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1.
Bingyuan Guo Yingying Sheng Dr. Ke Zhou Prof. Quansheng Liu Dr. Lei Liu Prof. Hai‐Chen Wu 《Angewandte Chemie (International ed. in English)》2018,57(14):3602-3606
A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex‐forming molecular beacon and a stem‐forming DNA component that is modified with a host–guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α‐hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point‐of‐care diagnostics with a portable nanopore kit in the future. 相似文献
2.
Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore 下载免费PDF全文
Graphene nanopore has been promising the ultra‐high resolution for DNA sequencing due to the atomic thickness and excellent electronic properties of the graphene monolayer. The dynamical translocation phenomena and/or behaviors underneath the blocked ionic current, however, have not been well unveiled to date for the translocation of DNA electrophoretically through a graphene nanopore. In this report, the assessment on the sensitivity of ionic current to instantaneous statuses of DNA in a 2.4 nm graphene nanopore was carried out based on the all‐atom molecular dynamics simulations. By filtering out the thermal noise of ionic current, the instantaneous conformational variations of DNA in a graphene nanopore have been unveiled from the fluctuations of ionic current, because of the spatial blockage effect of DNA against ionic current. Interestingly, the neighborhood effect of DNA against ionic current was also observed within a distance of 1.5 nm nearby the graphene nanopore, suggesting the further precise control for DNA translocation through a graphene nanopore in gene sequencing. Moreover, the sensitivity of the blocked ionic current toward the instantaneous conformations of DNA in a graphene nanopore demonstrates the great potential of graphene nanopores in the dynamics analysis of single molecules. 相似文献
3.
Xiu‐Hong Cai Shuo‐Hui Cao Sheng‐Lin Cai Yuan‐Yi Wu Muhammad Ajmal Yao‐Qun Li 《Electrophoresis》2019,40(16-17):2098-2103
Herein, we report the ultrasensitive DNA detection through designing an elegant nanopore biosensor as the first case to realize the reversal of current rectification direction for sensing. Attributed to the unique asymmetric structure, the glass conical nanopore exhibits the sensitive response to the surface charge, which can be facilely monitored by ion current rectification curves. In our design, an enzymatic cleavage reaction was employed to alter the surface charge of the nanopore for DNA sensing. The measured ion current rectification was strongly responsive to DNA concentrations, even reaching to the reversed status from the negative ratio (?6.5) to the positive ratio (+16.1). The detectable concentration for DNA was as low as 0.1 fM. This is an ultrasensitive and label‐free DNA sensing approach, based on the rectification direction‐reversed amplification in a single glass conical nanopore. 相似文献
4.
A Universal Strategy for Aptamer‐Based Nanopore Sensing through Host–Guest Interactions inside α‐Hemolysin 下载免费PDF全文
Ting Li Dr. Lei Liu Yuru Li Jiani Xie Prof. Dr. Hai‐Chen Wu 《Angewandte Chemie (International ed. in English)》2015,54(26):7568-7571
Nanopore emerged as a powerful single‐molecule technique over the past two decades, and has shown applications in the stochastic sensing and biophysical studies of individual molecules. Here, we report a versatile strategy for nanopore sensing by employing the combination of aptamers and host–guest interactions. An aptamer is first hybridized with a DNA probe which is modified with a ferrocene?cucurbit[7]uril complex. The presence of analytes causes the aptamer–probe duplex to unwind and release the DNA probe which can quantitatively produce signature current events when translocated through an α‐hemolysin nanopore. The integrated use of magnetic beads can further lower the detection limit by approximately two to three orders of magnitude. Because aptamers have shown robust binding affinities with a wide variety of target molecules, our proposed strategy should be universally applicable for sensing different types of analytes with nanopore sensors. 相似文献
5.
As a novel analytical method, nanopore sensing is widely applied in many fields such as nucleic acids sequencing, protein/peptides analysis, detection of metal ions and biomacromolecules including virus, bacteria, etc. With the growing public concerns on dietary safety and public security, there has been a greater demand on the detection of toxic molecules. With high sensitivity and selectivity, nanopore sensing is considered as a more powerful assay, and has been reported in many research articles. Accordingly, this paper surveys the application of nanopore sensing in detection of toxic molecules. 相似文献
6.
Nanopore sensor has been developed as a promising technology for DNA sequencing at the single‐base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G‐quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20‐nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105‐nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore‐based DNA sequencing at single‐base level. 相似文献
7.
Nanopore techniques are experiencing a gallop since it walked out the notebook and show its charm on the science arena. The nanoscale pore offers a single-molecule resolution with a label-free and high-selective manner for the research of molecular structures, molecular dynamics, single-molecule reactions and for a variety of applications in biophysics and bionanotechnology.In this review, we introduce the construction of three types of nanopore platforms along with the latest progress in DNA sensing,structure and dynamics analysis of peptides/proteins, and the detection of redox reactions with new sensing mechanisms. Then,we depict nanopore data processing methods which provide an insight of data mining under the background of big data. We could fully expect the great impact of nanopore techniques on not only for DNA sequencing and sensing applications, but also in protein sequencing and clinical diagnostics. 相似文献
8.
The field of nanopore sensing at the single‐molecular level is in a “boom” period. Such nanopores, which are either composed of biological materials or are fabricated from solid‐state substrates, offer a unique confined space that is compatible with the single‐molecular scale. Under the influence of an electrical field, such single‐biomolecular interfaces can read single‐molecular information and, if appropriately fine‐tuned, each molecule plays its individual ionic rhythm to compose a “molecular symphony”. Over the past few decades, many research groups have worked on nanopore‐based single‐molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore‐based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis. 相似文献
9.
10.
《中国化学》2018,36(9):875-885
In recent years, bio‐nanopore and solid‐state nanopore have been greatly improved for molecule bio‐sensing. Whereas, the development of this scientific field seems to have encountered a bottleneck due to their respective limitations. The small pore size of the former impedes the detection of large single molecule, and the latter is difficult to achieve similar accuracy and functional control. DNA origami plays a novel role to bring more opportunities for the development of nanopore technology since it is relatively easy to synthesize and modify. This review mainly focuses on introducing the DNA origami nanopore fabrication methods, characterization and application. Meanwhile, the challenges in the present DNA origami nanopore research are also discussed. 相似文献
11.
《Electrophoresis》2018,39(19):2410-2416
Baxα, a key tumor suppressor gene, will not be expressed correctly as a result of single nucleotide mutation in its microsatellite region; Instead, BaxΔ2, an isoform of Baxα, is often produced. In addition, lack of the exon 2 due to an alternative splicing, BaxΔ2 has the same sequence as Baxα except single base deletion from eight continuous guanines (G8) to G7. Most of the currently available methods for Bax∆2 detection are inefficient and time‐consuming, and/or require the use of labels or dyes. In this work, we reported a label‐free nanopore sensing strategy to differentiate between Baxα and BaxΔ2 with a DNA polymer as a molecular probe based on alternative spliced sequences. Two DNA molecules were designed to selectively detect Baxα and BaxΔ2, respectively. The method was rapid, accurate, and highly sensitive: picomolar concentrations of target nucleic acids could be detected in minutes. Our developed simple and fast nanopore‐based detection strategy is not only useful for distinguishing between Baxα and Bax∆2, but also provides a useful tool for detection of other single‐base mutations in genetic diagnosis. 相似文献
12.
Nanopore is a single‐molecule analysis method which also employed electrophoresis has achieved promising single‐molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid‐state nanopores with desirable diameters to study the structured single‐strand DNA of C‐rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single‐strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single‐molecule information. The solid‐state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule. 相似文献
13.
《中国科学:化学(英文版)》2017,(6)
Nanopores for DNA sequencing have drawn much attention due to their potentials to achieve amplification-free, low-cost, and high-throughput analysis of nuclei acids. The material configuration and fabrication of the nanopore has become one important consideration in the nanopore based DNA sequencing research. Among various materials, the newly emerged graphene has brought more opportunities to the development of sequencing technology because of its unique structures and properties. This review mainly focuses on the experimental aspects of graphene nanopore research including the nanopore fabrication methods and processes. Meanwhile, the challenges in the present graphene nanopore research including hydrophobicity, translocation velocity and noise are also addressed and discussed. 相似文献
14.
纳米孔道分析技术是一种低成本、快速、无需标记的单分子检测技术,仅有20多年的发展历史,在DNA单分子测序领域展示出较好的应用前景,现已有商业化的产品面世且趋于成熟.越来越多的研究表明,纳米孔可作为一个通用的单分子传感器.本文综述了生物纳米孔道分析技术对蛋白质、多肽和核酸等单个分子与孔道间相互作用、动力学和热力学过程的实时监测以及多种生物大分子和金属离子的定量检测等方面的研究进展.在纳米孔技术中,电化学检测系统也十分重要,本文还特别介绍了高带宽及超低电流分辨仪器和相关软件的相关进展. 相似文献
15.
Dr. Rachael R. Jetson Prof. Casey J. Krusemark 《Angewandte Chemie (International ed. in English)》2016,55(33):9562-9566
A sensing approach is applied to encode quantitative enzymatic activity information into DNA sequence populations. The method utilizes DNA‐linked peptide substrates as activity probes. Signal detection involves chemical manipulation of a probe population downstream of sample exposure and application of purifying, selective pressure for enzyme products. Selection‐induced changes in DNA abundance indicate sample activity. The detection of protein kinase, protease, and farnesyltransferase activities is demonstrated. The assays were employed to measure enzyme inhibition by small molecules and activity in cell lysates using parallel DNA sequencing or quantitative PCR. This strategy will allow the extensive infrastructure for genetic analysis to be applied to proteomic assays, which has a number of advantages in throughput, sensitivity, and sample multiplexing. 相似文献
16.
Yi‐Lun Ying Dr. Junji Zhang Rui Gao Prof. Yi‐Tao Long 《Angewandte Chemie (International ed. in English)》2013,52(50):13154-13161
Nanopore‐based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single‐molecule detection. The technology allows the real‐time, selective, high‐throughput analysis of nucleic acids through both biological and solid‐state nanopores. In this Minireview, the background and latest progress in nanopore‐based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore‐based detection. 相似文献
17.
Yu Wang Kiran M. Patil Shuanghong Yan Panke Zhang Weiming Guo Yuqin Wang Hong‐Yuan Chen Dennis Gillingham Shuo Huang 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2019,131(25):8520-8524
O6‐carboxymethylguanine (O6‐CMG) is a highly mutagenic alkylation product of DNA, triggering transition mutations relevant to gastrointestinal cancer. However, precise localization of a single O6‐CMG with conventional sequencing platforms is challenging. Here nanopore sequencing (NPS), which directly senses single DNA bases according to their physiochemical properties, was employed to detect O6‐CMG. A unique O6‐CMG signal was observed during NPS and a single‐event call accuracy of >95 % was achieved. Moreover, O6‐CMG was found to be a replication obstacle for Phi29 DNA polymerase (Phi29 DNAP), suggesting this lesion could cause DNA sequencing biases in next generation sequencing (NGS) approaches. 相似文献
18.
Nanopores based on α-hemolysin and MspA represent attractive sensing platforms due to easy production and operation with relatively low background noise. Such characteristics make them highly favorable for sequencing nucleic acids. Artificial lipid bilayer membranes, also referred to as black lipid membranes, in conjunction with membrane nanopores, can be applied to both the detection and highly efficient sequencing of DNA on a single-molecule level. However, the inherently weak physical properties of the membrane have impeded progress in these areas. Current issues impeding the ultimate recognition of the artificial lipid bilayer as a viable platform for detection and sequencing of DNA include membrane stability, lifespan, and automation. This review (with 105 references) highlights attempts to improve the attributes of the artificial lipid bilayer membrane starting with an overview on the present state and limitations. The first main section covers lipid bilayer membranes (BLM) in general. The following section reviews the various kinds of lipid bilayer membrane platforms with subsections on polymer membranes, solid-supported membranes, hydrogel-encapsulated membranes, shippable and storable membrane platforms, and droplet interface bilayers. A further section covers engineered biological nanopore sensor applications using BLMs with subsections offering a comparative view of different DNA sequencing methods, a detailed look at DNA Sequencing by synthesis using alpha-hemolysin nanopores, sequencing by synthesis using the MspA nanopore and quadromer map, and on limitations of sequencing based on synthesis technology. We present an outlook at the end that discusses current research trends on single-molecule sequencing to highlight the significance of this technology and its potential in the medical and environmental fields. 相似文献
19.
Harrell CC Choi Y Horne LP Baker LA Siwy ZS Martin CR 《Langmuir : the ACS journal of surfaces and colloids》2006,22(25):10837-10843
In this paper, we describe resistive-pulse sensing of two large DNAs, a single-stranded phage DNA (7250 bases) and a double-stranded plasmid DNA (6600 base pairs), using a conically shaped nanopore in a track-etched polycarbonate membrane as the sensing element. The conically shaped nanopore had a small-diameter (tip) opening of 40 nm and a large-diameter (base) opening of 1.5 microm. The DNAs were detected using the resistive-pulse, sometimes called stochastic sensing, method. This entails applying a transmembrane potential difference and monitoring the resulting ion current flowing through the nanopore. The phage DNA was driven electrophoretically through the nanopore (from tip to base), and these translocation events were observed as transient blocks in the ion current. We found that the frequency of these current-block events scales linearly with the concentration of the DNA and with the magnitude of the applied transmembrane potential. Increasing the applied transmembrane potential also led to a decrease in the duration of the current-block events. We also analyzed current-block events for the double-stranded plasmid DNA. However, because this DNA is too large to enter the tip opening of the nanopore, it could not translocate the pore. As a result, much shorter duration current-block events were observed, which we postulate are associated with bumping of the double-stranded DNA against the tip opening. 相似文献
20.
Nanopore has been developed to be a powerful,single-molecule analytical tool for sensing ions,small organic molecules and biomacromolecules such as proteins and DNAs.Generally,the identity of the analyte can be revealed by current amplitude changes and mean dwell time of the analyte binding events.In some cases,generation of highly characteristic current events affords an alternative way of analyte determination with high confidence level.However,we found that secondary structures in DNA/RNA hybrids might severely hinder the generation of signature events during their translocation through?-hemolysin nanopore.In this report,we propose a strategy to add a certain concentration of urea in the buffer solution for single channel recordings and validate that low concentration of urea can effectively denature the secondary structures in DNA hybrids and recover the generation of signature events.This finding might be useful in other secondary structure-related nanopore sensing activities. 相似文献