Synthesis of RNA Using 2‘-<i>O</i>-DTM Protection

Semenyuk, Andrey; Földesi, András; Johansson, Tommy; Estmer-Nilsson, Camilla; Blomgren, Peter; Brännvall, Mathias; Kirsebom, Leif A.; Kwiatkowski, Marek

doi:10.1021/ja0636587

Cited by 78 publications

(81 citation statements)

References 15 publications

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“…Furthermore, the TBDMS group is associated with relatively long coupling times (11) and insufficiently high coupling yields (12), though improvements based on the use of more powerful activators or less bulky 2′-hydroxyl protecting groups have been proposed (12). To resolve these pro-blems, three new protecting groups, bis(2-acetoxyethyl-oxy)methyl (ACE) (13), triisopropylsilyloxymethyl (TOM) (14), and more recently t -butyldithiomethyl (DTM) (15), have been developed. Though such protecting groups represent major improvements in the synthesis of RNA oligonucleotides (16), however, they still leave something to be desired in their practical application.…”

Section: Introductionmentioning

confidence: 99%

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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

Shiba¹,

Masuda²,

Watanabe³

et al. 2007

Nucleic Acids Research

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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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Section: Introductionmentioning

confidence: 99%

“…TOM-protected oligonucleotides, meanwhile, are not readily amenable to routine analysis and purification by HPLC because of the hydrophobic nature of the silyl group. Finally, DTM-amidites, particularly the G amidite, are somewhat unstable in acetonitrile solution (15). …”

Section: Introductionmentioning

confidence: 99%

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

Shiba¹,

Masuda²,

Watanabe³

et al. 2007

Nucleic Acids Research

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“…These results confirmed the above mentioned instability of uridine derivative 1a in the presence of this catalyst. 12 With other tested nucleosides 1b-1f only traces of products 2b-2f may be detected using TLC (entries [14][15][16][17][18][19]. The ratio of starting 1, product 2 and decomposition products were determined using TLC and PMR spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

Effective isomerization of 3', 5'-O-(tetraisopropyldisiloxane-1,3-diyl)nucleosides in the presence of trimethylsilyl trifluoromethanesulfonate

Kulikova¹,

Muradova²,

Mikhailov³

2008

Arkivoc

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Trimethylsilyl trifluoromethanesulfonate catalyze effective isomerization of 3′,5′-O-(tetraisopropyldisiloxane-1,3-diyl)nucleosides (1) in 1,2-dicloroethane at 0°C into 2′,3′-O-(tetraisopropyldisiloxane-1,3-diyl)-derivatives (2), which can be obtained in 55-90% yields. On the other hand nucleosides 1 were found to be stable in the presence of tin tetrachloride. Only in the case of uridine derivative 1a a substantial amount of isomerization product 2a was formed.

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“…Characterization data obtained from 1 H and 13 C NMR analysis of 2a are in agreement with those reported by Semenyuk et al . (23). …”

Section: Methodsmentioning

confidence: 99%

Permanent or reversible conjugation of 2′-O- or 5′-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences

Cieślak

Grajkowski

Ausín

et al. 2011

Nucleic Acids Research

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2′-O-Aminooxymethyl ribonucleosides are prepared from their 3′,5′-disilylated 2′-O-phthalimidooxymethyl derivatives by treatment with NH4F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2′-conjugates in yields of 69–82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2′-O-aminooxymethyl uridine provides permanent uridine 2′-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5′-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3′-O-levulinyl-5′-O-phthalimidooxymethyl precursor. Pyrenylation of 5′-O-aminooxymethyl thymidine and the sensitivity of the 5′-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2′-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2′-conjugate into an RNA sequence, the conjugation of 2′-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2′-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

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Synthesis of RNA Using 2‘-O-DTM Protection

Cited by 78 publications

References 15 publications

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

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

Effective isomerization of 3', 5'-O-(tetraisopropyldisiloxane-1,3-diyl)nucleosides in the presence of trimethylsilyl trifluoromethanesulfonate

Permanent or reversible conjugation of 2′-O- or 5′-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences

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