Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit

Jeffrey D. Munzar, Andy Ng and David Juncker ()
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Jeffrey D. Munzar: McGill University
Andy Ng: McGill University
David Juncker: McGill University

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: Abstract Duplexed aptamers (DAs) are ligand-responsive constructs engineered by hybridizing an aptamer with an aptamer-complementary element (ACE, e.g., a DNA oligonucleotide). Although DAs are commonly deployed, the binding dynamics of ternary ACE-aptamer–ligand systems remain underexplored, having been conventionally described by a conformational selection framework. Here we introduce aptamer-complementary element scanning (ACE-Scan) as a method to generate comprehensive hybridization, spontaneous off-rate, and induced fit ligand-binding landscapes for entire DA families. ACE-Scan reveals induced fit in DAs engineered from small molecule- and protein-binding DNA and RNA aptamers, as well as DAs engineered from the natural add riboswitch aptamer. To validate ACE-Scan, we engineer solution-phase ATP-specific DAs from 5 ACEs with varying spontaneous and induced fit off-rates, generating aptasensors with 8-fold differences in dynamic range consistent with ACE-Scan. This work demonstrates that ACE-Scan can readily map induced fit in DAs, empowering aptamers in biosensing, synthetic biology, and DNA nanomachines.

Date: 2018
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DOI: 10.1038/s41467-017-02556-3

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