Synthesis and properties of small interfering RNA duplexes carrying 5-ethyluridine residues

Abstract

Abstract. Oligoribonucleotides carrying 5-ethyluridine units were prepared using solidphase phosphoramidite chemistry. The introduction of the tert-butyldimethylsilyl group at the 2'-OH position proceeded in good yield and very high 2'-regioselectivity. RNA duplexes carrying 5-ethyluridine either at the sense or the guide strands display RNAi activity comparable to or slightly better than that of unmodified RNA duplexes. Gene suppression experiments using luciferase targets in SH-SY5Y cells show that the ethyl group is generally well accepted at all positions although a small decrease in RNA interference activity is observed when one 5-ethylU residue is incorporated in the 3' overhangs.

The synthesis and application of a diazirine-modified uridine analogue for investigating RNA–protein interactions

“…The impact of the modication on the duplex stability with both the complementary DNA and RNA strands seems to be negligible (DT m in the range of À1.4 to +0.5 C per modication; Table 2). A similar behavior has been observed for other C5-modied uridine analogues, [77][78][79] and therefore modi-cations located at the C5 position of pyrimidines are well-accommodated in the major groove and do not interfere with duplex formation and stability. 80,81…”

Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications

“…[68] For these reasons, we decided to study the intermediate sized analogue 5-ethyluridine (Figure 3). [73] The incorporation of 5-ethyluridine in siRNA was as well accepted as uridine and 5-methyluridine by the RNA interference machinery, however and unfortunately, 5-ethyluridine modification did not protect the oligonucleotides towards nuclease degradation. [73] A crucial structural parameter in nucleotides is the pucker of the furanose ring.…”

“…[73] The incorporation of 5-ethyluridine in siRNA was as well accepted as uridine and 5-methyluridine by the RNA interference machinery, however and unfortunately, 5-ethyluridine modification did not protect the oligonucleotides towards nuclease degradation. [73] A crucial structural parameter in nucleotides is the pucker of the furanose ring. In standard B-DNA, the pucker is 2'-endo or South (S) whereas A-DNA and RNA are characterized by 3'-endo or North (N) pucker of N-type conformation.…”

siRNA Modified with 2′‐Deoxy‐2′‐C‐methylpyrimidine Nucleosides

“…In view of these factors, different modifications in the 2′‐position of the ribose moiety have been evaluated: in particular, 2′‐ O ‐methyl, 2′‐deoxy‐2′‐F in the ribo and arabino configurations, 2′‐ O ‐aminoethyl, 2′‐aminopropyl, 2′‐guanidinoethyl, and 2′‐cyanoethyl derivatives . Other modified nucleosides assessed for siRNA performance included phosphorothioates, vinylphosphonates, LNA, and 5‐alkyl modifications, among others …”