A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA

Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (s...

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Bibliographic Details
Published in:Chemical science (Cambridge) 2019-01, Vol.1 (2), p.354-358
Main Authors: Hu, Zheng-Li, Li, Meng-Yin, Liu, Shao-Chuang, Ying, Yi-Lun, Long, Yi-Tao
Format: Article
Language:English
Subjects:
Deoxyribonucleic acid
DNA
Histograms
Lithium chloride
Lithium ions
Molecular dynamics
Oligonucleotides
Porosity
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Summary:Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA ( i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li + and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics. By developing lithium-ion-active aerolysin, for the first time we have achieved aerolysin detection of single-stranded DNA longer than 100 nt.
ISSN:2041-6520
2041-6539
DOI:10.1039/c8sc03927e