Energy Transfer from a Cationic Conjugated Polyelectrolyte to a DNA Photonic Wire: Toward Label-Free, Sequence-Specific DNA Sensing

Abstract

We demonstrate a label-free, sequence specific DNA sensor based on fluorescence resonant energy transfer (FRET) occurring between a cationic conjugated polyelectrolyte and a small intercalating dye, malachite green chloride. The sensor combines (1) conjugated polymer chain conformation changes induced by the binding with DNA, with the conjugated polymer wrapping/twisting around the DNA helical duplex and experiencing a 3-fold increase in its photoluminescence quantum yield and (2) FRET from the conjugated polymer to the intercalated DNA. Owing to its small size, the dye intercalates at maximal, one-to-one dye-to-base pair load, making the intercalated DNA a molecular photonic wire with dyes excitonically coupled and chiroptically active. Any sequence mismatch between probe and target DNA degrades the intercalated DNA photonic wire by decreasing its brightness, excitonic coupling, and chiroptical properties, and this provides a signal transduction method for the DNA sensor. Coupling of intercalated DNA with the conjugated polymer via FRET provides target signal amplification and increased sensitivity toward sequence mismatch, with the FRET efficiency decreasing with added DNA sequence mismatch.

Self-assembly and hybridization mechanisms of DNA with cationic polythiophene

“…9 The optical signature of the binding process of CPT with DNA, such as fluorescence amplification, has been exploited for the determination of very low concentrations of DNA, [10][11][12][13] for protein identification using CPT/DNA aptamer complexes, 14 and for the fabrication of new DNA biochips. 2,5,11,12,[15][16][17][18][19] The principle of these hybridization biosensors, as introduced by Heeger, Bazan, Leclerc and their colleagues, is that the CPE fluorescence is quenched when the polymer chain is bound to a singlestranded DNA, while the fluorescence is recovered or amplified only in the presence of the complementary strand, which can bear a fluorophore dye to exploit Fluorescence Resonance Energy Transfer (FRET). 2,5,11,12,[15][16][17][18][19] The principle of these hybridization biosensors, as introduced by Heeger, Bazan, Leclerc and their colleagues, is that the CPE fluorescence is quenched when the polymer chain is bound to a singlestranded DNA, while the fluorescence is recovered or amplified only in the presence of the complementary strand, which can bear a fluorophore dye to exploit Fluorescence Resonance Energy Transfer (FRET).…”

Tailoring Conformation-Induced Chromism of Polythiophene Copolymers for Nucleic Acid Assay at Resource Limited Settings

“…28 Another FRET-based strategy utilizing cationic poly(phenylenevinylene) and malachite green (as intercalating dye) was found to be sensitive between 10 and 1000 nM; however, assay did not provide naked eye detection. 29 Naked eye detection of nucleic acids by using mixtures of CPEs and gold nanoparticles were successfully presented pending validation with clinical samples. 30 Electrochemical approaches on quantitative analysis of miRNA have claimed subnanomolar detection sensitivities.…”

Labeling-free fluorescent detection of DNA hybridization through FRET from pyrene excimer to DNA intercalator SYBR green I

“…Homogeneous DNA hybridization assays based on fluorescence resonance energy transfer (FRET) between energy-transfer chromophore pairs are attractive because of their simplicity of operation and use of standard optical equipment . Recently, the FRET strategy employing water-soluble cationic conjugated polymers (CCP) with a large number of chromophoric repeat units, which enable the transfer of excitation energy along the whole backbone of the CCP to the reported chromophore via FRET, has been paid more attention for DNA detection with high sensitivity and selectivity (Feng et al, 2011;Jiang et al, 2009;Liu et al, 2014;Xu et al, 2005Xu et al, , 2010. Bazan and co-workers designed a three-color DNA detection assay with CCP and a fluorophorelabeled peptide nucleic acid strand through efficient FRET from CCP to the fluorophore (Liu and Bazan, 2004).…”