Retarding and manipulating of DNA molecules translocation through nanopores

Nanopores are emerging sensitive sensors that can detect and analyze single charged molecule. Nanopores present a promising approach for sequencing human gen- ome below US$1,000 because of its superior performance, such as high throughput and low cost. However, a dominant bottleneck, that is, the high translocation speed of DNA molecules, has to be overcome. This property decreases accuracy of nanopore sensors to the single-base level. In this review, we mainly introduce the recent research works of retarding and manipulating of DNA motion through nanopores by actively control of three forces, which are the driving force, interaction force between nanopore and molecule, and exterior drag force. Lastly, conclusion and further outlook are presented pore-based DNA sequencing on future directions of nano- technology.     

Translocation of polymer through nanopore: dissipative particle dynamics simulation

Dissipative particle dynamics simulations are performed to study the forced translocation of polymer through a nanopore inside which the polymer experiences a driving force F. Hydrodynamic interaction （HI） is taken into account for the polymer in good solvent. We find that the mean translocation time 〈t〉 scales with the polymer length N as 〈t〉 ~ N^a with α = 1.26 ± 0.03 close to a theoretical pre- diction, and the probability distribution of t can be described by a Gaussian function. Our results show that the dynamics of polymer translocation with the HI is different from that without the HI. However, the exponent 6 in the scaling 〈t〉 ~ F^-δ is found not to be affected by the HI effect.     

DNA sequencing technology based on nanopore sensors by theoretical calculations and simulations

DNA sequencing based on nanopore sensors is a promising tool for third-generation sequencing technol- ogy because of its special properties, such as revolutionized speed and low cost. With about two decades of nanopore technology development, the pioneering work has dem- onstrated the ability of nanopores to perform single-mole- cule detection and DNA sequencing. However, the microscopic mechanisms of DNA transport dynamics through nanopores remain largely unknown. Currently, DNA microscopic transport in a nanopore is difficult to characterize and several unexpected experimental obser- vations are equivocal. This limitation can be resolved using theoretical calculations and simulations. These computa- tional methods can monitor the entire dynamic process that DNA undergoes in solution at a single-atom resolution that can accurately unveil the mystery of DNA transport dynamics and predict certain unexpected phenomena. This paper mainly reports the recent applications of computa- tional and simulation methods applied to the study of DNA transport through both biological and synthetic nanopores. We hope the theoretical calculations and simulations of DNA transport through nanopores can benefit the design of DNA sequencing devices.     

Investigation of self-assembled protein dimers through an artificial ion channel for DNA sensing

Artificial nanopores have become promising tools for sensing DNA. Here, we report a new technique for sensing DNA through a conical-shaped nanopore embed- ded in track-etched polyethylene terephthalate （PET） membrane. Two different streptavidin-conjugated mono- valent DNA probes were prepared that can bind to two distinct segments （at either end） of the target DNA. The size of target DNA-linked to the two streptavidin-conju- gated monovalent DNA probes is double that of the indi- vidual probes. By precisely controlling the tip diameter of the conical nanopore embedded in the PET polymer, events due to the translocation of the streptavidin-conjugated monovalent DNA probes through the nanopore can be fil- tered and purposely undetected, whereas the current pulses due to the translocation of the target DNA-induced self- assembled complexes can be detected. The two streptavi- din-conjugated DNA probes cannot be linked by multi- mismatched DNA. Therefore, multi-mismatched （non- specific） DNA will not induce any current pulse signatures. The current pulse signatures for the self-assembled com- plex can be used to confirm the presence of the target DNA. The size-dependent detection of self-assembled complexes on the molecular level shows strong promise for the detection of biomolecules without interference from the probes.     

An integrated software system for analyzing nanopore data

We presented an integrated software system for analyzing nanopore data. This self-developed software provided rapid processes for accurate location, classifica- tion, and evaluation of every individual blockade. Using the proposed software, statistical analysis could be achieved easily and conveniently. The results of β-Amyloid 42 dem- onstrated that our data process could rapidly extract duration time and current amplitudes. In addition, our data process could accurately carry out statistical fittings.     

An integrated current measurement system for nanopore analysis

Nanopore-based techniques have attracted increasing attention as a unique tool for single-molecule analysis. To accurately detect individual motions of each single molecule, nanopore techniques are used to develop an ultrasensitive current measurement system. This work proposes an integrated current measurement system con- taining an amplifier system and a current signal acquisition system with a high current resolution and a high temporal resolution for nanopore analysis. The exploration and achievements in instrument and signal processing endow nanopore techniques with reliability, affordability, and portability, which make a great leap toward its real applications.     

Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces

A nanopore on an impermeable membrane, which separates two chambers containing electrolytic solu- tion, can be used as a nanometre-sized Coulter counter for single-molecule biological sensing. With an applied poten- tial, charged molecules are electrically dragged through the pore, and the analytical information is sequentially read out from the current blockades. Nucleic acid, which is an elec- trically charged polymer, is an ideal analyte for nanopore analysis and nanopore sequencing. With the advantages of high-speed, label-free and single-molecule resolution, a nanopore sequencer is considered to be the most promising candidate for the third-generation DNA sequencing. In this review, a brief history of nanopore sequencing to date is summarized and discussed along with future prospects. Although successfully demonstrated for known viral gen- ome sequences, the nanopore sequencing technique still requires missing pieces like improved accuracy, automation and throughput for clinical diagnosis-level applications.     

四川盆地周缘牛蹄塘组页岩微观孔隙结构特征

以四川盆地周缘地区下寒武统牛蹄塘组富有机质页岩为研究对象,通过X衍射全岩分析、低温液氮吸/脱附等实验方法技术对研究区页岩储层微观孔隙结构进行了系统研究;并探讨了控制纳米尺度微观孔隙结构的主要原因。结果表明:四川盆地周缘牛蹄塘组富有机质页岩矿物组分中石英、长石等脆性矿物含量较高,其次是黏土矿物;页岩微孔结构复杂,多为开放型空隙,以管状孔和平行壁的狭缝状孔为主;微观孔隙孔径主要分布在2~10 nm,以微孔为主。通过分析控制该区页岩储层微观孔隙结构的主要因素,认为有机碳含量是控制纳米级孔隙发育的主要因素,同时也是页岩气赋存的重要物质基础。