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Effect of nanopore size on poly(dT)_(30) translocation through silicon nitride membrane

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Science China(Technological Sciences) 2013年第10期56卷 2398-2402页

作者： SI Wei sha jingjie LIU Lei QIU YingHua CHEN YunFei Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments Southeast University

The nanopore size effect on translocation of poly(dT)30through Si3N4 membrane is *** this paper,we report that the speed of the poly(dT)30 transport through Si3N4 nanopores can be slowed down by half through increasing the nanopore diameter from 4.8 nm to 10.8 *** results are consistent with our simulation ***,the current blockage induced by DNA passing through the nanopore is less obvious as pore diameter is larger,which is in good agreement with the theoretical *** conclusion about DNA transport through nanopores is beneficial for the design of DNA sequencing devices.

关键词： solid-state nanopore nanopore technology single molecule sensor molecular dynamics simulation slow down

Integrated solid-state nanopore devices for third generation DNA sequencing

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Science China(Technological Sciences) 2014年第10期57卷 1925-1935页

作者： WU GenSheng ZHANG Yin SI Wei sha jingjie LIU Lei CHEN YunFei Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments Southeast University

Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale *** is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial *** integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event,such as transverse tunneling current,local potential change,and capacitance oriented voltage *** this mini review,the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented.

关键词： DNA sequencing solid-state nanopore spatial resolution integrated sensors

Temperature effect on translocation speed and capture rate of nanopore-based DNA detection

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Science China(Technological Sciences) 2015年第3期58卷 519-525页

作者： ZHANGYin WU GenSheng MA Jian YUAN Zhishan SI Wei LIU Lei sha jingjie CHEN YunFei Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments School of Mechanical Engineering Southeast University

We study the effects of electrolyte temperature on DNA molecule translocation experimentally without and with a temperature gradient across nanopore *** same temperatures on both electrolyte chambers are first *** DNA molecule translocation time is measured to be 2.44 ms at 2°C in both chambers,which is 1.57 times longer than at 20°*** the temperature difference effect is characterized in both *** results show that the DNA translocation speed can be slowed down as long as one side temperature is lowered,irrespective of the temperature gradient *** indicates that the thermophoretic driving force generated by a temperature gradient has no obvious effect on the threading speed of DNA molecules,while the main reason for the slowed DNA translocation speed is the increased ***,the capture rate of DNA molecules is enhanced under a temperature gradient condition,and the capture rate during DNA translocation from hot side at 21°C to cold one at 2°C is 1.7 times larger than that under the condition of both chambers at 20°***,an optimized configuration is proposed to acquire higher capture rates and lower DNA translocation speeds.

关键词： nanopore DNA detection temperature translocation speed capture rate

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

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Chinese Science Bulletin 2014年第35期59卷 4929-4941页

作者： Wei Si Yin Zhang Gensheng Wu jingjie sha Lei Liu Yunfei Chen Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments Southeast University

DNA sequencing based on nanopore sensors is a promising tool for third-generation sequencing technology because of its special properties,such as revolutionized speed and low *** about two decades of nanopore technology development,the pioneering work has demonstrated the ability of nanopores to perform single-molecule detection and DNA ***,the microscopic mechanisms of DNA transport dynamics through nanopores remain largely ***,DNA microscopic transport in a nanopore is difficult to characterize and several unexpected experimental observations are *** limitation can be resolved using theoretical calculations and *** computational 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 *** paper mainly reports the recent applications of computational and simulation methods applied to the study of DNA transport through both biological and synthetic *** hope the theoretical calculations and simulations of DNA transport through nanopores can benefit the design of DNA sequencing devices.

关键词： DNA测序技术可计算性纳米孔传感器模拟应用程序原子分辨率微观机制

Retarding and manipulating of DNA molecules translocation through nanopores

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Chinese Science Bulletin 2014年第35期59卷 4908-4917页

作者： Yin Zhang Gensheng Wu Wei Si jingjie sha Lei Liu Yunfei Chen Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments School of Mechanical EngineeringSoutheast University

Nanopores are emerging sensitive sensors that can detect and analyze single charged *** present a promising approach for sequencing human genome below US$1,000 because of its superior performance,such as high throughput and low ***,a dominant bottleneck,that is,the high translocation speed of DNA molecules,has to be *** property decreases accuracy of nanopore sensors to the single-base *** 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 ***,conclusion and further outlook are presented on future directions of nanopore-based DNA sequencing technology.

关键词： DNA分子纳米孔操纵易位传感器精度 DNA测序延缓纳米技术

Investigation on the interaction length and access resistance of a nanopore with an atomic force microscopy

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Science China(Technological Sciences) 2017年第4期60卷 552-560页

作者： SI Wei YANG HaoJie LI Kun WU GenSheng ZHANG Yin KAN YaJing XIE Xiao sha jingjie LIU Lei CHEN YunFei Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering Southeast University Nanjing 210096 China Key Laboratory of MEMS of Ministry of Education Southeast University Nanjing 210096 China

Nanopore devices have attracted a lot of attention for their potential application in DNA sequencing. Here, we study how an occluding object placed near a nanopore affects its access resistance by integrating an atomic force microscopy with a nanopore sensor. It is found that there exists a critical hemisphere around the nanopore, inside which the tip of an atomic force microscopy will affect the ionic current. The radius of this hemisphere, which is a bit smaller than the theoretical capture radius of ions, increases linearly with the applied bias voltage and quadratically with the nanopore diameter, but is independent of the operation modes and scanning speeds of the atomic force microscopy. A theoretical model is also proposed to describe how the tip position and geometrical parameters affect the access resistance.

关键词： solid-state nanopore ionic current access resistance interaction length AFM capture radius

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LiCl溶液中基于固态纳米孔的DNA检测

东南大学学报（自然科学版） 2016年第5期46卷 982-986页

作者：沙菁 石鸿佼徐冰东南大学江苏省微纳生物医疗器械设计与制造重点实验室南京211189 东南大学机械工程学院南京211189

采用阳离子体积较小的LiCl溶液作为缓冲液,研究DNA在不同浓度下通过固态纳米孔时的行为特征,以探究DNA的过孔机理.实验结果表明,当LiCl溶液浓度从0.1 mol/L变化到1.0 mol/L时,由DNA过孔所引起的相对阻塞离子电流信号比值从0.014 42降低... 详细信息

采用阳离子体积较小的LiCl溶液作为缓冲液,研究DNA在不同浓度下通过固态纳米孔时的行为特征,以探究DNA的过孔机理.实验结果表明,当LiCl溶液浓度从0.1 mol/L变化到1.0 mol/L时,由DNA过孔所引起的相对阻塞离子电流信号比值从0.014 42降低至0.002 79,而DNA完全通过纳米孔所需时间从0.30 ms增加至1.87 ms.对比1 mol/L KCl,Na Cl,LiCl三种溶液中DNA的过孔结果发现,在LiCl溶液中DNA的过孔时间分别为KCl,Na Cl溶液中的6.2和5.3倍,说明LiCl溶液能够有效降低DNA的过孔速度.此外,实验发现LiCl溶液中DNA主要以线性非折叠和折叠2种形态过孔.因此,增加LiCl溶液浓度可延长DNA的过孔时间,但会使相对阻塞离子电流信号幅值降低.

关键词：纳米孔 LiCl溶液 DNA 阻塞离子电流过孔时间

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数字化无阀微泵内微流体泵送运动的理论解析

中国机械工程 2007年第20期18卷 2472-2476页

作者：沙菁 侯丽雅章维一东南大学南京210096 南京理工大学南京210094

对研制出的新型基于微流体数字化技术的数字化无阀微泵的泵送实验现象进行理论分析研究。提出数字化无阀微泵内的微流体概念,该微流体受外加周期性扰动,其边界流和中间流间产生速度差异,由于粘性力、惯性力交替作用,使微流体运动,中间... 详细信息

对研制出的新型基于微流体数字化技术的数字化无阀微泵的泵送实验现象进行理论分析研究。提出数字化无阀微泵内的微流体概念,该微流体受外加周期性扰动,其边界流和中间流间产生速度差异,由于粘性力、惯性力交替作用,使微流体运动,中间流克服表面张力的作用得以喷射出去,实现数字化无阀微泵泵送。推导了中间流的运动公式,分析认为中间流与边界流存在着滞后效应,调整扰动周期长短,可实现离散流、连续流。

关键词：数字化无阀微泵数字化微流体技术边界流中间流粘性力

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固态纳米孔对蛋白质易位的实验研究

化学学报 2017年第11期75卷 1121-1125页

作者：沙菁 徐冰陈云飞杨颜菁东南大学江苏省微纳生物医疗器械设计与制造重点实验室南京211189 东南大学机械工程学院南京211189 南京医科大学口腔疾病研究江苏省重点实验室南京210029 南京医科大学附属口腔医院口腔预防科南京210029

蛋白质因其多样性和功能性,是生物体内一类非常重要的分子.通常蛋白质的表征需要借助荧光或者酶的标记.而纳米孔技术,得益于免标记、单分子检测等优势,为蛋白质的表征提供了新方向.我们使用固态纳米孔完成了单个蛋白质分子及蛋白质-蛋... 详细信息

蛋白质因其多样性和功能性,是生物体内一类非常重要的分子.通常蛋白质的表征需要借助荧光或者酶的标记.而纳米孔技术,得益于免标记、单分子检测等优势,为蛋白质的表征提供了新方向.我们使用固态纳米孔完成了单个蛋白质分子及蛋白质-蛋白质结合物的检测.可以发现,外部电压和电解质溶液的酸碱度会直接影响蛋白质分子表面带电量,从而加快或延迟其在孔内的易位时间.抗原、抗体本质上都是蛋白质,两者之间具有高度特异性.通过比较抗体溶液在添加特异性抗原前后的易位事件,实现了单个蛋白质分子和蛋白质-蛋白质结合物的区分.未来,纳米孔技术有望应用于多蛋白质分子的辨识、蛋白质分子相互作用机制等方面的研究.

关键词：牛血清蛋白(BSA) 抗原抗体固态纳米孔单分子检测