Chemical Synthesis of LNA-2-thiouridine and Its Influence on Stability and Selectivity of Oligonucleotide Binding to RNA

Abstract

Hybridization to RNA is important for many applications, including antisense therapeutics, RNA interference, and microarray screening. Similar thermodynamic stabilities of A-U and G-U base pairs result in difficulties in selective binding of matched and mismatched RNA duplexes. Moreover, A-U pairs are weaker than G-C pairs so that binding is sometimes weak when many A-U pairs are present. It is known, however, that replacement of uridine with 2-thiouridine significantly improves binding and selectivity. To test for additional improvement of binding and of the specificity for binding A over G, LNA-2-thiouridine was synthesized for the first time and incorporated into many LNA-2-O-methylRNA/RNA duplexes. UV melting was used to measure the thermodynamic effect of replacing 2'-O-methyluridine with 2'-O-methyl-2-thiouridine or LNA-2-thiouridine. The 2-thiouridine usually enhances binding and selectivity. Selectivity is optimized when a single 2-thiouridine is placed at an internal position in a duplex.

Synthesis and Biological Evaluation of 4′‐C,3′‐O‐Propylene‐Linked Bicyclic Nucleosides

“…[18] dehyde and sodium hydroxide afforded the corresponding aldol, which was then trapped by reduction with sodium borohydride to yield the desired diol 23. [19] According to previously reported examples, the less hindered 5Јβ-hydroxy group of diol 23 was stereoselectively protected as a silyl ether in 64 % yield. [11b,17] The structure of 24 was confirmed by NOE correlation between the methylene bearing the free hydroxy function and the methyl of the isopropylidene group oriented toward the endo face of the bicyclic system (see Supporting Information).…”

“…Spectroscopic data of this compound were consistent with those reported by Kierzek et al, see ref. [19] . …”

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

“…Studies on thioxo- and azapyrimidine nucleosides are an inspiring subject of investigation due to their very special biochemical [3–7] and biophysical properties in comparison with the natural pyrimidine nucleosides in order to understand the impact of such modifications as monomers or constituents of oligonucleotides [8–14]. Thioxopyrimidine nucleosides as such, as well as building blocks of artificial oligonucleotides demonstrate promising antiviral activity in various experiments [15–22].…”

“…Regarding the chemical synthesis of this class of pyrimidine nucleosides various approaches were published (see, e.g., [8–11 14–16 23–24]; reviewed by Vorbrüggen and Ruh-Pohlenz [25]). On the contrary, only few publications are available on the enzymatic synthesis of these nucleosides.…”

Nucleotides and nucleic acids; oligo- and polynucleotides

“…121 2-Thiouridine-LNA has been synthesised and incorporated into oligomers where it was shown that as expected the 2-thioU-LNA:A base pair was more stable than the usual LNA-U:A base pair. 122 The 2'-amino analogues of LNA have been one of the most widely studied LNA analogues. The 2'-amino-b-L-LNA analogue (26) has been synthesised and when incorporated into a-DNA forms stable parallel stranded duplexes with RNA.…”