Engineering self-contained DNA circuit for proximity recognition and localized signal amplification of target biomolecules

Abstract

Biomolecular interactions have important cellular implications, however, a simple method for the sensing of such proximal events is lacking in the current molecular toolbox. We designed a dynamic DNA circuit capable of recognizing targets in close proximity to initiate a pre-programmed signal transduction process resulting in localized signal amplification. The entire circuit was engineered to be self-contained, i.e. it can self-assemble onto individual target molecules autonomously and form localized signal with minimal cross-talk. α-thrombin was used as a model protein to evaluate the performance of the individual modules and the overall circuit for proximity interaction under physiologically relevant buffer condition. The circuit achieved good selectivity in presence of non-specific protein and interfering serum matrix and successfully detected for physiologically relevant α-thrombin concentration (50 nM–5 μM) in a single mixing step without any further washing. The formation of localized signal at the interaction site can be enhanced kinetically through the control of temperature and probe concentration. This work provides a basic general framework from which other circuit modules can be adapted for the sensing of other biomolecular or cellular interaction of interest.

Proximity-dependent initiation of hybridization chain reaction

“…An HCR-based technique has recently been described in a proof-of-concept paper for detection of α-thrombin in solution 12 . In their approach the authors used a protector oligonucleotide (P) to block the HCR-initiating oligonucleotide (I2) in an aptamer against α-thrombin.…”

Programming DNA‐Based Systems through Effective Molarity Enforced by Biomolecular Confinement

“…used the binding‐induced DNA strand displacement strategy in conjunction with a nanopore technology and performed amplification‐free detection of a protein biomarker enabled by the electrical signal generated by the output DNA strand . Through a rational design of the interacting DNA modules, it is possible to implement the binding‐induced strategy for constructing more complex DNA assemblies, such as three‐way DNA junctions, and for controlling synthetic DNA circuits with protein‐responsive activation (Figure a) . Colocalization‐enabled DNA networks can also be deployed in vitro and utilized as tools to study and image receptor proteins on the cell surface.…”

Applications of Catalytic Hairpin Assembly Reaction in Biosensing

“…In the past few decades, nucleic acids have been investigated in “dynamic DNA nanotechnology” instead of depending on the simple phosphate‐sugar backbone. Dynamic DNA nanotechnology includes the dynamic displacement and movement of nanostructures stimulated with the transitions of nucleic acids, such as DNA tweezers, DNA walkers, DNA dendrimers, and DNA circuits . Among them, toehold‐mediated strand displacement (TMSD), which is powered by the free energy of strand displacement, is a typical example.…”