Oligonucleotide-Peptide Conjjugates for RNA Cleavage

RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions

“…Our recent work (Patutina et al, 2017(Patutina et al, , 2019Staroseletz, Williams et al, 2017;Williams et al, 2015) and earlier studies from other groups (Mironova et al, 2002;Mironova, Boutorine et al 2004;Mironova et al, 2006Mironova et al, , 2007Pyshnyi et al, 1997) demonstrated that the biological activity of this class of bioconjugates can only be achieved through chemical conjugation of the catalytic peptide with the oligonucleotide component. This suggested that the oligonucleotide component may induce an 'active' conformation of the peptide to make it catalytically active by some unclear molecular interactions between the oligonucleotide and peptide components.…”

“…Earlier, C1 and C2 conjugates were evaluated against the linear (e.g. non-structured) complementary oligoribonucleotide 5 0 -[P 32 ]-GAUUGAAAAUCCCC, which corresponded to a sequence from the anticodon arm of E.Coli tRNA Phe (Pyshnyi et al, 1997 and had some sequence similarity with RNA 1 studied in this research. In contrast to the data presented here (see Figure 2(A)) showing clear Pyr-A preference in cleavage of 5 0 -[ 32 P]-RNA-HIV-1, both conjugates demonstrated exclusive G-X base-specificity for the site-directed cleavage of this short, linear complementary target, mainly at G1-A2 and G5-A6 positions.…”

“…We have recently developed a new class of catalytic bioconjugates, as synthetic ribonucleases using amphipathic peptides, which only cleave RNA when conjugated to oligonucleotide recognition motifs (Mironova et al, 2002;Mironova, Boutorine et al, 2004;Mironova et al, 2006Mironova et al, , 2007Patutina et al, 2017Patutina et al, , 2019Pyshnyi et al, 1997;Staroseletz, Williams et al, 2017;Williams et al, 2015). These RNA-targeting synthetic nucleases are chemically-engineered by conjugation of short, catalytically-inactive peptides with oligonucleotide recognition motif components, which range from fully-through poorlyto non-complementary to the target RNA, in order to produce novel biologically-active molecules capable of recognizing and cleaving RNA sequences quantitatively.…”

“…Peptidyl-oligonucleotide conjugates (POCs) designed to date have the ability to cleave RNA at two different extremes: (i) either sequence-specifically (Mironova et al, 2002;Patutina et al, 2017Patutina et al, , 2019Pyshnyi et al, 1997;Staroseletz, Williams et al, 2017;Williams et al, 2015) by site-directed cleavage of the regions adjacent to the RNA hybridization sites, but in a non-catalytic manner; or (ii) non-specifically at non-complementary regions, which were located distantly from the major RNA binding region, but with a high level of catalytic turnover (Mironova, Boutorine et al, 2004;Mironova et al, 2006Mironova et al, , 2007. These data provided some experimental indications that peptidyl-oligonucleotide conjugates may interact differently with the complementary and non-complementary regions of RNA sequences.…”

Cleavage of yeast tRNAPhe with complementary oligonucleotide conjugated to a small ribonuclease mimic

“…Attempts have been made to design RNA cleaving oligonucleotide conjugates with small organic RNA cleaving groups. Cleaving of RNA was shown to occur in complexes of RNA with complementary oligonucleotides bearing an ethylenediamine residue [24–27], alternating amino acids with basic and hydrophobic side chains [28] and constructs with imidazole groups [10–12,29,30].…”