DNA Strand Displacement Driven by Host–Guest Interactions

Abstract

Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications�from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host−guest-driven toeholdmediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.

Challenges and Opportunities of Functionalized Cucurbiturils for Biomedical Applications

“…Finally, Jayawickramarajah and co-workers used the CB [7] •ADA host−guest pair as a surrogate to replace the regularly used base pair for DNA strand displacement, modulating enzyme activity and layered reactions detecting specific microRNA. 91 This method is a positive alternative to the traditional base-pair-driven, toehold-mediated strand displacement, enhancing the diversity of the toolbox for the manipulation of the function of dynamic DNA machines. Recently, Wang and co-workers employed supramolecular systems based on hyaluronic acid (HA)-modified CB [7] (CB [7]-HA, Figure 15) and TPP-PEG-ADA (TPP: triphenylphosphonium, a well-known moiety targeting mitochondria) 92 to get some control on the biological properties of mitochondria (Figure 16).…”

The pivotal role of non-covalent interactions in single-molecule charge transport

“…It can also provide a reaction chamber by maintaining space proximity between two individual molecules, and give information about reaction kinetics. [127][128][129][130] By this means, Yuan et al showed that single-molecule junctions formed in an STM-BJ setup could provide a testbed to detect temporal signals from reactants in ultra-low concentrations, which are invisible to methods such as mass spectroscopy. 131 They used hostguest assembly to study the conductance change during complexation of 1,2-bis(4-pyridinyl)ethylene (BPE) monomer and CB [8], and finally the dimerization product to BPE2@CB [8] upon UV irradiation.…”

Dual-Signal Integrated Aptasensor for Microcystin-LR Detection via In Situ Generation of Silver Nanoclusters Induced by Circular DNA Strand Displacement Reactions

“…The DNA strand displacement reaction (SDR) is a procedure whereby DNA strands undergo structural changes based on binding force differences for exporting new dsDNA. , If the SDR is performed repeatedly, it can constitute a circular DNA SDR (CD-SDR). , CD-SDR is an entropy-initiated self-assembly reaction that offers the merits of dynamics, manipulability, high controllability, and mild reaction conditions, opening the door to the design of novel sensing strategies. – Therefore, the present study envisages the use of the target as a primer to complete trace detection of the target by means of the signal accumulation of CD-SDR.…”