Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers

Chemical Science
Jeffrey D MunzarDavid Juncker

Abstract

Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1.8 to 0.7). To validate these unexpected findings, we developed a non-equilibrium surface-based assay that only signals induced fit binding, and corroborated the results from the solution-based assay. Our findings indicate that ACEs regulate ATP DA ligand binding dynamics, opening new avenues for the study and design of ligand-responsive nucleic acids.

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Citations

Dec 7, 2019·Computer Methods in Biomechanics and Biomedical Engineering·Haoyao CaoTinghui Zheng
Nov 9, 2019·Nature Communications·Brandon D WilsonH Tom Soh
Jul 28, 2020·Journal of Materials Chemistry. B, Materials for Biology and Medicine·Keitel Cervantes-SalgueroMatteo Palma
Feb 2, 2019·Chemical Society Reviews·Jeffrey D MunzarDavid Juncker
Jun 11, 2021·Analytical and Bioanalytical Chemistry·Annelies DillenJeroen Lammertyn
Jan 5, 2018·Analytical Chemistry·Benmei WeiAlexis Vallée-Bélisle

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Methods Mentioned

BETA
biosensing
biosensors
FRET
fluorescence assay
Fluorescence
biosensor

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