Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

Abstract

The strand displacement competition assay is based on the dynamic equilibrium of the competitive hybridization of two oligonucleotides (A and B) to a third oligonucleotide (S). In the presence of an analyte that binds to a specific affinity-moiety conjugated to strand B, the equilibrium shifts, which can be detected by a shift in the fluorescence resonance energy transfer signal between dyes attached to the DNA strands. In the present study we have integrated an ATP aptamer in the strand B and demonstrated the optical detection of ATP. Furthermore we explore a new readout method using a split G-quadruplex DNAzyme for colorimetric readout of the detection of streptavidin by the naked eye. Finally, we integrate the whole G-quadruplex DNAzyme system in a single DNA strand and show that it is applicable to colorimetric detection.

Modular DNA strand-displacement controllers for directing material expansion

“…We next asked how we might couple the unlocking process to biomolecular circuits, allowing inputs other than nucleic acid signals or combinations of inputs to trigger material shape change. However, the concentrations of Key strand required to trigger swelling are higher than the 1 nM to 1 µM typical for the outputs of biomolecular circuits 20 , 32 – 35 , 37 , 38 , 42 – 48 .…”

“…1c ) 31 . We hypothesized that upstream DNA circuits such as amplifiers 32 – 34 , translators 35 , 36 , or logic circuits 37 , 38 could release DNA outputs that might direct this expansion. These circuits could in turn take different types or concentrations of chemical stimuli as inputs.…”

“…Crosslinks were designed to switch from an inactive to an active state via a toehold-mediated DNA strand-displacement process 39 , 40 . The strand that unlocks the crosslink is a short DNA strand of a form that can be the output of DNA strand-displacement logic 37 , 38 or sensing 35 , 36 , 41 circuits. We designed the locking strand to minimize leaky swelling of locked gels in an iterative process outlined in Supplementary Note 1 and Supplementary Figs.…”

“…A Cofactor strand can bind the ATP sensor complex to partially separate the two strands of the complex. The ATP-bound sensor can then displace the Catalyst from the Catalyst source complex 35 . This system of interactions ensures that Catalyst can be released at a significant rate only when ATP and the Cofactor are both present in solution.…”

Strand Displacement Amplification for Multiplex Detection of Nucleic Acids

“…Whilst several isothermal amplification platforms, such as nucleic acid sequence based amplification (NASBA) [1], strand displacement amplification (SDA) [2][3][4][5], loop-mediated isothermal amplification (LAMP) [6], rolling circle amplification (RCA) [7], recombinase polymerase amplification (RPA) [8], and Helicase dependent Isothermal DNA Amplification (HAD) [9,10] have been developed. These amplification platforms can achieve linear or exponential dsDNA accumulation, and some of which can be purchased as kits and integrated in portable devices [5], so no expensive instruments are needed, but there are still challenges in multiplexing, primer design, and stringency in experimental design.…”