Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor

Wang, Sen; Liang, Liyuan; Tang, Jing; Cai, Yong; Zhao, Chuanqi; Fang, Shaoxi; Wang, Huabin; Weng, Ting; Wang, Liang; Wang, Deqiang

doi:10.1039/d0ra05083k

Cited by 10 publications

(4 citation statements)

References 52 publications

(55 reference statements)

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“…These G4 structures induced different blocking currents while translocation through CDM-Nanopore. Also, G4 structures would reversibly fold and melted dynamically in the confined nanopore environment. − In addition, the translocations of λ-DNA molecules demonstrate that the capture rate increased significantly after the addition of formamide into DNA translocation experiments with CDM-Nanopore, as shown in Figure S7.…”

Section: Resultsmentioning

confidence: 98%

“…The telomere sequences (5′-(AG 3 T 2 )4–3′) were chosen to assess the molecular detection performance of the proposed CDM-Nanopore with G4 structures. − According to the previous work of our group, we knew that the telomere sequence spontaneously formed a highly ordered secondary structure in the presence of some ions, called G4. − The G4 structures with a small size of 24 bp were used to verify the sensitivity of the fabricated CDM-Nanopore. According to the formula calculation with eq 1, the pore diameter we used for molecular detection was ∼3.8 nm.…”

Section: Resultsmentioning

confidence: 99%

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Cross Disjoint Mortise Confined Solid-State Nanopores for Single-Molecule Detection

Liu

Xie

Fang

et al. 2021

ACS Appl. Nano Mater.

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Solid-state nanopores have attracted widespread attention in the singlemolecule detection application. However, getting controllable nanopores with high sensitivity and robustness requires a revolutionary breakthrough in nanopore fabrication. As a convenient and low-cost nanopore fabrication method, the controlled dielectric breakdown technology can hardly control the position and number of nanopores. This work proposes a concept of cross disjoint mortise confined solid-state nanopore (CDM-Nanopore) fabricated using a focused gallium ion beam and controlled dielectric breakdown technologies. A confined domain formed by the two cross disjoint mortise structures localizes the position for nanopore fabrication with a controlled dielectric breakdown method. The ion translocation analyses and noise performance of CDM-Nanopore were experimentally demonstrated with excellent sensitivities for long-term molecular detection due to their robustness and low noise characteristics of cross disjoint mortise structures. The surface charges have a great effect on the capture rate for DNA translocation in the confined nanopore while adding the formamide into G-quadruplex translocation experimentally. Besides, the COMSOL simulation results verify that the CDM-Nanopore has the same electrical properties as the conventional nanopore with the same effective thickness. These provide insight into an understanding of DNA translocation in the CDM-Nanopore to enable the localized nanopore fabrication with the controlled dielectric breakdown technology. Our results can be used to expand the membrane nanopores to zero-depth nanopores for molecular sensing and DNA/RNA sequencing.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Cross Disjoint Mortise Confined Solid-State Nanopores for Single-Molecule Detection

Liu

Xie

Fang

et al. 2021

ACS Appl. Nano Mater.

Self Cite

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“…[ 73‐74 ] Lately, Wang and coworkers reported a label‐free approach for the detection of inter‐, intra‐, and tandem molecular G‐quadruplexes in different cation buffers with solid‐state nanopores, and used the method to monitor the folding process of single‐molecule G‐quadruplexes. [ 75 ] Li and coworkers used an α ‐HL nanopore to analyze the interaction between a G‐quadruplex structure formed by the human telomere sequence and a small molecule ligand, pyridostatin (PDS), revealing that PDS could promote the folding and stability of G‐quadruplex structures. [ 76 ] In addition, translocation studies demonstrated that PDS and K + have a synergistic effect on the stability of G‐quadruplex structures when simultaneously bound to one G‐quadruplex (Figure 11).…”

Section: Analysis Of Biomolecular Structuresmentioning

confidence: 99%

Recent Advances in Nanopore Sensing†

Cui

Zhuge

et al. 2021

Chin. J. Chem.

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Nanopore sensing is developing into a powerful label‐free approach to investigate the features of biomolecules at the single‐molecule level. When a charged molecule is captured within a nanopore, it modulates the ionic current, which can be recorded in real time to reveal the properties of the target molecule. To date, nanopores have been used to sense a variety of analytes, including DNA, RNA, proteins, enzymes, small molecules, cancer cells, and metal ions, and can also provide information on biomolecular structures. In this review, we highlight the progress made in nanopore sensing over the past five years (2016—2020), and provide an outlook on future developments and directions in the field

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“…As a powerful single-molecule platform, nanopore has played an important role in DNA sequencing, − sensing of various biomolecules, − detection of cancer cells, , evaluation of enzyme activity, − ion detection, − and analysis of DNA and RNA secondary structure. − In particular, α-hemolysin (α-HL) nanopores possess a natural advantage for capturing and analyzing folded structures because of their large nanocavity volume (∼40 nm 3 ) . To date, α-HL has successfully identified the characteristics of DNA secondary structures that are challenging to observe by bulk measurements. , For example, Gu et al studied the two-tetrad G-quadruplex adopted by the thrombin-binding aptamer captured within the α-HL vestibule and the unraveling of its kinetics upon binding with different cations .…”

Section: Introdutionmentioning

confidence: 99%

Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures

Cui

Zhou

et al. 2021

ACS Sens.

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i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3− 10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.

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Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor

Abstract: Nanopore detection of single-molecule G-quadruplexes.

Cited by 10 publications

References 52 publications

Cross Disjoint Mortise Confined Solid-State Nanopores for Single-Molecule Detection

Cross Disjoint Mortise Confined Solid-State Nanopores for Single-Molecule Detection

Recent Advances in Nanopore Sensing†

Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures

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