Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 6 (2), 1225-1229

DNA Cross-Triggered Cascading Self-Amplification Artificial Biochemical Circuit

Affiliations

DNA Cross-Triggered Cascading Self-Amplification Artificial Biochemical Circuit

Ji Nie et al. Chem Sci.

Abstract

The construction of compact and robust artificial biochemical circuits based on nucleic acids can help researchers to understand the essential mechanisms of complex biological systems, and design sophisticated strategies for various requirements. In this study, a novel DNA cross-triggered cascading self-amplification artificial biochemical circuit was developed. Once triggered by trace amounts (as low as 2 amol) of either of two fully independent oligonucleotide factors under homogeneous isothermal conditions, the circuit simultaneously amplified both factors by 105-107 fold, which was proved using mass spectrometry. The compact and robust circuit was successfully used to construct a multi-input Boolean logic operation and a sensitive DNA biosensor based on the dual-amplification of both the target and reporter. The circuit showed great potential for signal gain in complicated molecular programming, and flexible control of nucleic acid nanomachines in biochemical network systems and nanotechnology.

Figures

Scheme 1
Scheme 1. The principle of the cross-triggered cascading self-amplification artificial biochemical circuit.
Fig. 1
Fig. 1. (A) The strand displacement amplification (SDA) circuit triggered by the oligonucleotide factor X. The factor Y is created in a simple linear amplification manner. (The same circuit with factor Y priming Y′X′ is not displayed.) The insert illustrates the fluorescence monitoring of the X/X′Y′ linear circuit triggered by 1 nM X (a) and the Y/Y′X′ circuit triggered by 1 nM Y (b). Line c represents the control experiment performed in the absence of X or Y. (B) and (D) are the real-time fluorescence curves of the cross-triggered cascading self-amplification circuit triggered by different concentrations of the factor X and Y, respectively ((a) 1 nM, (b) 100 pM, (c) 10 pM, (d) 1 pM, (e) 100 fM, (f) 0). (C) and (E) display the relationships between the POI values and the concentrations of factor X and Y, respectively. Experimental conditions: 100 nM X′Y′, 100 nM Y′X′, 0.4 U μL–1 Nt.BstNBI, and 0.05 U μL–1 Vent (exo-) polymerase. In the strand displacement experiment (A), the unrelated template is removed from the corresponding reaction system. Error bars: standard deviation (SD), n = 3.
Fig. 2
Fig. 2. (A) Mass spectrum of the oligonucleotides X and Y produced in the circuit. (B) and (C) display the amounts of X and Y produced in the circuit when triggered by different concentrations of X ((a) 10 pM, (b) 1 pM, (c) 100 fM). The initial concentration is not able to be measured by the mass spectrometer. For the triggering factor, the added amount is used as the initial concentration. For the generated factor Y in (C), it is assumed that the added trigger X can prime the relevant template and generate an equal amount of factor Y in the first cycle in split-second time. Error bars: SD, n = 3.
Fig. 3
Fig. 3. (A) The equivalent electronic circuit, the fluorescence intensity for different combinations of the three inputs and a truth table for the logic operation. Experimental conditions: 375 μM dNTPs, 100 nM X′Y′, 100 nM Y′X′, and 0.05 U μL–1 Vent (exo-) polymerase are treated as the work units. The three inputs are 0.4 U μL–1 Nt.BstNBI, 1 nM X, and 1 nM Y. The output signal is obtained at 30 min and is monitored by real-time fluorescence PCR. The threshold is set at 5000 a.u. (B) A schematic illustration and quantification of the performance of the dual-amplification (target XT and reporter YG4) biosensor via the cross-triggered cascading circuit. Error bars: SD, n = 3.

Similar articles

See all similar articles

Cited by 3 articles

References

    1. Sprinzak D., Elowitz M. B. Nature. 2005;438:443–448. - PubMed
    1. Isaacs F. J., Dwyer D. J., Collins J. J. Nat. Biotechnol. 2006;24:545–554. - PubMed
    1. Seeman N. C. Trends Biochem. Sci. 2005;30:119–125. - PMC - PubMed
    1. Bath J., Turberfield A. J. Nat. Nanotechnol. 2007;2:275–284. - PubMed
    1. Zhu J., Zhang L., Dong S., Wang E. ACS Nano. 2013;7:10211–10217. - PubMed
Feedback