Sequence-dependent hybridizability of DNA-monoconjugated nanoparticles: Kinetic complexity unveiled by a dimerization assay

doi:10.52396/JUST-2021-0195

Abstract

Abstract: Understanding DNA hybridization kinetics is highly important for nucleic acid detections, genomic biotechniques, and DNA nanotechnology. DNA-conjugated nanomaterials offer versatile functionalities for DNA-programmable nanoassembly with superfine controls toward bioanalytical and nanotechnological applications. Although small molecule end-tagging does not incur much attenuation of DNA’s hybridizability, nanoparticle-conjugation greatly suppresses the hybridization kinetics of DNA strands. The impeded hybridization not only decreases the efficiency in building complicated nanostructures, but also causes difficulty in realizing rapidly responsive sensors and nanomotors. With monovalent DNA-nanoparticle conjugates as an ideal system, this work aims to unveil the kinetic complexity of hybridization-driven dimeric assembly assayed by agarose gel electrophoresis. Our results point out a coexistence of different factors that can affect the hybridization kinetics of DNA-conjugated nanoparticles, including: the rigidity of a DNA spacer proximal to the nanoparticle surface; the base-stacking between the spacer and a hybridized domain; the inherent base-sequence-dependent DNA hybridizability; and the spatially confined movement of the hybridization sequences. The dimeric hybridization assay offers a reliable platform for kinetic evaluation of DNA-conjugated nanoparticles to enable structurally complicated and rapidly functioning analytical devices and bio-labelling nanoprobes.

Key words: electrophoresis, DNA, hybridization kinetics, nanoparticles, monoconjugates

CLC Number:

Q523
TB383.1

WANG Jiannan, ZHENG Yuanqin, LI Yulin, DENG Zhaoxiang. Sequence-dependent hybridizability of DNA-monoconjugated nanoparticles: Kinetic complexity unveiled by a dimerization assay[J]. Journal of University of Science and Technology of China, 2021, 51(11): 802-812.

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