Single‐molecule, hybridization‐based strategies for short nucleic acids detection and recognition with nanopores

Abstract

DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore-and hybridization-based DNA detection, and explores a range of state-ofthe-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.

Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis

“…In response to the pressing need for a deeper understanding of the intrinsic heterogeneity and internal dynamics of individual molecules, nanopores have emerged as highly sensitive and versatile analytical tools enabling label-free, high-throughput, and low-cost characterization of individual molecules. Nanopore sensors are extremely versatile single-molecule sensors employed for both qualitative and quantitative analysis, and representative applications include polynucleotide detection and gene sequencing [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ], polypeptide secondary structure recognition [ 15 , 16 , 17 , 18 ], protein structure analysis [ 19 , 20 , 21 , 22 , 23 ], small molecule and metal ion detection [ 24 , 25 , 26 , 27 , 28 ], polymer analysis [ 29 , 30 ], and virus and bacteria detection [ 31 , 32 , 33 , 34 , 35 , 36 , 37 ].…”

Highlights on the current state of proteomic detection and characterization with nanopore sensors

“…The second review, by Luchian and co-workers [22] focuses on the development of hybridization schemes for selective enhancement of short nucleic acids. This review is of particular interest for this special issue because it covers the role of peptide nucleic acids play in improving nucleic acid detection, a relatively new idea with considerable potential in nanopore sensing.…”

“…The review primarily focuses on using noise analysis as a powerful tool for investigating polymer–pore interactions, and compares these results to the direct resistive pulse methods more frequently encountered in the literature. The second review, by Luchian and co‐workers [22] focuses on the development of hybridization schemes for selective enhancement of short nucleic acids. This review is of particular interest for this special issue because it covers the role of peptide nucleic acids play in improving nucleic acid detection, a relatively new idea with considerable potential in nanopore sensing.…”

A Single‐Molecule Insight into the Ionic Strength‐dependent, Cationic Peptide Nucleic Acids‐Oligonucleotides Interactions

“…[2][3][4][5][6][7][8] PNAs high binding affinity and sequence selectivity toward DNAs, biochemical stability and facile functionalization, made them attractive for oligonucleotide sensing applications. [9] Despite the lack of electrostatic repulsion between the uncharged PNA backbone and negatively charged DNAs or RNAs, the ionic conditions proved relevant for PNA-dsDNA interactions, [10] and in a landmark paper, authors have presented compelling evidence that high concentrations of salt (> 1 M) led to a lowering of the PNA-DNA duplexes melting temperature and hence augmented structural destabilization. [11] Lack of PNAs intrinsic electric charge, rendering them ideally suited for hybridization with polynucleotides in physiologically low salts, proved counterproductive in other applications, due to PNA reduced solubility compared to native nucleic acids and poor cellular uptake.…”

“…PNAs constitute a unique class of polynucleotides binding ligands capable of interacting with their target sites efficiently and in a highly sequence‐specific manner, are less susceptible to biological degradation by nucleases, proteases, and peptidases, do not require high salt concentration for binding due to the absence of Coulombic repulsion interactions manifested between negatively charged DNA strands, and are useful in nucleic acid detection systems and as antisense molecules, and became an extremely useful research tool in many assays and diagnostics [2–8] . PNAs high binding affinity and sequence selectivity toward DNAs, biochemical stability and facile functionalization, made them attractive for oligonucleotide sensing applications [9] …”