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Efimov VA, Aralov AV, Klykov VN, Chakhmakhcheva OG. Synthesis of RNA by the rapid phosphotriester method using azido-based 2'-O-protecting groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:846-65. [PMID: 20183623 DOI: 10.1080/15257770903170286] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The azidomethyl and 2-(azidomethyl)benzoyl as 2'-OH protecting groups are reported for preparation of oligoribonucleotides by the phosphotriester solid-phase method using O-nucleophilic intramolecular catalysis. The procedures for the synthesis of the corresponding monomer synthons were developed and the usefulness of the application of 2'-O-azidomethyl and 2'-O-2-(azidomethyl)benzoyl groups was examined in the synthesis of different RNA fragments with a chain length of 15-22 nucleotides. The azidomethyl group was found to be more preferable for effective synthesis of oligoribonucleotides. Hybridization properties of RNAs toward their complementary oligonucleotides were examined before and after the removal of 2'-O-azidomethyl groups.
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Affiliation(s)
- V A Efimov
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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52
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Beaucage SL, Reese CB. Recent advances in the chemical synthesis of RNA. ACTA ACUST UNITED AC 2009; Chapter 2:Unit 2.16 1-31. [PMID: 19746354 DOI: 10.1002/0471142700.nc0216s38] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As a consequence largely of recent developments in RNA interference (RNAi) research, the availability of rapid and efficient methods for the chemical synthesis of RNA sequences has become a matter of considerable urgency. This unit is concerned mainly with work that has been carried out, especially in the past decade, on the design of new and improved methods of RNA synthesis. The main criteria for the choice of protecting groups for the 2'-hydroxy functions of the ribonucleoside building blocks, which is arguably the most crucial strategic decision to be made, are discussed. A number of new ether-, acetal-, orthoester-, and ester-based 2'-protecting groups are described and their application, mainly in phosphoramidite-based solid-phase synthesis, is discussed in some detail. Brief consideration is also given to solution-phase RNA synthesis, which may well prove to be of great importance if a systemic drug is developed and multikilogram quantities of synthetic RNA sequences are required.
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53
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Lackey JG, Mitra D, Somoza MM, Cerrina F, Damha MJ. Acetal levulinyl ester (ALE) groups for 2'-hydroxyl protection of ribonucleosides in the synthesis of oligoribonucleotides on glass and microarrays. J Am Chem Soc 2009; 131:8496-502. [PMID: 19485360 DOI: 10.1021/ja9002074] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a synthetic strategy that permits both the growth and deprotection of RNA chains that remain attached to a solid polymer support or chip surface. The key synthons for RNA synthesis are novel 5'-O-DMTr 2'-acetal levulinyl ester (2'-O-ALE) ribonucleoside 3'-phosphoramidite derivatives. In the presence of 4,5-dicyanoimidazole (DCI) as the activator, these monomers coupled to Q-CPG solid support with excellent coupling efficiency (approximately 98.7%). The method was extended to the light directed synthesis of poly rU and poly rA on a microarray through the use of a 5'-O-(2-(2-nitrophenyl)propoxycarbonyl)-2'-O-ALE-3'-phosphoramidite derivative. A two-stage deprotection strategy was employed to fully deblock the RNA directly on the Q-CPG or microarray support without releasing it from the support's surface: phosphate group deblocking with NEt(3) in acetonitrile (ACN) (2:3 v/v; 1 h, r.t.) followed by removal of the 2'-O-ALE groups under mild hydrazinolysis conditions (0.5-4 h, r.t.). This last treatment also removed the levulinyl (Lv) group on adenine (N(6)) and cytosine (N(4)) and the dimethylformamidine (dmf) group on guanine (N(2)). The chemistry and methods described here pave the way to the fabrication of microarrays of immobilized RNA probes for analyzing molecular interactions of biological interest.
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Affiliation(s)
- Jeremy G Lackey
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 2K6
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54
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Martin AR, Lavergne T, Vasseur JJ, Debart F. Assessment of new 2'-O-acetalester protecting groups for regular RNA synthesis and original 2'-modified proRNA. Bioorg Med Chem Lett 2009; 19:4046-9. [PMID: 19560920 DOI: 10.1016/j.bmcl.2009.06.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 06/03/2009] [Accepted: 06/05/2009] [Indexed: 11/29/2022]
Abstract
New base-labile acyloxymethyl groups were evaluated to protect 2'-OH functions of ribonucleotides for regular RNA synthesis in order to shorten the deprotection procedure upon ammonia. These same acetalester groups were assessed in 2'-modified proRNA as biolabile 2'-protections removable by cell enzymes to generate parent RNA. Demasking of 2'-modified pro-uridylates was studied in cell extracts.
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Affiliation(s)
- Anthony R Martin
- IBMM, UMR 5247 CNRS-UM1-UM2, cc1704, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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55
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Lavergne T, Bertrand JR, Vasseur JJ, Debart F. A base-labile group for 2'-OH protection of ribonucleosides: a major challenge for RNA synthesis. Chemistry 2008; 14:9135-8. [PMID: 18767078 DOI: 10.1002/chem.200801392] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Lavergne
- Equipe Oligonucléotides Modifiés, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier 1-, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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56
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Ohgi T, Kitagawa H, Yano J. Chemical synthesis of oligoribonucleotides with 2'-O-(2-cyanoethoxymethyl)-protected phosphoramidites. ACTA ACUST UNITED AC 2008; Chapter 2:Unit 2.15. [PMID: 18819083 DOI: 10.1002/0471142700.nc0215s34] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An RNA synthetic method with 2-cyanoethoxymethyl (CEM) as the 2'-hydroxyl protecting group allows the synthesis of long oligoribonucleotides from CEM-amidites with an efficiency and final purity comparable to that obtained in DNA synthesis. The CEM-amidites give a high coupling efficiency, because the CEM group minimizes steric hindrance in the coupling reaction. The CEM group shows satisfactory stability under solid-phase synthetic conditions, avoids the generation of asymmetric centers, and is easily cleaved to give the final product. This unit describes the synthesis of the four CEM-amidites, the preparation of reagents, the solid-phase synthesis of oligoribonucleotides on an automated DNA synthesizer, and their deprotection.
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Affiliation(s)
- Tadaaki Ohgi
- Discovery Research Laboratories, Nippon Shinyaku Co., Ltd., Ibaraki, Japan
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57
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Cieślak J, Grajkowski A, Kauffman JS, Duff RJ, Beaucage SL. The 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleosides in the solid-phase synthesis of oligoribonucleotides. J Org Chem 2008; 73:2774-83. [PMID: 18327953 DOI: 10.1021/jo702717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Emerging RNA-based technologies for controlling gene expression have triggered a high demand for synthetic oligoribonucleotides and have motivated the development of ribonucleoside phosphoramidites that would exhibit coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites. To fulfill these needs, the novel 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleoside phosphoramidites 9a-d has been implemented (Schemes 1 and 2). The solid-phase synthesis of AUCCGUAGCUAACGUCAUGG was then carried out employing 9a-d as 0.2 M solutions in dry MeCN and 5-benzylthio-1H-tetrazole as an activator. The coupling efficiency of 9a-d averaged 99% within a coupling time of 180 s. Following removal of all base-sensitive protecting groups, cleavage of the remaining 2'-[4-(N-methylamino)benzyl] acetals from the RNA oligonucleotide was effected in buffered 0.1 M AcOH (pH 3.8) within 30 min at 90 degrees C. RP-HPLC and PAGE analyses of the fully deprotected AUCCGUAGCUAACGUCAUGG were comparable to those of a commercial RNA oligonucleotide sharing an identical sequence. Enzymatic digestion of the RNA oligomer catalyzed by bovine spleen phosphodiesterase and bacterial alkaline phosphatase revealed no significant amounts of RNA fragments containing (2'-->5')-internucleotidic phosphodiester linkages or noteworthy nucleobase modifications.
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Affiliation(s)
- Jacek Cieślak
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
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58
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Turcatti G, Romieu A, Fedurco M, Tairi AP. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res 2008; 36:e25. [PMID: 18263613 PMCID: PMC2275100 DOI: 10.1093/nar/gkn021] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Fluorescent 2′-deoxynucleotides containing a protecting group at the 3′-O-position are reversible terminators enabling array-based DNA sequencing by synthesis (SBS) approaches. Herein, we describe the synthesis of a new family of 3′-OH unprotected cleavable fluorescent 2′-deoxynucleotides and their evaluation as reversible terminators for high-throughput DNA SBS strategies. In this first version, all four modified nucleotides bearing a cleavable disulfide Alexa Fluor® 594 dye were assayed for their ability to act as a reversible stop for the incorporation of the next labeled base. Their use in SBS leaded to a signal–no signal output after successive addition of each labeled nucleotide during the sequencing process (binary read-out). Solid-phase immobilized synthetic DNA target sequences were used to optimize the method that has been applied to DNA polymerized colonies or clusters obtained by in situ solid-phase amplification of fragments of genomic DNA templates.
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Affiliation(s)
- Gerardo Turcatti
- Manteia Predictive Medicine S.A., Zone Industrielle, Coinsins, CH-1267, Switzerland.
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59
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Chow CS, Mahto SK, Lamichhane TN. Combined Approaches to Site-Specific Modification of RNA. ACS Chem Biol 2008; 3:30-37. [PMID: 18177002 DOI: 10.1021/cb7002225] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Both natural and unnatural modifications in RNA are of interest to biologists and chemists. More than 100 different analogues of the four standard RNA nucleosides have been identified in nature. Unnatural modifications are useful for structure and mechanistic studies of RNA. This Review highlights chemical, enzymatic, and combined (semisynthesis) approaches to generate site specifically modified RNAs. The availability of these methods for site-specific modifications of RNAs of all sizes is important in order to study the relationships between RNA chemical composition, structure, and function.
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Affiliation(s)
- Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Santosh K. Mahto
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
| | - Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202
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60
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Somoza Á. Protecting groups for RNA synthesis: an increasing need for selective preparative methods. Chem Soc Rev 2008; 37:2668-75. [DOI: 10.1039/b809851d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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61
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Saneyoshi H, Ando K, Seio K, Sekine M. Chemical synthesis of RNA via 2′-O-cyanoethylated intermediates. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.07.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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62
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63
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Shiba Y, Masuda H, Watanabe N, Ego T, Takagaki K, Ishiyama K, Ohgi T, Yano J. Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2'-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate. Nucleic Acids Res 2007; 35:3287-96. [PMID: 17459888 PMCID: PMC1904286 DOI: 10.1093/nar/gkm202] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A long RNA oligomer, a 110mer with the sequence of a precursor-microRNA candidate, has been chemically synthesized in a single synthesizer run by means of standard automated phosphoramidite chemistry. The synthetic method involved the use of 2-cyanoethoxymethyl (CEM), a 2′-hydroxyl protecting group recently developed in our laboratory. We improved the methodology, introducing better coupling and capping conditions. The overall isolated yield of highly pure 110mer was 5.5%. Such a yield on a 1-μmol scale corresponds to 1 mg of product and emphasizes the practicality of the CEM method for synthesizing oligomers of more than 100 nt in sufficient quantity for biological research. We confirmed the identity of the 110mer by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, as well as HPLC, electrophoretic methods, and RNase-digestion experiments. The 110mer also showed sense-selective specific gene-silencing activity. As far as we know, this is the longest chemically synthesized RNA oligomer reported to date. Furthermore, the identity of the 110mer was confirmed by both physicochemical and biological methods.
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Affiliation(s)
| | | | | | | | | | | | - Tadaaki Ohgi
- *To whom correspondence should be addressed. Tel: +81-29-850-6243; Fax: +81-29-850-6217;
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64
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Zhou C, Pathmasiri W, Honcharenko D, Chatterjee S, Barman J, Chattopadhyaya J. High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions. CAN J CHEM 2007. [DOI: 10.1139/v07-025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During the F–-promoted deprotection of the oligo–RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is formed as a by-product. The TVS formed has been shown to react with the exocyclic amino functions of adenosine (A), guanosine (G), and cytidine (C) of the fully deprotected oligo–RNA to give undesirable adducts, which are then purified by HPLC and unambiguously characterized by 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) NMR and mass spectroscopic analysis. The relative nucleophilic reactivities of the nucleobases toward TVS have been found to be the following: N6–A > N4–C > N2–G > > N3–U. This reactivity of TVS toward RNA nucleobases to give various Michael adducts could, however, be suppressed by using various amines as scavengers. Among all these amines, morpholine and piperidine are the most efficient scavenger for TVS, which gave highly pure oligo–RNA even in the crude form and can be used directly in RNA chemical biology studies.Key words: RNA synthesis, RNA alkylation, p-tolyl vinyl sulphone, Michael addition.
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65
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Abstract
Following the introduction of the first successful automated DNA synthesizer by Applied Biosystems Inc. (ABI) in 1983, the company was in a position to consider the commercialization of additional chemistries to enable the automated synthesis of RNA oligonucleotides or other analogs. This retrospective account provides a personal view of how ABI collaborated with Professor Kelvin K. Ogilvie in 1986 to commercialize automated RNA synthesis, using the 2′-O-alkylsilyl-protected monomers that he pioneered. The influence of end-user scientific applications on this decision-making process is highlighted, together with the influence of such applications on subsequent commoditization of RNA. Hopefully, these perspectives will provide chemists with further appreciation of the sometime complex and unpredictable interplay between academically interesting chemistry and evolving scientific applications that influence commercialization, and vice versa.Key words: RNA, synthesis, automated, 2′-O-alkylsilyl phosphoramidite, siRNA.
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66
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Lackey JG, Sabatino D, Damha MJ. Solid-phase synthesis and on-column deprotection of RNA from 2'- (and 3'-) O-levulinated (Lv) ribonucleoside monomers. Org Lett 2007; 9:789-92. [PMID: 17279762 DOI: 10.1021/ol0629521] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[reaction: see text] The solid-phase synthesis of oligoribonucleotides derived from ribonucleosides esterified at the 2'- (or 3'-) position with the levulinyl (Lv) group is described. The oligomers can be released from the solid support as 2'-O-Lv ester derivatives or fully deprotected while still attached to the solid support.
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Affiliation(s)
- Jeremy G Lackey
- Department of Chemistry, McGill University, Montreal, QC, Canada
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67
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Semenyuk A, Kwiatkowski M. A base-stable dithiomethyl linker for solid-phase synthesis of oligonucleotides. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2006.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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68
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Zhou C, Honcharenko D, Chattopadhyaya J. 2-(4-Tolylsulfonyl)ethoxymethyl (TEM)-a new 2'-OH protecting group for solid-supported RNA synthesis. Org Biomol Chem 2006; 5:333-43. [PMID: 17205178 DOI: 10.1039/b614210a] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 2-(4-tolylsulfonyl)ethoxymethyl (TEM) as a new 2'-OH protecting group is reported for solid-supported RNA synthesis using phosphoramidite chemistry. The usefulness of the 2'-O-TEM group is exemplified by the synthesis of 12 different oligo-RNAs of various sizes (14-38 nucleotides long). The stepwise coupling yield varied from 97-99% with an optimized coupling time of 120 s. The synthesis of all four pure phosphoramidite building blocks is also described. Two new reliable parameters, delta(C2')-delta(C3') and delta(H2')-delta(H3'), have been suggested for the characterization of isomeric 2'-O-TEM and 3'-O-TEM as well as other isomeric mono 2'/3'-protected ribonucleoside derivatives. The most striking feature of this strategy is that the crude RNA prepared using our 2'-O-TEM strategy is sufficiently pure (>90%) for molecular biology research without any additional purification step, thereby making oligo-RNAs easily available at a relatively low cost, saving both time and lab resources.
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Affiliation(s)
- Chuanzheng Zhou
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, S-751 23, Uppsala, Sweden
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