Date of Award




Document Type

Master's Thesis

Degree Name

Master of Science (MS)


Department of Chemistry

Content Description

1 online resource (ii, vi, 60 pages) : illustrations (some color)

Dissertation/Thesis Chair

Jia Sheng

Committee Members

Ting Wang, Maksim Royzen


base pair, oligonucleotides, phosphoramidites, RNA modification, solid-phase synthesis, Nucleosides, Transfer RNA, Ribonucleosides, Uridine

Subject Categories



RNA plays an essential role in many biological processes by acting as both genetic information carriers, catalyst and regulator. Natural RNAs usually contain nucleoside analogs from the four common ribonucleosides. There are over 150 chemical modification have been discovered in natural RNA molecules. 5-cyanomethyl uridine is a native modification that has been discovered in total tRNAs from Haloarcula marismortui. This modification in the anticodon wobble position affects the codon recognition, and leads the mutant tRNA to bind not only to AUA but also to AUU and AUG. We synthesized 5-cyanomethyl uridine (cnm5U) and its derivative 5-cyanouridine (cn5U), which has the strong electron-withdrawing group (-CN) directly linking to the uracil. We incorporated them into RNA duplexes through the phosphoramidite building blocks and solid-phase synthesis. Furthermore, the base pairing stability and specificity studies of cnm5U and cn5U RNA duplexes indicated that cnm5U slightly decreases the RNA duplex stability but retains the base pairing preference. However, the cn5U dramatically decreases the base pairing stability between U-A and other non-canonical pairs. In addition, the cn5U shows the higher preference on G than A.

Included in

Chemistry Commons