Pattern Recognition of microRNA Expression in Body Fluids using Nanopore Decoding at Sub-femtomolar Concentration

This paper describes nanopore decoding for microRNA (miRNA) expression patterns using DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type-specificity, and therefore simple strategies for miRNA-pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore measurement. With this system, we succeeded in distinguishing miRNA expression patterns in the plasma of BDC patients using a label-free method and in real-time. Moreover, our dgDNA-miRNAs complexes can be captured by the nanopore at ultralow concentration, such as 0.1 fM. Such nanopore decoding with dgDNAs could be applied as a simple and early diagnostic tool for cancer in the future.

Pattern Recognition of microRNA Expression in Body Fluids using Nanopore Decoding at Sub-femtomolar Concentration

This paper describes nanopore decoding for microRNA (miRNA) expression patterns using DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type-specificity, and therefore simple strategies for miRNA-pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore measurement. With this system, we succeeded in distinguishing miRNA expression patterns in the plasma of BDC patients using a label-free method and in real-time. Moreover, our dgDNA-miRNAs complexes can be captured by the nanopore at ultralow concentration, such as 0.1 fM. Such nanopore decoding with dgDNAs could be applied as a simple and early diagnostic tool for cancer in the future.

Isothermal digital detection of microRNAs using background-free molecular circuit

MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.

Isothermal digital detection of microRNA using background-free molecular circuit

MicroRNA, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design DNA circuit that converts, threshold, amplifies and report the presence of a specific microRNA, down to the femtomolar concentration. Using a leak-absorption mechanism, we were able to suppress non-specific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNA: by partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.

Fabrication of N-Type Silicon Nanowire Biosensor for Sub-10-Femtomolar Concentration of Immunoglobulin

A simple fabrication process of an n-type silicon nanowire (SiNW) biosensor for sub-10 femtomolar (fM) concentration immunoglobulin detection was presented in this work. The SiNWs with different widths of 80-190 nm were fabricated using electron beam lithography and reaction ion etching techniques. The electrical characteristics of SiNWs with various widths were measured. And it can be observed that thin SiNW has high resistance, which is in agreement with electrical resistance theory. Furthermore, the surface of the fabricated SiNW was functionalized by 3-aminopropyltriethoxysilane for making the biosensor device to detect the binding of immunoglobulin G (IgG) molecules. The responsivity of the biosensor was investigated by observing electrical performance in response due to IgG with various concentration from 6 fM to 600 nanomolar (nM). The resistance changing ratio based on the current voltage (I-V) characteristics was analyzed and it increased with increasing of the IgG concentration. As a result, it demonstrated that the n-type SiNW biosensor has the ability to detect the IgG molecules with low concentration of 6 fM.

T7 bacteriophage induced changes of gold nanoparticle morphology: biopolymer capped gold nanoparticles as versatile probes for sensitive plasmonic biosensors

The morphological changes of gold nanoparticles induced by T7 virus (bacteriophage) and the determination of its femtomolar concentration by a plasmonic method are presented.