Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

Abstract

Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A–U rich RNA duplex by a neomycin (Neo)–polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin–PCDA monomer (Neo–PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly(rA)–poly(rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo–PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly(rA)–poly(rU) is added into the system. Furthermore, poly(PCDA)/Neo–PCDA shows a clear specificity for poly(rA)–poly(rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo–PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.