Oligo(2′-O-methylribonucleotides) and their derivatives: III. 5′-Mono- and 5′-bispyrenyl derivatives of oligo(2′-O-methylribonucleotides) and their 3′-modified analogues: Synthesis and properties

Abstract

5'-Pyrenylmethylphosphoramidite and 5'-bispyrenylmethylphosphordiamidite derivatives of oligo(2'-O-methylribonucleotides) and their analogues with thymidine attached at their 3'-termini by a 3'-3'-phosphodiester internucleotide bond (inverted thymidine) were synthesized. The effect of the pyrene residue(s) on the thermal stability of duplexes of the modified oligonucleotides with RNA and DNA was studied. A possibility of detection of hybridization of 5'-mono- and 5'-bispyrenyl derivatives with RNA and DNA targets in solution was demonstrated according to the changes in fluorescence. 5'-Pyrenylmethylphosphoramidite derivatives of oligo(2'-O-methylribonucleotides) and their inverted analogues were shown to serve as sensitive probes for the detection of oligonucleotide substitutions in RNA and DNA by the method of thermal denaturation of the formed duplexes detected according to changes in their fluorescence.

Multipyrene Tandem Probes for Point Mutations Detection in DNA

“…5′-Phosphorylated oligomers contained 3′-“inverted” thymidine to increase their stability towards 3′-exonucleases. Coupling of pyrene residues to 5′- or 3′-terminal phosphate of oligo(2′-O-methylribonucleotides) was realized by analogy with [ 29 ], using greater excess of 1-pyrenylmethylamine to increase the yields of the conjugates. In case of monopyrene-labeled conjugates Ia–IVa synthesis the activation of terminal phosphate was followed by removal of activating reagents and nucleophilic catalyst excess.…”

“…5′-Phosphorylation of oligo(2′-O-methylribonucleotides) I, II was performed by analogy with [ 27 ]. The molar extinction coefficients of pyrene conjugates were calculated as the sum of the molar extinction coefficients of the corresponding oligonucleotides and that of one or two pyrene residues attached to the oligomer (24000 M −1 cm −1 at 260 nm) [ 28 , 29 ]. Synthesized conjugates were characterized by MALDI TOF MS spectra recorded with REFLEX III (Bruker Daltonics, Germany) mass spectrometer.…”

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

“…Krasheninina et al developed and studied three variants of pyrene excimer-forming 2′- O -methyl RNA probes, namely linear probes, dual probes, and MBs for the detection of RNA [ 82 , 83 , 84 , 85 ]. The probes were obtained via simple and efficient postsynthetic labeling method as described in [ 86 , 87 ].…”

“…The probes are 2′- O -methyl RNAs containing a 5′-bispyrenylmethylphosphorodiamidate group (bispyrene group) at the 5′-end ( 5′Nbpyr monomer) and a fluorescence quencher ( BHQ1 ) at the 3′-end ( Figure 11 a). The incorporation of a pyrene moiety was performed with the use of simple and efficient postsynthetic method of modification via the Mukaiyama reaction with nucleophilic catalysis according to [ 86 , 87 ].…”

Fluorescently labeled single-walled carbon nanotubes and their hybrids with oligonucleotides

“…5' Monopyrenyl oligonu cleotide conjugates Pyr22, PyrHEG22, Pyr17, and PyrHEG17 were synthesized according to [18] and purified by preparative polyacrylamide gel electro phoresis. The structure of the conjugates was con firmed by MALDI TOF mass spectroscopy and UV and fluorescence spectroscopy.…”