miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

Abstract

Please cite this article as: Patutina OA, Bichenkova EV, Miroshnichenko SK, Mironova NL, Trivoluzzi LT, Burusco KK, Bryce RA, Vlassov VV, Zenkova MA, miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells, Biomaterials (2017Biomaterials ( ), doi: 10.1016Biomaterials ( / j.biomaterials.2017 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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

“…In fact, the binding affinity of the PNA incorporating guanidinium moiety toward single-stranded RNA (relevant to this study) was shown to be 14 times lower than that toward double-stranded RNA (Krishna et al, 2019). These results seemed to agree with our molecular modeling simulations, which demonstrated the possibility of hydrogen bonding interactions between the arginine sidechain with the N 7 and carbonyl O atoms of guanosine residues (Patutina et al, 2017). However, these interactions appeared to be ancillary, whereas the network of ionic interactions between arginine residues with backbone phosphate groups of RNA was shown to dominate such interactions.…”

“…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.…”

“…This synergistic combination of the individual properties of the two components yields a new catalytic entity, which is capable of catalyzing the cleavage of phosphodiester bonds in RNA under physiological conditions, with a rate enhancement factor of RNA cleavage reaching 10 8 in some cases, as compared to non-catalyzed reaction (Mironova et al, 2007). We have recently demonstrated that this type of biologically-active conjugates can selectively knock down highly-oncogenic miR-21 by irreversible cleavage and thereby down-regulate abnormal expression in lymphosarcoma cells, thus leading to a reduction in proliferative activity of tumor cells (Patutina et al, 2017(Patutina et al, , 2019.…”

“…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.…”

A Trisbenzimidazole Phosphoramidite Building Block Enables High-Yielding Syntheses of RNA-Cleaving Oligonucleotide Conjugates

“…Although in modern life sciences gapmers [2,14,15] and siRNAs [16] are the preferred tools for achieving the site-specific cleavage of RNA strands, there is still interest in synthetic ribonucleases and recent years have seen important progress in the field. Effective catalysts that are based on metal ions [17][18][19][20][21][22][23], guanidines or polyamines [24][25][26][27], peptide conjugates [28][29][30][31][32], and deoxyribozymes [33,34] have been described. Starting from heterocyclic guanidine analogs [35], we have investigated the conjugates of tris(2-aminobenzimidazoles) and different types of oligonucleotides, such as DNA [36], PNA [37,38], or DNA-LNA mixmers [39], which were shown to act as sequence-specific metal-free RNA cleavers.…”