C₃-symmetric opioid scaffolds are pH-responsive DNA condensation agents

Abstract

Herein we report the synthesis of tripodal C3-symmetric opioid scaffolds as high-affinity condensation agents of duplex DNA. Condensation was achieved on both supercoiled and canonical B-DNA structures and identified by agarose electrophoresis, viscosity, turbidity and atomic force microscopy (AFM) measurements. Structurally, the requirement of a tris-opioid scaffold for condensation is demonstrated as both di- (C2-symmetric) and mono-substituted (C1-symmetric) mesitylene-linked opioid derivatives poorly coordinate dsDNA. Condensation, observed by toroidal and globule AFM aggregation, arises from surface-binding ionic interactions between protonated, cationic, tertiary amine groups on the opioid skeleton and the phosphate nucleic acid backbone. Indeed, by converting the 6-hydroxyl group of C3-morphine (MC3) to methoxy substituents in C3-heterocodeine (HC3) and C3-oripavine (OC3) molecules, dsDNA compaction is retained thus negating the possibility of phosphate—hydroxyl surface-binding. Tripodal opioid condensation was identified as pH dependent and strongly influenced by ionic strength with further evidence of cationic amine-phosphate backbone coordination arising from thermal melting analysis and circular dichroism spectroscopy, with compaction also witnessed on synthetic dsDNA co-polymers poly[d(A-T)2] and poly[d(G-C)2]. On-chip microfluidic analysis of DNA condensed by C3-agents provided concentration-dependent protection (inhibition) to site-selective excision by type II restriction enzymes: BamHI, HindIII, SalI and EcoRI, but not to the endonuclease DNase I.

Efficient DNA Condensation by a C3‐Symmetric Codeine Scaffold

“…While internalization of DNA/Ligand particles with diameters of between 50 and 100 nm is a relatively rapid process, particles up to 500 nm have shown good cell membrane transport, but an upper size limit of ≥1 μm is generally accepted . In contrast to previously reported MC3 (which has a similar molecular structure to HC3 ), AFM studies conducted with plasmid DNA (pUC19) identified large DNA aggregates ≥1 μM with visible free plasmid in the surrounding surface area . CC3 , on the other hand, produces tightly packed particles that may offer improved transfection efficacy and protection from endonuclease activity.…”

“…This work focuses on the non‐analgesic use of opioids as a bio‐renewable resource capable of packaging DNA. While opioids are predominantly used for their potent analgesic properties, serving as one of the major drug classes within the pharmaceutical industry,, specific architectures were recently identified to have DNA binding properties . In that study, we identified morphine ( MC3 ), oripavine ( OC3 ) and heterocodeine ( HC3 ) C 3 ‐opioids could condense DNA.…”

“…While opioids are predominantly used for their potent analgesic properties, serving as one of the major drug classes within the pharmaceutical industry, [12,13] specific architectures were recently identified to have DNA binding properties. [14] In that study, we identified morphine (MC3), oripavine (OC3) and heterocodeine (HC3) C 3 -opioids could condense DNA. It was postulated that nucleic acid aggregation arises from ionic bridging between the cationic piperidine ring on the opioid skeleton and the negatively charged phosphate backbone.…”

“…[28] In contrast to previously reported MC3 (which has a similar molecular structure to HC3), AFM studies conducted with plasmid DNA (pUC19) identified large DNA aggregates � 1 μM with visible free plasmid in the surrounding surface area. [14] CC3, on the other hand, produces tightly packed particles that may offer improved transfection efficacy and protection from endonuclease activity.…”

A propeller‐like small molecule as a novel G‐quadruplex DNA binder: The study of fluorescent sensing property and preferential interactions with human telo21 structure

“…Interestingly, in recent years, some efforts have also been contributed to develop C 3 ‐symmetric molecules in areas of catalysis and materials science, metal ions sensing, and biomolecular interaction and stabilization . However, examples found from the literature of designing C 3 ‐symmetric molecules for biological or biomolecular‐related investigations such as targeting amino acids and DNA are very rare. In the present study, we attempted to design a propeller‐like (C 3 ‐symmetric as shown in Scheme ) small organic molecule for the study of molecular interaction and fluorescent detection of human telomere G‐quadruplex DNA (telo21) under physiological conditions because telo21 DNA has the unique structural features that are able to contribute biological significance in telomere maintenance, transcription regulation and anti‐tumour chemotherapy …”