Enhanced Binding Affinity of siRNA Overhang‐Binding Fluorescent Probes by Conjugation with Cationic Oligopeptides for Improved Analysis of the siRNA Delivery Process

Abstract

Carrier‐mediated delivery of small interfering RNAs (siRNAs) into the living cells is important for the realization of siRNA therapeutics that can silence target genes through RNA interference. We recently proposed a new strategy for analyzing the siRNA delivery process based on affinity labeling with a peptide nucleic acid (PNA)‐based fluorescent probe (PyAATO; Py: pyrene, A: adenine; TO: thiazole orange) capable of selectively binding to the overhanging structures of siRNAs. We have prepared new probes with improved binding affinity by conjugation with a cationic oligopeptide. The probe, carrying six lysine residues (PyAATO‐Lys6 (Lys6)), displayed a 39‐fold increase in affinity, compared with that of the parent probe containing no oligopeptides. Thermodynamic characterization revealed that enhanced affinity resulted from the favorable polyelectrolyte effect, due to the electrostatic interaction between lysine residues and phosphate anions of the RNA duplexes near the overhanging structure. Lys6 showed the improved imaging ability of the carrier‐mediated siRNA delivery process in living cells, in which 20 nm siRNA could be analyzed and was considered to show the minimal off‐target effects.

Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule

“…This structure, called the promoter, can be selectively recognized by RNA-dependent RNA polymerase (RdRp), which triggers both transcription to mRNA and replication into the complementary RNA. This promoter region has emerged as an important target for biochemical and therapeutic applications because the sequences are not involved in the gene variations related to pathogenesis and antiviral resistance. , Following our previous works on molecular probes targeting biologically important RNAs such as miRNA, − siRNA − and rRNA, − we are interested in the design of fluorogenic probes capable of binding to the IAV RNA promoter with a view toward the sensing of IAV RNA as well as the screening of novel anti-influenza drugs.…”

Self-Assembly of Nicotinic Acid-Conjugated Selenopeptides into Mesotubes

“…Peptide bioconjugates, a class of compounds that combine peptides with other biomolecules, provide a platform to develop new biomaterials. , Such conjugates specifically and uniquely improve the activity of biomolecules due to their biofunctionality, biodegradability, and biocompatibility. , The self-assembly of peptides with different biomolecules such as biotin, porphyrin, and nucleotides has been explored by many research groups. − In this regard, small peptide conjugates are very helpful to understand the role of different noncovalent interactions in supramolecular self-assemblies. ,,, For instance, aromatic π interactions have been utilized in nanotube fabrication of homodipeptide phenylalanine (F) and are exploited to morph wide nanostructures using different aromatic substituents. , The transformation of a fibrillar biotin nanostructure to a soft spherical morphology upon conjugation with di-tryptophan emphasizes the importance of heteroatoms in the π stacking interaction along with the hydrogen bonding and van der Waals interactions …”

Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes

“…Much attention has been paid to the design of fluorescent probes capable of selective binding to specific structures in DNAs and RNAs [1,2]. This class of fluorescent probes has been designed to bind abasic (apyrimidinic or apurinic; AP) sites [3][4][5][6][7][8], bulges [9,10], mismatched sites [11,12] and overhanging structures [13][14][15], by which the biological functions of these noncanonical base-pairs have been examined. Moreover, these fluorescent probes have great potential to be applied for the analysis of target DNAs and RNAs based on their binding-induced fluorescence signaling.…”