DNA nanotechnology approaches for microRNA detection and diagnosis

Abstract

MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

In Silico and In Cell Analysis of Openable DNA Nanocages for miRNA Silencing

“…In line, a minimal DNA cage was designed for encapsulation of small RNAs and conditional release in the presence of selected trigger strands [26], and DNA nanotubes, carrying multiple DNA segments, were proposed for capturing overexpressed oncogenic miRNAs [9]. DNA-based nanostructures, mainly based on a tetrahedral geometry, were implemented for miRNA biosensing, using electrochemical, optical, and microscopic strategies as sensing approaches [17]. For example, tetrahedral DNS immobilized on the surface of a gold electrode have been proposed for electrochemical sensing of microRNAs, showing enhanced accessibility to the target when compared to linear single-stranded probes [27].…”

“…Tetrahedral DNA cages have been modified with the use of DNA oligonucleotides with pH-sensitive i-motif, to encapsulate an enzyme inside them [14]. DNA nanostructures have also been functionalized to selectively interact with intracellular miRNA, mainly to detect their concentration, using electrochemical current or fluorescence signals [15][16][17]. Here, taking advantage of our experience matured in the last years in the characterization of different types of fully covalently octahedral DNA nanocages [11,12,[18][19][20][21], including their receptor-mediated cell targeting and their efficacy in selective drug delivery [5,22,23], we propose a new nanostructure for a possible therapeutic use as an efficient captor of the oncogenic miR21.…”

How to Perform miRacles: A Step‐by‐Step microRNA Detection Protocol Using DNA Nanoswitches

“…DNA nanotechnology has provided an alternative route to building devices and machines with desired applications (Chandrasekaran, Anderson, Kizer, Halvorsen, & Wang, ) including biosensing (Chandrasekaran, Punnoose, et al., ). For microRNA detection, different groups have used DNA nanostructures in combination with nanoparticles (Qi et al., ; Qu et al., ), hybridization chain reaction (Ge et al., ), and transition metal dichalcogenide nanosheets (Xiao et al., ).…”

“…The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or the American Heart Association. Some parts of the text in the introduction and commentary sections are reproduced or adapted from references (Chandrasekaran, MacIsaac, et al, 2019, and(Chandrasekaran, Punnoose, et al, 2019), both of which are by the authors and are open access with permission for reuse.…”

l-DNA-Based Catalytic Hairpin Assembly Circuit

“…Owing to its simplicity, DNA strand-displacement reactions have been widely used for engineering molecular devices, including motors and walkers [4][5][6][7], reconfigurable DNA nanostructures [8,9], and logic circuits [10][11][12]. Importantly, such devices can be easily interfaced with regulatory nucleic acids (e.g., mRNAs and microRNAs) via WC base pairing [13,14], making them particularly well suited for applications in bioengineering and disease diagnosis.…”