DNA Origami Sensor That Controls Gene Expression

Self-assembled nucleic acid structures such as DNA origami are examples of the integration of materials engineering and synthetic biology. These nanostructures are being used as nanomachines to perform various roles in drug delivery,¹ biology,² photonics,³ semiconductors,⁴ and molecular computation.^5,6 In this study, we designed and synthesized a self-assembled DNA complex that detects microRNA biomarkers (miR146, miR151 miR193 and miR212) that are specific to lung cancer and produces a fluorescence signal and a proof of concept RNA output. Two fluorophores (a donor and acceptor pair) were placed at the DNA origami with an optimum inter-distance of ~2 nm and FRET (Förster resonance energy transfer) was used to monitor the activity of the nanomachine (Fig. 1a). In the closed state, the donor and acceptor dyes are in close proximity, leading to a high FRET value (state 1, Fig. 1b). Addition of microRNA mimics (i.e. DNA strands with identical genetic content), triggers strand displacement of the DNA locks on the closed origami. As a result the DNA origami conformation switches to an open state and thus the donor and acceptor dyes become distant, leading to a low FRET value (state 0, fig 1b). Once opened by the aforementioned keys, transcription of a target DNA molecule showed multifold increase in the RNA production (Fig. 1b). This study successfully demonstrates that DNA origami can be programed to control transcription, an essential step in gene expression, providing a tool for controlling biomolecular reactions for nanomedicine, synthetic biology, biotechnology and molecular computating.

References

(1)   Zadegan et al., Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami, ACS Nano 2012.

(2)   Reif & LaBean, DNA Nanotechnology and its Biological Applications, in Bio-Inspired and Nanoscale Integrated Computing 2009.

(3)   Klein et al., Multi-Scaffold DNA Origami Nanoparticle Waveguides, Nano Letters 2013.

(4)   Zhirnov, et al., Nucleic Acid Memory, Nature Materials 2016.

(5)   Zadegan et al., Construction of a Fuzzy and Boolean Logic Gates Based on DNA, Small, 2015.

(6)   Yurke et al., A DNA-fuelled molecular machine made of DNA, Nature 2000.