Improved Sensitivity of Intramolecular Strand Displacement Based on Localization of Probes

Simulation-Guided Rational Design of DNA Walker-Based Theranostic Platform

Biomolecule-functionalized nanoparticles represent a type of promising biomaterials in biomedical applications owing to their excellent biocompatibility and versatility. DNA-based reactions on nanoparticles have enabled emerging applications including intelligent biosensors, drug delivery, and biomimetic devices. Among the reactions, strand hybridization is the critical step to control the sensitivity and specificity of biosensing, and the efficiency of drug delivery. However, a comprehensive understanding of DNA hybridization on nanoparticles is still lacking, which may differ from the process in homogeneous solutions. To address this limitation, coarse-grained model-based molecular dynamic simulation is harnessed to disclose the critical factors involved in intermolecular hybridization. Based on simulation guidance, DNA walker-based smart theranostic platform (DWTP) based on "on-particle" hybridization is developed, showing excellent consistency with simulation. DWTP is successfully applied for highly sensitive miRNA 21 detection and tumor-specific miRNA 21 imaging, driven by tumor-endogenous APE 1 enzyme. It enables the precise release of antisense oligonucleotide triggered by tumor-endogenous dual-switch miRNA 21 and APE 1, facilitating effective gene silencing therapy with high biosafety. The simulation of "on-particle" DNA hybridization has improved the corresponding biosensing performance and the release efficiency of therapeutic agents, representing a conceptually new approach for DNA-based device design.

A General Signal Amplifier of Self-Assembled DNA Micelles for Sensitive Quantification of Biomarkers

Owing to the excellent structural rigidity and programmable reaction sites, DNA nanostructures are more and more widely used, but they are limited by high cost, strict sequence requirements, and time-consuming preparation. Herein, a general signal amplifier based on a micelle-supported entropy-driven circuit (MEDC) was designed and prepared for sensitive quantification of biomarkers. By modifying a hydrophobic cholesterol molecule onto a hydrophilic DNA strand, the amphiphilic DNA strand was first prepared and then self-assembled into DNA micelles (DMs) driven by hydrophobic effects. The as-developed DM showed unique advantages of sequence-independence, easy preparation, and low cost. Subsequently, amplifier units DMF and DMTD were successfully fabricated by connecting fuel strands and three-strand duplexes (TDs) to DMs, respectively. Finally, the MEDC was triggered by microRNA-155 (miR-155), which herein acted as a model analyte, resulting in dynamic self-assembly of poly-DNA micelles (PDMs) and causing the recovery of cyanine 3 (Cy3) fluorescence as the DMTD dissociated. Benefiting from the "diffusion effect", the MEDC herein had a nearly 2.9-fold increase in sensitivity and a nearly 97-fold reduction in detection limit compared to conventional EDC. This amplifier exhibited excellent sensitivity of microRNAs, such as miR-155 detection in a dynamic range from 0.05 to 4 nM with a detection limit of 3.1 pM, and demonstrated outstanding selectivity with the distinguishing ability of a single-base mismatched sequence of microRNAs. Overall, the proposed strategy demonstrated that this sequence-independent DNA nanostructure improved the performance of traditional DNA probes and provided a versatile method for the development of DNA nanotechnology in biosensing.

Simulation-Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

DNA-based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse-grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided-LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation-guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL^-1 , respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.

Hybridization-based DNA biosensing with a limit of detection of 4 fM in 30 s using an electrohydrodynamic concentration module fabricated by grayscale lithography

Speeding up and enhancing the performances of nucleic acid biosensing technologies have remained drivers for innovation. Here, we optimize a fluorimetry-based technology for DNA detection based on the concentration of linear targets paired with probes. The concentration module consists of a microfluidic channel with the shape of a funnel in which we monitor a viscoelastic flow and a counter-electrophoretic force. We report that the technology performs better with a target longer than 100 nucleotides (nt) and a probe shorter than 30 nt. We also prove that the control of the funnel geometry in 2.5D using grayscale lithography enhances sensitivity by 100-fold in comparison to chips obtained by conventional photolithography. With these optimized settings, we demonstrate a limit of detection of 4 fM in 30 s and a detection range of more than five decades. This technology hence provides an excellent balance between sensitivity and time to result.

Engineering a high-efficient DNA amplifier for biosensing application based on perylene decorated Ag microflowers as novel electrochemiluminescence indicators

DNA-based amplifiers with high programmability and accurate molecular recognition ability have become a versatile platform for target amplification. However, the random diffusion of capture probes (CPs) in most DNA amplifiers limits the target recognition efficiency, affecting the limit of detection. Herein, a high-efficient DNA amplifier was developed by localizing the CPs consisted of the unique palindromic tails and target recognition sequences on Au nanoparticle modified magnetic beads (Au@MBs). In the presence of target K-ras gene, the CPs with high local concentration and orientation could capture the target efficiently to expose their palindromic tails, which could act as primers to trigger the polymerization for target recycling. More importantly, the polymerization products could involve in the next recycle and produce abundant mimic targets (MTs) continuously, thereby achieving the detection of trace K-ras gene. Meanwhile, a novel electrochemiluminescence (ECL) indicator of a thin-layer of perylene (Pe) molecules decorated Ag microflowers (Pe@Ag MFs) was obtained based on the reaction between the perylene cation radical (Pe^•+) and Ag atoms. The obtained Pe@Ag MFs exhibited desirable ECL performance because (i) a thin-layer of Pe molecules could reduce the inner filter effect and inactive emitters, (ii) the Ag MFs as coreaction accelerator could react with S₂O₈^2- to produce more SO₄^•- and shorten the distance between Pe^•- and SO₄^•- to significantly enhance the ECL intensity of Pe with less energy loss. This work paves the way for the development of efficient amplification strategy and offers a paradigm for the preparation of high-efficiency ECL indicators.

micro-RNA 21 detection with a limit of 2 pM in 1 min using a size-accordable concentration module operated by electrohydrodynamic actuation

We present a fluorimetry-based technology for micro-RNA-21 (miR-21) sensing based on the concentration of miR-molecular beacon (MB) complexes and flushing of unbound MB. This concentration module consists of a microfluidic channel with the shape of a funnel operated with electrohydrodynamic actuation. We report a limit of detection of 2 pM in less than 1 min for miR-21 alone, and then demonstrate that miR-21 levels, measured in fine needle biopsy samples, from patients with pancreatic cancer correlate with the reference technique of reverse-transcription polymerase chain reaction (RT-PCR). Altogether, this technology has promising clinical performances for the follow-up of patients with cancer.

DNA Transformations for Diagnosis and Therapy

Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.

Spatially Constrained DNA Nanomachines To Accelerate Kinetics in Response to External Input: Design and Bioanalysis

Cells take advantage of the spatial organization to accelerate the reaction kinetics of diverse components within a crowded intracellular environment. Inspired by this, we hereby designed a principle of spatial constraint to overcome limitations of response kinetics in DNAzyme-powered DNA nanomachines. First, we proposed the type-1 of spatially constrained DNA nanomachines (scDN-1) by co-localizing the aptamer probe and power unit (DNAzyme), allowing the DNA nanomachines to accomplish faster cyclic cleavage of DNAzyme as intramolecular reactions. To expand the scDN into the clinical practice, Type 2 spatially constrained DNA nanomachines (scDN-2) with constrained antibody probes were then constructed through Holliday junction assembly, which increased the effective local concentration to obtain the improved kinetics. With an accelerated response kinetics, this design principle allows DNA nanomachines to accomplish the response to tumor markers in real patients' samples within 30 min, significantly broadening the bioanalytical applications of DNA nanomachines to clinical practice.