2'-DeoxypseudoUridine

2^'-DeoxypseudoUridine

2^'-DeoxypseudoUridine belongs to the C-glycosides that linked by C-C bond rather than usual C1-N1 bond found in uridine. Especially, glycosidic bond of 2^'-deoxypseudoUridine is that C-C bond between C5 of uracil and C1 of the deoxyribose sugar. 2^'-DeoxypseudoUridine can be served as one of the modified deoxyribonucleosides to participate in the synthesis of DNA oligonucleotides, resulting in modified DNA. It is well known that pseudoUridine is the most common RNA modification, and pseudoUridine has important roles for abundant non-coding RNAs (ncRNAs), including tRNA, rRNA and small nuclear RNA (snRNA), and the pseudouridylation of mRNA have been studied in many literatures. Given the biological importance of pseudoUridine, 2^'-deoxypseudoUridine modified DNA may present unexpected discoveries and applications.

Application of 2^'-DeoxypseudoUridine

2^'-deoxypseudoUridine can be used as the block buildings of DNA oligodeoxynucleotides to afford modified DNA. The incorporation of 2^'-deoxypseudoUridine into triplex DNA has been reported. Triplex DNA is a supramolecular structure that is formed by an antiparallel DNA duplex and a single-stranded triplex forming oligonucleotide (TFO). There are two binding modes of the DNA triplex, antiparallel and parallel. In antiparallel and parallel binding modes, TFO forms reverse-Hoogsteen and Hoogsteen base pairs with the DNA strand, and the orientation of TFO and the DNA strand is antiparallel and parallel, respectively. Under the background that triplex DNA formation is a powerful tool for gene targeting applications, it is necessary to overcome their sequence limitation that triplex DNA requires the sequences of DNA duplex must be homopurine-homopyrimidine, and TFO must be homopyrimidine. Various sets of artificial bases that recognize four canonical nucleobases in the DNA duplex have been developed. Study shown that 2^'-deoxypseudoUridine as the thymidine analogs that formed Watson-Crick base pairs with adenine. The triplex formation was successfully used in the inhibition of transcription of the DNA duplex modified by the modified bases, such as 2^'-deoxypseudoUridine.

Synthesis of 2^'-deoxypseudoUridine

It has been reported an efficient synthesis of 2^'-deoxypseudoUridine through the palladium-mediated coupling of a glycal with a nitrogen heterocycle with unprotected NH group. In addition, 1-Methyl-2^'-deoxypseudoUridine, as 2^'-deoxypseudoUridine derivative, which can be synthesized from glycal and 5-iodo-1-methyluracil by the palladium-catalyzed Heck reaction.

What^'s more, oligonucleotides incorporating modified bases can be synthesized on an automated DNA/RNA synthesizer. For the synthesis of oligodeoxynucleotide incorporating deoxypseudoUridine, the cyanoethyl group was removed before cleavage from solid support by washing with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in acetonitrile to avoid the cyanoethylation of the pseudoUridine base. After removal of the cyanoethyl group, the solid supports were treated with aqueous ammonia to afford oligodeoxynucleotide containing deoxypseudoUridine. And the oligonucleotides can be purified by reversed-phase HPLC.