The synthesis of 2′-homouridine, its incorporation into a dinucleoside monophosphate and hydrolytic behaviour of the dimer

Double-Headed 2'-Deoxynucleotides That Hybridize to DNA and RNA Targets via Normal and Reverse Watson-Crick Base Pairs

Through the use of modified nucleotides, synthetic nucleic acids have found several fields of application within biotechnology and in the pharmaceutical industry. We have previously introduced nucleotides with an additional functional nucleobase linked to C2' of arabinonucleotides (B_X). These double-headed nucleotides fit neatly into DNA·DNA duplexes, where they can replace the corresponding natural dinucleotides and thus condense the molecular information. Here, we introduce a 2'-deoxy version of the B_X design with inversion of the C2' stereochemistry (^dSB_X) with the aim of obtaining improved RNA recognition. Specifically, ^dSB_X analogues with cytosine or isocytosine attached to C2' of 2'-deoxyuridine (^dSU_C and ^dSU_iC) were synthesized and evaluated in duplexes. Whereas the ^dSB_X design did not outperform the B_X design in terms of mimicking dinucleotides in nucleic acid duplexes, it was able to engage in reverse Watson-Crick pairing using its 2'-base. This was evident from the ability of the ^dSU_C cytosine to form stable mis-matching base pairs with opposite cytosines identified as hemiprotonated C·C⁺ pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearing ^dSU_iC monomer. Very stable duplexes were obtained with ^dSU_C/iC monomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the ^dSB_X design.

Synthesis of nucleosides with additional nucleobases

The syntheses of two nucleosides with additional nucleobases in the 2'-position are presented. The nucleosides have two- and one-carbon linkers to the additional nucleobase, respectively. The two nucleosides are synthesized from different strategies. The nucleoside with two carbons in the linker has been incorporated into oligonucleotides and showed stabilization of a tree-way junction.

Synthesis of functionalised nucleosides for incorporation into nucleic acid-based serine protease mimics

The synthesis of nucleosides modified with an extra imidazole, carboxyl and hydroxyl group is described. These nucleosides can be incorporated into an oligonucleotide duplex, thus generating a novel type of serine protease mimic.

Synthesis of 2‘-C-α-(Hydroxyalkyl) and 2‘-C-α-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA

Nucleoside analogues bearing 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkyl substitutes have numerous applications in RNA chemistry and biology. In particular, they provide a strategy to probe the interaction between the 2'-hydroxyl group of RNA and water. To incorporate these nucleoside analogues into oligonucleotides for studies of the group II intron (Gordon, P. M.; Fong, R.; Deb, S.; Li, N.-S.; Schwans, J. P.; Ye, J.-D.; Piccirilli, J. A. Chem. Biol. 2004, 11, 237), we synthesized six new phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-(hydroxyalkyl)cytidine (36: R = -(CH2)2OH; 38: R = -(CH2)3OH; 40: R = -(CH2)4OH) and 2'-deoxy-2'-C-alpha-alkylcytidine (37: R = -CH2CH3; 39: R = -(CH2)2CH3; 41: R = -(CH2)3CH3) from cytidine or uridine via 2'-C-alpha-allylation, followed by alkene and alcohol transformations. Phosphoramidites 36 and 37 were prepared from cytidine in overall yields of 14% (10 steps) and 7% (11 steps), respectively. Phosphoramidites 38 and 39 were prepared from uridine in overall yields of 30% (10 steps) and 13% (11 steps), respectively. Phosphoramidites 40 and 41 were synthesized from uridine in overall yields of 21% (13 steps) and 25% (14 steps), respectively.

Synthesis of the Phosphoramidite Derivatives of 2‘-Deoxy-2‘-C-α-methylcytidine and 2‘-Deoxy-2‘-C-α-hydroxymethylcytidine: Analogues for Chemical Dissection of RNA's 2‘-Hydroxyl Group

Oligonucleotides containing 2'-C-alpha-methyl and 2'-C-alpha-hydroxymethyl modifications enable strategies for delineation of the distinctive role fulfilled by the 2'-hydroxyl group in RNA structure and function. Synthetic routes to the phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-methylcytidine (14%, 15 steps) and 2'-deoxy-2'-C-alpha-hydroxymethylcytidine (19%, 10 steps) from methyl 3,5-di-O-(4-chlorobenzyl)-alpha-d-ribofuranoside are developed.

Synthesis and transcription studies on 5'-triphosphates derived from 2'-C-branched-uridines: 2'-homouridine-5'-triphosphate is a substrate for T7 RNA polymerase

The 5'-triphosphates of 2'-hydroxymethyluridine (2'-homouridine) and 2'-hydroxyethyluridine were prepared from the corresponding acetyl-protected nucleosides by initial phosphitylation with 2-chloro-5,6-benzo-1,2,3-dioxaphosphorin-4-one. 2'-Acetamidouridine 5'-triphosphate was prepared in an analogous fashion from uridine 2'-C-, 3'-O-gamma-butyrolactone, in which the 3'-hydroxyl group is internally protected as the lactone. Subsequent treatment with ammonia gave the required acetamido triphosphate. All three triphosphates were investigated as substrates for T7 RNA polymerase and a Y639F mutant of this enzyme. 2'-Homouridine triphosphate was found to be a substrate for the wild-type enzyme in the presence of manganese and was specifically incorporated into short RNA transcripts (20 and 21 nucleotides in length). The presence of the analogue within the transcripts was confirmed through its resistance to alkaline hydrolysis. Gel electrophoretic analysis also showed that 2'-homouridine could be multiply incorporated into a transcript with a length of 75 nucleotides. This is the first report of a 2'-deoxy-2'-alpha-C-branched nucleoside 5'-triphosphate acting as a substrate for T7 RNA polymerase. The 2'-hydroxyethyl- and 2'-acetamido -uridine triphosphates were not substrates for the enzymes.