1
|
Hasegawa S, Inagaki M, Kato S, Li Z, Kimura Y, Abe H. Synthesis of nucleoside oligophosphates by electrophilic activation of phosphorothioate. Org Biomol Chem 2023; 21:3997-4001. [PMID: 37186249 DOI: 10.1039/d2ob02260e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We herein report a new synthetic method for nucleoside oligophosphates based on electrophilic activation of 5'-phosphorothioate nucleotides. The treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently afforded the key activated species, electrophilic thioester nucleotides (EPT-Ns), which were coupled with various phosphate reagents to afford the target nucleoside oligophosphates, including an mRNA cap analog.
Collapse
Affiliation(s)
| | | | - Shunichi Kato
- Graduate School of Science, Nagoya University, Japan.
| | - Zhenmin Li
- Graduate School of Science, Nagoya University, Japan.
| | | | - Hiroshi Abe
- Graduate School of Science, Nagoya University, Japan.
- CREST, Japan Science and Technology Agency, Japan
- Institute for Glyco-core Research (iGCORE), Japan
| |
Collapse
|
2
|
Epple S, El-Sagheer AH, Brown T. Artificial nucleic acid backbones and their applications in therapeutics, synthetic biology and biotechnology. Emerg Top Life Sci 2021; 5:691-697. [PMID: 34297063 PMCID: PMC8726046 DOI: 10.1042/etls20210169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022]
Abstract
The modification of DNA or RNA backbones is an emerging technology for therapeutic oligonucleotides, synthetic biology and biotechnology. Despite a plethora of reported artificial backbones, their vast potential is not fully utilised. Limited synthetic accessibility remains a major bottleneck for the wider application of backbone-modified oligonucleotides. Thus, a variety of readily accessible artificial backbones and robust methods for their introduction into oligonucleotides are urgently needed to utilise their full potential in therapeutics, synthetic biology and biotechnology.
Collapse
Affiliation(s)
- Sven Epple
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Afaf H. El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| |
Collapse
|
3
|
Yamaoka K, Oikawa R, Abe N, Nakamoto K, Tomoike F, Hashiya F, Kimura Y, Abe H. Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells. Chembiochem 2021; 22:3273-3276. [PMID: 34519401 DOI: 10.1002/cbic.202100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/11/2021] [Indexed: 11/10/2022]
Abstract
Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.
Collapse
Affiliation(s)
- Kazuki Yamaoka
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ryota Oikawa
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| |
Collapse
|
4
|
Adhireksan Z, Sharma D, Lee PL, Bao Q, Padavattan S, Shum WK, Davey GE, Davey CA. Engineering nucleosomes for generating diverse chromatin assemblies. Nucleic Acids Res 2021; 49:e52. [PMID: 33590100 PMCID: PMC8136823 DOI: 10.1093/nar/gkab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/09/2021] [Accepted: 02/04/2021] [Indexed: 01/01/2023] Open
Abstract
Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Here we show that nucleosomal constructs with cohesive-ended DNA can be designed that assemble into different types of circular configurations or continuous fibers extending throughout crystals. We demonstrate the utility of the method for characterizing nucleosome compaction and linker histone binding at near-atomic resolution but also advance its application for tackling further problems in chromatin structural biology and for generating novel types of DNA nanostructures. We provide a library of cohesive-ended DNA fragment expression constructs and a strategy for engineering DNA-based nanomaterials with a seemingly vast potential variety of architectures and histone chemistries.
Collapse
Affiliation(s)
- Zenita Adhireksan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Deepti Sharma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Phoi Leng Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Qiuye Bao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sivaraman Padavattan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Wayne K Shum
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Gabriela E Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| | - Curt A Davey
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
| |
Collapse
|
5
|
Nakamoto K, Abe H. Chemical Synthesis of Circular RNAs with Phosphoramidate Linkages for Rolling-Circle Translation. Curr Protoc 2021; 1:e43. [PMID: 33657267 DOI: 10.1002/cpz1.43] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, many types of circular RNAs have been reported in human cells. One interesting aspect of circular RNAs is their translation into proteins. We previously discovered that circular RNA without a stop codon can be translated into long repeating peptides via rolling-circle translation in both prokaryotic and eukaryotic systems. Because the rate-limiting step of translation-ribosome binding-occurs only once in rolling-circle translation, the translation efficacy is very efficient compared to translation of linear mRNAs. However, preparation of circular RNAs involves costly and time-consuming enzymatic methods, and there was no practical non-enzymatic method. We recently reported a chemical synthesis strategy using short RNA fragments and one or two phosphoramidate linkages. In this article, we describe the chemical synthesis and purification methods for preparation of circular RNAs for rolling-circle translation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 3'-amino-modified guanosine controlled-pore glass Basic Protocol 2: Solid-phase synthesis of linear RNA fragments Basic Protocol 3: Chemical synthesis of circular RNAs.
Collapse
Affiliation(s)
| | - Hiroshi Abe
- Graduate School of Science, Nagoya University, Aichi, Japan
| |
Collapse
|
6
|
Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
Collapse
Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| |
Collapse
|
7
|
Zhou QY, Zhong XY, Zhao LL, Wang LJ, Zhou YL, Zhang XX. High-throughput ultra-sensitive discrimination of single nucleotide polymorphism via click chemical ligation. Analyst 2020; 145:172-176. [PMID: 31724655 DOI: 10.1039/c9an01672d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) have been proven to be important biomarkers for disease diagnosis, prognosis and disease pathogenesis. Here, taking the advantages of a self-assembled oligonucleotide sandwich structure and robust chemical reactions, we have developed a simple, high-throughput and effective colorimetric analytical technique termed CuAAC-based ligation-assisted assays (CuAAC-LA) for SNP detection using a DNA-BIND 96-well plate. With the 5'-azide and 3'-alkyne groups labelled on two oligonucleotide probes, the target DNA can direct a Cu(i)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction. Since the small difference in duplex stability caused by a single-nucleotide mismatch was amplified by the steric effects of these reactive groups for the ligation reaction of an unstable duplex, CuAAC-LA exhibited an ultra-sensitive discrimination ability for a mutant type target in the presence of large amounts of wild type targets. As low as 0.05% SNP could be clearly detected, which was better than most previously reported methods by various DNA ligases, indicating that a simple and rapid synthetic method i.e., the DNA template-directed click reaction held the potential to replace the ligase for SNP detection.
Collapse
Affiliation(s)
- Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | | | | | | | | | | |
Collapse
|
8
|
Shivalingam A, Taemaitree L, El-Sagheer AH, Brown T. Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly. Angew Chem Int Ed Engl 2020; 59:11416-11422. [PMID: 32153132 PMCID: PMC7383975 DOI: 10.1002/anie.202000209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Joining oligonucleotides together (ligation) is a powerful means of retrieving information from the nanoscale. To recover this information, the linkages created must be compatible with polymerases. However, enzymatic ligation is restrictive and current chemical ligation methods lack flexibility. Herein, a versatile ligation platform based on the formation of urea and squaramide artificial backbones from minimally modified 3′‐ and 5′‐amino oligonucleotides is described. One‐pot ligation gives a urea linkage with excellent read‐through speed, or a squaramide linkage that is read‐through under selective conditions. The squaramide linkage can be broken and reformed on demand, while stable pre‐activated precursor oligonucleotides expand the scope of the ligation reaction to reagent‐free, mild conditions. The utility of our system is demonstrated by replacing the enzymatically biased RNA‐to‐DNA reverse transcription step of RT‐qPCR with a rapid nucleic‐acid‐template‐dependent DNA chemical ligation system, that allows direct RNA detection.
Collapse
Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Lapatrada Taemaitree
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Department of Science and Mathematics, Suez University, Faculty of Petroleum and Mining Engineering, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| |
Collapse
|
9
|
Shivalingam A, Taemaitree L, El‐Sagheer AH, Brown T. Squaramides and Ureas: A Flexible Approach to Polymerase‐Compatible Nucleic Acid Assembly. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Arun Shivalingam
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Lapatrada Taemaitree
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Afaf H. El‐Sagheer
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
- Department of Science and Mathematics Suez University Faculty of Petroleum and Mining Engineering Suez 43721 Egypt
| | - Tom Brown
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| |
Collapse
|
10
|
Nakamoto K, Abe N, Tsuji G, Kimura Y, Tomoike F, Shimizu Y, Abe H. Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation. Chem Commun (Camb) 2020; 56:6217-6220. [DOI: 10.1039/d0cc02140g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circular RNA without a stop codon enables rolling circle translation. we carried out one-pot chemical synthesis of circular RNA from RNA fragments. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.
Collapse
Affiliation(s)
| | - Naoko Abe
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
| | - Genichiro Tsuji
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- National Institute of Health Sciences
| | | | - Fumiaki Tomoike
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- Faculty of Science
| | | | - Hiroshi Abe
- Graduate School of Science
- Nagoya University
- Nagoya
- Japan
- JST CREST, Science and Technology Agency
| |
Collapse
|
11
|
Kanavarioti A. HPLC methods for purity evaluation of man-made single-stranded RNAs. Sci Rep 2019; 9:1019. [PMID: 30705318 PMCID: PMC6356003 DOI: 10.1038/s41598-018-37642-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
Synthetic RNA oligos exhibit purity decreasing as a function of length, because the efficiency of the total synthesis is the numerical product of the individual step efficiencies, typically below 98%. Analytical methods for RNAs up to the 60 nucleotides (nt) have been reported, but they fall short for purity evaluation of 100nt long, used as single guide RNA (sgRNA) in CRISPR technology, and promoted as pharmaceuticals. In an attempt to exploit a single HPLC method and obtain both identity as well as purity, ion-pair reversed-phase chromatography (IP-RP) at high temperature in the presence of an organic cosolvent is the current analytical strategy. Here we report that IP-RP is less suitable compared to the conventional ion-exchange (IEX) for analysis of 100nt RNAs. We demonstrate the relative stability of RNA in the denaturing/basic IEX mobile phase, lay out a protocol to determine the on-the-column stability of any RNA, and establish the applicability of this method for quality testing of sgRNA, tRNA, and mRNA. Unless well resolving HPLC methods are used for batch-to-batch evaluation of man-made RNAs, process development will remain shortsighted, and observed off-target effects in-vitro or in-vivo may be partially related to low purity and the presence of shorter sequences.
Collapse
Affiliation(s)
- Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95762, USA.
| |
Collapse
|