DNA nanotechnology assisted nanopore-based analysis

Abstract

Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

DNA Manipulation and Single-Molecule Imaging

“…The four types of DNA bases were distinguished according to the blockade current, according to the specific interactions between the DNA-origami plate layers and the different DNA bases. Thus, the translocation speeds and detection of DNA in a nanopore can be controlled by the interactions between target biomolecules and the DNA scaffold [ 116 , 117 ]. By introducing various modifications (e.g., sensing elements, such as DNA, fluorophores, and FRET (see Section 3.1.3 ), and moving parts) at specific sites of DNA origami, DNA-origami nanopores have provided new insight as a powerful tool for single-molecule detection [ 116 , 117 ].…”

“…Thus, the translocation speeds and detection of DNA in a nanopore can be controlled by the interactions between target biomolecules and the DNA scaffold [116,117]. By introducing various modifications (e.g., sensing elements, such as DNA, fluorophores, and FRET (see Section 3.1.3), and moving parts) at specific sites of DNA origami, DNA-origami nanopores have provided new insight as a powerful tool for single-molecule detection [116,117]. In the near future, DNAorigami nanopores may be achieved in the development of variable and dynamic nanopore structures.…”

Recent Advances in Liposome-Based Molecular Robots

“…Nanopore technologies also offer a potential in designing chemical sensors for molecular robots [ 76 , 77 , 78 , 79 , 80 ]. In this technology, pore-forming transmembrane proteins are reconstituted into the lipid bilayer, and a target molecule passes through the nanopore.…”

Analytical and Structural Studies for the Investigation of Oxidative Stress in Guanine Oligonucleotides

“…This result was based on earlier studies that demonstrated the possible distinction of the abasic site versus G:C base pair positioned in the latch zone at the top of the α-HL vestibule [48][49][50]. Nanopore sequencing of oligonucleotides is a promising method, yet its robustness still needs improvement [51]. Endogenous level of OG in genomic DNA is relatively low and may not be easily detected by Sanger sequencing.…”

“…Nanopore sequencing of oligonucleotides is a promising method, yet its robustness still needs improvement [51]. Endogenous level of OG in genomic DNA is relatively low and may not be easily detected by Sanger sequencing.…”