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Issue 3, 2017
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Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers

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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.

Graphical abstract: Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers

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Publication details

The article was received on 06 Sep 2016, accepted on 07 Dec 2016 and first published on 08 Dec 2016


Article type: Edge Article
DOI: 10.1039/C6SC03993F
Citation: Chem. Sci., 2017,8, 2251-2256
  • Open access: Creative Commons BY license
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    Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers

    J. D. Munzar, A. Ng, M. Corrado and D. Juncker, Chem. Sci., 2017, 8, 2251
    DOI: 10.1039/C6SC03993F

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