TY - JOUR

T1 - Detection of the Enzymatic Cleavage of DNA through Supramolecular Chiral Induction to a Cationic Polythiophene

AU - Fossépré, Mathieu

AU - Trévisan, Marie E.

AU - Cyriaque, Valentine

AU - Wattiez, Ruddy

AU - Beljonne, David

AU - Richeter, Sébastien

AU - Clément, Sébastien

AU - Surin, Mathieu

N1 - Publisher Copyright: © 2019 American Chemical Society.

PY - 2019

Y1 - 2019

N2 - Water-soluble ?-conjugated polymers are increasingly envisioned in biosensors, in which their unique optical and electronic properties permit a highly sensitive detection of biomolecular targets. In particular, cationic ?-conjugated polymers are attractive for DNA sensing technologies, through the use of the fluorescence signals either in physiological solutions or in thin films. However, in the context of enzymatic activity assays, fluorescence-based methods require covalently labeling DNA with a dye or an antibody and are limited to short time scale due to dye photobleaching. In this frame, we report here a novel possible approach to probe the cleavage of DNA by a restriction enzyme, in continuous and without covalently labeled DNA substrate. This is achieved by exploiting unique chiroptical signals arising from the chiral induction of DNA to a poly[3-(6′-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] upon interaction. The cleavage of DNA by HpaI, an endonuclease enzyme, is monitored through circular dichroism (CD) signals in the spectral range where the polymer absorbs light, i.e., far away from the spectral ranges of both DNA and the enzyme. We compare the results to a conventional noncontinuous assay by polyacrylamide gel electrophoresis, and we demonstrate that induced CD signals are effective in probing the enzymatic activity. By means of molecular dynamics simulations and calculations of CD spectra, we bring molecular insights into the structure of DNA/polymer supramolecular complexes before and after the cleavage of DNA. We show that the cleavage of DNA modifies the dynamics and the organization of the polymer backbone induced by the DNA helix. Altogether, our results provide detailed spectroscopic and structural insights into the enzymatic cleavage of DNA in interaction with a ?-conjugated polymer, which could be helpful for developing chiroptical detection tools to monitor the catalytic activity in real time.

AB - Water-soluble ?-conjugated polymers are increasingly envisioned in biosensors, in which their unique optical and electronic properties permit a highly sensitive detection of biomolecular targets. In particular, cationic ?-conjugated polymers are attractive for DNA sensing technologies, through the use of the fluorescence signals either in physiological solutions or in thin films. However, in the context of enzymatic activity assays, fluorescence-based methods require covalently labeling DNA with a dye or an antibody and are limited to short time scale due to dye photobleaching. In this frame, we report here a novel possible approach to probe the cleavage of DNA by a restriction enzyme, in continuous and without covalently labeled DNA substrate. This is achieved by exploiting unique chiroptical signals arising from the chiral induction of DNA to a poly[3-(6′-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] upon interaction. The cleavage of DNA by HpaI, an endonuclease enzyme, is monitored through circular dichroism (CD) signals in the spectral range where the polymer absorbs light, i.e., far away from the spectral ranges of both DNA and the enzyme. We compare the results to a conventional noncontinuous assay by polyacrylamide gel electrophoresis, and we demonstrate that induced CD signals are effective in probing the enzymatic activity. By means of molecular dynamics simulations and calculations of CD spectra, we bring molecular insights into the structure of DNA/polymer supramolecular complexes before and after the cleavage of DNA. We show that the cleavage of DNA modifies the dynamics and the organization of the polymer backbone induced by the DNA helix. Altogether, our results provide detailed spectroscopic and structural insights into the enzymatic cleavage of DNA in interaction with a ?-conjugated polymer, which could be helpful for developing chiroptical detection tools to monitor the catalytic activity in real time.

KW - chiral induction

KW - circular dichroism

KW - DNA

KW - enzymatic assay

KW - molecular modeling

KW - polythiophene

U2 - 10.1021/acsabm.9b00123

DO - 10.1021/acsabm.9b00123

M3 - Journal article

AN - SCOPUS:85067973971

VL - 2

SP - 2125

EP - 2136

JO - ACS Applied Bio Materials

JF - ACS Applied Bio Materials

SN - 2576-6422

IS - 5

ER -