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Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA

“…The corresponding phosphoramidite was generated by using a similar approach as Höbartner and coworkers,31 but employing the DPC-protected precursor (compound 5 ). In our hands, compound 5 gave higher yields in the m 2 G phosphoramidite (compound 8 ) synthesis (Supplementary material) than the methods reported previously 31,32. The synthesis could be performed on a reasonably high scale to produce sufficient amounts of amidite 8 for multiple couplings.…”

Chemical Synthesis of Oligoribonucleotide (ASL of tRNALysT. brucei) Containing a Recently Discovered Cyclic Form of 2‐Methylthio‐N6‐threonylcarbamoyladenosine (ms2ct6A)

“…Although chemical synthesis of RNA oligomers containing the t 6 A or ms 2 t 6 A units by the phosphoramidite approach using the ultra‐mild protected monomers is feasible, this approach is inappropriate for synthesis of RNAs bearing ms 2 ct 6 A because of the aforementioned instability of the hydantoin ring in even slightly alkaline media. Therefore, we decided to explore an alternative post‐synthetic methodology in which the ms 2 t 6 A→ms 2 ct 6 A cyclization is performed in the already assembled oligoribonucleotide containing the ms 2 t 6 A unit.…”

“…(Note: in a similar approach, used by Chheda and Hong for the synthesis of t 6 A , the “isocyanated” O ‐benzyl‐ l ‐threonine benzyl ester was reacted with 2′,3′,5′‐tri‐ O ‐acetyl‐adenosine and the product was obtained with a moderate 48 % yield . In a “mirror” reaction of the “isocyanated” adenosine with O ‐ tert ‐butyldimethylsilyl‐ l ‐threonine p ‐nitrophenylethyl ester the urethane nucleoside product was obtained in only 19 % yield ) afforded the TBDMS/TMSE derivative of ms 2 t 6 A in 50 % overall yield, compared with 40 % reported for the use of O ‐ tert ‐butyldimethylsilyl‐ l ‐threonine‐(2‐(4‐nitrophenyl)ethyl) ester intermediate .…”

Reliable Chemical Synthesis of Oligoribonucleotides (RNA) with 2′-O-[(Triisopropylsilyl)oxy]methyl(2′-O-tom)-Protected Phosphoramidites

“…In all such analyses, the products exhibited the correct mass, indicating the correct sequence composition and the absence of protecting groups. Several MS data of RNA sequences prepared from 2'-O-tom phosphoramidites are published [13] [18 ± 21] [28]. In Fig.…”

“…By having adapted our RNA chemistry to the established DNA chemistry, the 2'-O-tom-protected building blocks can be combined with all of these modifications and even with 2'-O-tbdmsprotected RNA phosphoramidites [28]. This work was supported by the ETH Z¸rich.…”