Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

Cao, Chunhua; Ying, Yi‐Lun; Hu, Zheng‐Li; Liao, Dong-Fang; Tian, He; Long, Yi‐Tao

doi:10.1038/nnano.2016.66

Cited by 363 publications

(345 citation statements)

References 31 publications

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“…Similar to previous reports, Long’s group in 2016 21 (see the detailed protocol of 2017 23 ) determined that ARP could not capture long, single-stranded DNA molecules, but this conductance variation could discriminate the length of high-concentrations (1 μM) of short (2–10 nt) poly(dA) oligonucleotides at a single nucleotide resolution (Fig. 2a) under a wide range of pH conditions where the ARP remained stable.…”

Section: Direct Discrimination Of a T C And G Nucleobases As Well supporting

confidence: 83%

“…19,20 Compared to other reported biological nano-pores, ARP exhibits the advantage of stability over a broad pH range. 21,22 …”

Section: Arp Structurementioning

confidence: 99%

“…Using the total internal reflection fluorescence (TIRF) experiment (Fig. 2c), Long’s group identified that a 5′-AA-3′ dinucleotide with a 3′−6-carboxyfluorescein fluorophore tag 21 and a 5′-ACTG-3′ tetranucleotide with a 5′-hexachloro-fluorescein tag 24 can translocate from cis to trans through the ARP. Conversely, the 5′-ACTG-3′ tetranucleotide does not produce any current signals during cis or trans translocation through alpha-hemolysin, the most widely used nanopore system.…”

Section: Direct Discrimination Of a T C And G Nucleobases As Well mentioning

confidence: 99%

See 2 more Smart Citations

The aerolysin nanopore: from peptidomic to genomic applications

Wang

Tian

2018

Nanoscale

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The aerolysin pore (ARP) is a newly emerging nanopore that has been extensively used for peptide and protein sensing. Recently, several groups have explored the application of ARP in detecting genetic and epigenetic markers. This brief review summarizes the current applications of ARP, progressing from peptidomic to genomic detection; the recently reported site-directed mutagenesis of ARP; and new genomic DNA sensing approaches, and their advantages and disadvantages. This review will also discuss the perspectives and future applications of ARP for nucleic acid sequencing and biomolecule sensing.

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Section: Direct Discrimination Of a T C And G Nucleobases As Well supporting

confidence: 83%

“…19,20 Compared to other reported biological nano-pores, ARP exhibits the advantage of stability over a broad pH range. 21,22 …”

Section: Arp Structurementioning

confidence: 99%

Section: Direct Discrimination Of a T C And G Nucleobases As Well mentioning

confidence: 99%

See 1 more Smart Citation

The aerolysin nanopore: from peptidomic to genomic applications

Wang

Tian

2018

Nanoscale

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“…The technologies presented above show the future potential for the identification of epigenetic modification or single nucleotide polymorphism on DNA using the nanopore-nucleic acid interaction [52,53,61,62]. In addition, the nanopore coupled with a complementary DNA would facilitate the early detection of pathogenic DNA, shown in the detection of the anthrax-related DNA of Bacillus anthracis [63].…”

Section: Chemical and Biomolecular Sensingmentioning

confidence: 99%

Membrane protein-based biosensors

Misawa

Osaki

Takeuchi

2018

J. R. Soc. Interface.

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This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.

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“…It has been broadly investigated for various genetic, 19–23 epigenetic, 24–27 and proteomic 28–30 detection strategies. 31 Many excellent studies have demonstrated nanopore’s single-nucleotide sensitivity 32–34 and ability to detect single-nucleotide polymorphism.…”

mentioning

confidence: 99%

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

et al. 2018

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Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D drivermutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wildtype DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

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Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

Cited by 363 publications

References 31 publications

The aerolysin nanopore: from peptidomic to genomic applications

The aerolysin nanopore: from peptidomic to genomic applications

Membrane protein-based biosensors

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations

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