/bf00472512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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