High-Affinity RNA Targeting by Oligonucleotides Displaying Aromatic Stacking and Amino Groups in the Major Groove. Comparison of Triazoles and Phenyl Substituents

Abstract

Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.

Double-headed nucleotides introducing thymine nucleobases in the major groove of nucleic acid duplexes

“…This might indicate that the duplex structure has moved towards an A/B-intermediate type as seen before with consecutive incorporations of 5-modified pyrimidine nucleotides. 31,33 The modified DNA : RNA duplexes formed by ON11-14, on the other hand, are showing the same clear A/B-type structures as with the single modified duplexes formed by ON7-10. With the abasic site in the dsDNA, the picture is also the same as with ON7-10.…”

“…The residue was purified by flash chromatography (0-100% EtOAc in petroleum ether) to give the product 13 (337 mg, 89%) as a white foam. R f 0.32 (9 : 1 EtOAc/petroleum ether); 31 To a stirred solution of compound 10 (288 mg, 0.395 mmol) in DCM (10 mL) was added N,N-diisopropylethylamine (270 µL, 1.578 mmol) followed by 2-cyanoethyl N,N-diisopropylphosphoramidochloridite (264 µL, 1.183 mmol). The reaction mixture was stirred at room temperature for 2 h. The reaction was quenched by the addition of MeOH (0.5 mL) and then added EtOAc (20 mL).…”

“…The residue was purified by flash chromatography (0-100% EtOAc in petroleum ether) to give the product 15 (103 mg, 54%) as a white foam. R f 0.30 (9 : 1 EtOAc/petroleum ether); 31 …”

Strain Promoted Click Chemistry of 8-Azidopurine and 5-Azidopyrimidine Nucleosides and Nucleotides with Cyclooctynes and Applications to Living Cell Imaging

“…127 The excellent photophysical properties of the target compounds 99 -107 along with an intact hydrogen-bonding pattern make these analogues promising fluorescent probes of nucleic acids. The Nielsen group synthesized 5-modifed 2'-deoxyuridine nucleosides using copper catalyzed click chemistry 109,130 and later incorporated into oligonucleotides using a solid phase oligonucleotide synthesis to give analogues 114 and 115, Figure 11.…”

Azido- and Triazolyl-modified Nucleoside/tide Analogues: Chemistry, Fluorescent Properties, and Anticancer Activities

“…41,65,66 The AmdU 5'-triphosphate (AmdUTP, 20) was found to be a substrate for DNA polymerases and PCR amplification. 57 Moreover, the clickable triazole adducts of 5-AdU 67 were incorporated into oligodeoxynucleotides; but, an attempt to synthesize the peptide-siRNA covalent conjugates from AmdU-derived triazole was unsuccessful. 53 The 5-(1-azidovinyl)-2'-deoxyuridine (AvdU, 21) proved inhibitory to the replication of HSV-1 and VZV and became highly cytostatic against HSV-1 and HSV-2 TK gene transfected FM3A tumor cells; the cytostatic effect was enhanced by 5-fold after short exposure to UV irradiation at 254 nm.…”