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. 2013 Jan 14;49(4):397-9.
doi: 10.1039/c2cc36878a. Epub 2012 Nov 28.

Controlling the function of DNA nanostructures with specific trigger sequences

Stijn Deborggraeve  1 , Jian Yuan Dai, Yi Xiao, Hyongsok Tom Soh
Affiliations

Controlling the function of DNA nanostructures with specific trigger sequences

Stijn Deborggraeve et al. Chem Commun (Camb). .

Abstract

We report a hybridization-based switching mechanism with single-base specificity that can be readily integrated with functional DNA nanostructures. As an exemplar, we have developed a switchable DNAzyme (SDZ) that only becomes activated in the presence of a perfectly matched trigger sequence and operates effectively at room temperature.

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Figures

Fig. 1
Fig. 1
Proof-of-concept and dynamic range of the SDZ. (A) Fluorescence emission spectra following incubation of the SDZ molecule (15 nM) with 10 nM PM trigger, MM trigger or no trigger sequence. We incubated samples for three hours at room temperature with 400 nM substrate with excitation at λ = 590 nm. (B) Fluorescence signals with one sigma standard deviations from PM and MM trigger sequences at varying concentrations. Inset shows the initial linear increase in fluorescence observed at low concentrations of trigger DNA.
Fig. 2
Fig. 2
Time-course measurements of the fluorescence (A) and DF (B) with one sigma standard deviations of our SDZ over 5 hours, obtained with 15 nM SDZ, 10 nM PM or MM trigger sequence and 400 nM substrate.
Scheme 1
Scheme 1
The SDZ molecule consists of a triple-stem probe integrated with a 10-23 DNAzyme motif, paired with a fluorescence/quencher-modified DNA/RNA chimeric substrate. In its native state, the probe renders the DNAzyme (blue) inactive by incorporating it into a thermodynamically stable triple-stem structure. (Top) Only a perfectly matched trigger sequence (PM trigger, green) can disrupt this structure and activate the DNAzyme, which cleaves the substrate and results in increased fluorescence. (Bottom) In contrast, trigger DNAs containing a single nucleotide mismatch (MM trigger, orange) cannot open the native structure and the DNAzyme remains inactive.
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