title: C 3-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.
authors.affiliation: School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
authors.forename: Natasha
authors.initials: N
authors.lastname: McStay
authors.affiliation: School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
authors.forename: Zara
authors.initials: Z
authors.lastname: Molphy
authors.affiliation: School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
authors.forename: Alan
authors.initials: A
authors.lastname: Coughlan
authors.affiliation: School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland.
authors.forename: Attilio
authors.initials: A
authors.lastname: Cafolla
authors.affiliation: School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
authors.forename: Vickie
authors.initials: V
authors.lastname: McKee
authors.affiliation: Department of Chemistry, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia nicholas.gathergood@ttu.ee.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Gathergood
authors.affiliation: School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland andrew.kellett@dcu.ie.
authors.forename: Andrew
authors.initials: A
authors.lastname: Kellett
mesh_terms: D000701:Analgesics, Opioid / Q000138:chemical synthesis / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D046210:Microfluidic Analytical Techniques; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration
chemical_list: D000701:Analgesics, Opioid; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific