Acridine−N Peptide Conjugates Display Enhanced Affinity and Specificity for boxB RNA Targets

Abstract

Arginine-rich peptides and small-molecule intercalating agents utilize distinct molecular mechanisms for RNA recognition. Here, we combined these distinct binding modules in an effort to create conjugate ligands with enhanced affinity and specificity using the bacteriophage λ N peptide/boxB interaction as a model system. We first designed and synthesized a series of peptide-acridine conjugates using portions of the RNA-binding domain of N protein (11- and 22- residue peptide segments), then compared the binding affinity, specificity, salt dependence, and structural properties of the RNA-peptide and RNA-peptide-acridine conjugate complexes using steady-state fluorescence, CD spectroscopy, NMR, and native gel mobility shift assays (GMSA). These analyses revealed that the full-length peptide-acridine conjugate displayed substantially improved RNA-binding affinity (~80-fold; Kd ~ 15 pM) relative to the peptide alone (Kd ~ 1.2 nM). In accordance, we also observed specificity enhancement (~25-fold) as determined by comparing binding of the best conjugate to a cognate λ boxB RNA with that to a noncognate P22 RNA hairpin (80-fold vs. 3.2-fold enhancement). Furthermore, the observed binding enhancement was unique to the full length conjugate with a flexible linker, implying that the structural context of acridine presentation was critical. Taken together, our observations support the idea that peptide- and intercalation-based binding can be combined to create a new class of high-affinity, high-specificity RNA-binding ligands.

‘Acridines’ as New Horizons in Antifungal Treatment

“…Conjugates of acridines or acridones in antimicrobial therapy have not been so widely analyzed, although their highly valuable mode of action was discovered. A significant improvement over DNA intercalating acridine binders was demonstrated for peptide derivatives with amino acid sequences localized at positions 4 and 9 of the tricyclic ring [51,52]. PACs were recognized to selectively bind RNA, according to the mechanism named "threading intercalation."…”

Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors

“…5b presents the computed signal when N protein is recognized by a 6 nm thick bio-functionalization layer (see the Supplementary Information †) over the surface of an In 2 O 3 based nano-wire (Table 2S †) for five different binding orientations. In fact the experimentally employed bio-functionalization layer was tailored to capture the RNA sensing fragment of N protein, 33 but it is not known if N protein would approach the capture agent from the top or the side. As previously noted, different approaching directions give different signals.…”

Synthesis of new 1H‐spiro[acridine‐9,3′‐indoline]‐1,2′(2H,10H)‐dione derivatives using aqueous ethanol as a reaction medium

“…During the recent years, acridine‐based compounds attract major interest because of their distinct properties and applications in the field of biology and industry [1,2]. The key features of the acridine derivatives are their ability for DNA binding [3], RNA binding [4], and human topoisomerase inhibitor activities [5] Moreover, acridine derivatives play a significant role as bioactive compounds such as antiherpes [6], antibacterial [7], antifungal [8], antiviral [9], anticancer [10], anti‐HIV [11], antitumor [12], Alzheimer's diseases [13], and antiproliferative [14] agents. In addition to the above potential properties, acridine moieties are found to have wide applications in organic light emitting diodes (OLEDs) [15], thermal activated delayed fluorescence (TADF) [16], chemiluminescence [17], radiotherapy (RT) [18], dyes‐sensitized photovoltaics [19], and organic semiconductors [20].…”

“…During the recent years, acridine-based compounds attract major interest because of their distinct properties and applications in the field of biology and industry [1,2]. The key features of the acridine derivatives are their ability for DNA binding [3], RNA binding [4], and human topoisomerase inhibitor activities [5] Moreover, acridine derivatives play a significant role as bioactive compounds such as antiherpes [6], antibacterial [7], antifungal [8], antiviral [9], anticancer [10], anti-HIV [11], antitumor [12], Alzheimer's diseases [13], and antiproliferative [14] agents.…”