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Kinetics of Toehold-Mediated DNA Strand Displacement Depend on FeII4L4 Tetrahedron Concentration.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Nguyen, Bao-Nguyen T 
Nitschke, Jonathan R  ORCID logo  https://orcid.org/0000-0002-4060-5122

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 FeII4L4 tetrahedral cage. Our results show that the presence of a flexible phosphate group and a minimum toehold segment length are essential for FeII4L4 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.

Description

Keywords

DNA strand displacement, fluorescence, kinetics, metal−organic cage, molecular interaction

Journal Title

Nano Lett

Conference Name

Journal ISSN

1530-6984
1530-6992

Volume Title

21

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/M008258/1)
European Research Council (647144)
European Research Council (695009)
Engineering and Physical Sciences Research Council (EP/P027067/1)
EPSRC (EP/T031603/1)
George and Lilian Schiff Foundation Studentship; Winton Programme for the Physics of Sustainability; St. John’s Benefactors’ Scholarship