Kinetics of Toehold-Mediated DNA Strand Displacement Depend on Fe<sup>II</sup><sub>4</sub>L<sub>4</sub> Tetrahedron Concentration.
basic_science · Level V
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- Record sourced from PubMed, PMID 33508195.
- Also identified by DOI 10.1021/acs.nanolett.0c04125 and PMC identifier 7886027.
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Abstract
The toehold-mediated strand displacement reaction (SDR) is a powerful enzyme-free tool for molecular manipulation, DNA computing, signal amplification, etc. However, precise modulation of SDR kinetics without changing the original design remains a significant challenge. We introduce a new means of modulating SDR kinetics using an external stimulus: a water-soluble Fe<sup>II</sup><sub>4</sub>L<sub>4</sub> tetrahedral cage. Our results show that the presence of a flexible phosphate group and a minimum toehold segment length are essential for Fe<sup>II</sup><sub>4</sub>L<sub>4</sub> binding to DNA. SDRs mediated by toehold ends in different lengths (3-5) were investigated as a function of cage concentration. Their reaction rates all first increased and then decreased as cage concentration increased. We infer that cage binding on the toehold end slows SDR, whereas the stabilization of intermediates that contain two overhangs accelerates SDR. The tetrahedral cage thus serves as a versatile tool for modulation of SDR kinetics.