Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Small Oligonucleotides Detection in Three-Dimensional Polymer Network of DNA-PEG Hydrogels

Version 1 : Received: 1 June 2021 / Approved: 9 June 2021 / Online: 9 June 2021 (11:45:54 CEST)

How to cite: Mazzarotta, A.; Caputo, T.M.; Raiola, L.; Battista, E.; Netti, P.A.; Causa, F. Small Oligonucleotides Detection in Three-Dimensional Polymer Network of DNA-PEG Hydrogels. Preprints 2021, 2021060264 (doi: 10.20944/preprints202106.0264.v1). Mazzarotta, A.; Caputo, T.M.; Raiola, L.; Battista, E.; Netti, P.A.; Causa, F. Small Oligonucleotides Detection in Three-Dimensional Polymer Network of DNA-PEG Hydrogels. Preprints 2021, 2021060264 (doi: 10.20944/preprints202106.0264.v1).

Abstract

The control of the three-dimensional (3D) polymer network structure is important for permselective materials when specific biomolecules detection is needed. Here we investigate conditions to obtain a tailored hydrogel network that combine both molecular filtering and molecular capture capabilities for biosensing applications. Along this line short oligonucleotide detection in a displacement assay is set within PEGDA hydrogels synthetized by UV radical photopolymerization. To provide insights on the molecular filter capability, diffusion studies of several probes (sulforhodamine G and dextrans) with different hydrodynamic radii were carried out using NMR technique. Moreover, fluorometric analyses of hybridization of DNA oligonucleotides inside PEGDA-hydrogels shed light on the mechanisms of recognition in 3D, highlighting that mesh size and crowding effect greatly impact of hybridization mechanism onto polymer network. Finally, we found the best probe density and diffusion transport conditions to allow the specific oligonucleotide capture and detection inside PEGDA-hydrogels for oligonucleotide detection and the filtering out of higher molecular weight molecules.

Subject Areas

PEGDA Hydrogels; 3D recognition; diffusion; strand displacement assay.

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