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.     

以病毒的230 kb DNA分子为模板的DNA序列测定

目的：为确认Tn3-gpt已插入小鼠巨细胞病毒(mouse cytomegalovirus,MCMV)基因组的特定位置,改进大分子病毒DNA的测序方法,建立以230kb DNA为模板直接进行DNA序列测定的方法。方法：待测MCMV的Tr3-gpt插入突变株感染NIH3T3细胞后,从培养液中制备病毒颗粒并从中纯化得到基因组DNA,以此DNA为模板,合成的寡核苷酸为引物,用热循环方法按Promega公司的DNA Cycle Sequencing System试剂盒的方法进行测序。结果：获得纯度较高可直接作为模板进行测序的：DNA,测序所得放射自显影图片条带清晰明亮,间隔正常,分辨率较高,可顺利读出插入位点的MCMV的DNA序列,证实Tn3-gpt插入在特定的位置。结论：长达230kb的大分子病毒DNA可直接作为模板,用热循环测序方法进行测序,无需切割成小片段后才进行测序。     

羟乙基纤维素/聚丙烯酰胺共混物在DNA测序研究中的应用

利用合成的中等分子量的线性聚丙烯酰胺（LPA）和羟乙基纤维素（HEC）构成的共混聚合物网络对标准DNA样品BigDyeTeminatorV3.1进行测序研究。研究了LPA/HEC的比例,温度,电压等对分离效果的影响。实验证明该聚合物网络同时具有LPA对DNA优良的筛分性能和HEC对毛细管内壁动态涂覆的能力。用2.5%w/v的这种介质在没有对软件系统优化的情况下,73min内对标准DNA的读写长度可达900个碱基。     

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.     

DNA宏条形码技术在动植物法医鉴定中的应用进展

DNA宏条形码技术是随着2代高通量测序技术的发展而出现的一种物种鉴别技术.该技术结合了DNA条形码技术和高通量测序技术的优点,可以对混合样本中的多物种来源进行同步鉴定.本研究介绍DNA宏条形码技术的含义以及目前的应用需求,分析DNA宏条形码技术在食品、药品监管、打击野生动植物犯罪、刑事案件侦查等司法实践中的应用现状,总...     

基于遗传算法的工艺过程排序研究

面向特征加工的工艺过程排序是计算机辅助工艺规划中一个非常突出的难点问题.首先对特征之间的约束关系进行分类,利用特征关系图来描述基本的合理性约束,并将最优性约束的满足程度视为工艺路线优化的判断标准.然后利用遗传算法来实现工艺过程排序,改进了编码规则并实现了解码算法,方便了适应度的计算,从而提高了排序算法的有效性.最后给出了应用实例.     

DNA序列分析中克隆片段在M13的缺失及质粒载体的应用

应用新的亚克隆载体BLUESCRIPT M13克服了外源DNA缺失问题.采用外切核酸酶Ⅲ快速亚克隆法,在不知道任何内切酶位点的情况下,也能获得一系列适应于DNA顺序分析的重叠衔接克隆.用超螺旋双股DNA直接序列分析程序,简化了DNA序列分析工作.     

一种基于传感器的Android应用行为分析技术

大多数针对恶意软件识别的研究都是基于应用程序接口(Application Program Interface,API)调用来实现的,但是目前基于API的研究大都没有考虑到设备的状态,设备状态能够直接体现程序运行的外部环境,这对分析应用的行为有着重要作用。本文提出一种基于传感器的应用行为识别技术,首先,通过传感器数据来判断设备实时状态;然后,结合API调用时序和图形用户界面(Graphic User Interface,GUI)首屏时序产生的多元时序数据,设计算法识别应用行为的恶意性;最后,设计实现包括静态打桩、动态行为监控和传感器实时状态采集的恶意行为分析原型系统,选取典型案例验证了本文提出方法的准确性,并通过黑盒测试验证了本文恶意应用识别方法的有效性。     

基于联系数系统态势排序综合评判方法及应用

联系数是把研究对象各个侧面的测度函数联系起来的一种数,基于联系数的系统态势排序充分利用联系数所提供的信息,可以替代模糊综合评判中的取大取小算法,避免系统综合评判因采用模糊数学中取大取小算法造成的信息丢失问题,评判结果可靠,算法简捷。     

基于半导体陶瓷技术的二氧化碳传感器研究

采用硬质酸盐方法制备出纳米BaTiO3粉末,利用半导体陶瓷技术掺杂CeO-AgNO3制造出对CO2气体敏感的功能材料.基于CaCO3和RuO2制作电极,NiCr丝加热.CO2气体传感器当加热到400~450℃时,CO2体积分数为100×10-6~2 000×10-6,传感器的特征阻值由600 kΩ变化到150 kΩ,函数关系呈良好的全对数线性,同时测定了元件的温度特性和湿度特性,提出了此种传感器工作时,为提高传感器测试准确性,应考虑环境温湿度补偿技术.     

DNA modular subtraction algorithm based on linear self-assembly

This paper presents a DNA algorithm based on linear self-assembly which gives the result of the modular subtraction operation of two nonnegative integers. For two n-bit nonnegative integers A and B, the algorithm gives the result of A-B mod 2 ⁿ . An extended borrow tag which indicates the relation of the minuend and the subtrahend is included in the resulting strand so that the pre-classification based on A>B or B>A is not required before the experiment. From the resulting strand, we can draw the information of operation result, operands, borrow, and the tag of the relation between the minuend and the subtrahend. The algorithm takes advantage of the parallelism characteristic of DNA computing: while given two sets of operands (one the minuend set and the other subtrahend set), the modular subtraction operation of these two sets can be achieved by a parallel processing procedure. The feasibility of the algorithm is based on a known experiment. The algorithm is of spontaneous characteristic which prevents the scale of the experimental procedures from growing with the length of the operands. As for the length of the operands n, there are O(n) kinds of strands required in the experiment, and the biochemical experimental procedures can be accomplished in constant number of steps.     

基于EDA技术的智能机器猫的仿真及设计

EDA技术是电子设计的发展趋势,是电子信息技术发展的杰出成果。尤其是Multisim电路仿真软件和Ultiboard印制板设计软件的出现,将EDA技术提高到了一个更高的水平。系统选取了一种简易的电池驱动玩具——电动机器猫,并利用EDA开发工具Multisim9和Ultiboard软件进行设计仿真,将其改装成能进行一定智能控制的电动玩具。     

序批式活性污泥法处理豆类加工废水

采用序批式活性污泥法处理豆类加工废水 ,获得了稳定、高效的处理效果。通过研究曝气时间和进水有机负荷对去除效果的影响 ,结果表明 ,曝气时间对处理效果影响很大 ,系统抗冲击负荷能力较强。并在此基础上 ,提出根据处理水的排放地点不同 ,确定不同的曝气时间 ,从而达到降低运行成本的目的     

DNA纳米机器药物递送研究进展

 天然分子机器是细胞正常功能（包括DNA复制、细胞内物质运输、离子平衡和细胞运动等）的重要执行者。受天然分子机器的启发,人工分子机器的概念被提出并逐步实践。DNA分子独特的理化性质使得其可作为自组装基元用于构建分子机器类纳米结构。DNA纳米结构具有形状可设计性、精确的可寻址性、结构动态响应性及良好的生物相容性,可以作为一种良好的药物递送载体材料。通过可寻址的负载特定功能元件从而构建DNA纳米载体和治疗型DNA纳米机器,可以靶向性地将药物传递到病变组织和细胞,响应性地释放药物,提高药物的细胞摄取率并降低其毒副作用,有望成为优秀的药物递送系统。基于DNA纳米结构的药物载体已经被用于递送小分子药物、寡核苷酸类药物和蛋白药物。以每类药物分子中的典型药物为例,介绍了DNA纳米载体和DNA纳米机器药物递送系统的研究进展,并讨论了其所面临的挑战及可能的发展趋势。     

A novel DNA computing model based on RecA-mediated triple-stranded DNA structure

The field of DNA computing emerged in 1994 after Adleman’s paper was published. Henceforth,a few scholars solved some noted NP-complete problems in this way. And all these methods of DNA computing are based on conventional Watson-Crick hydrogen bond of doublehelical DNA molecule. In this paper, we show that the triple-stranded DNA structure mediated by RecA protein can be used for solving computational problems. Sequence-specific recognition of double-stranded DNA by oligonucleotide-directed triple helix (triplex) formation is used to carry out the algorithm. We present procedure for the 3-vertex-colorability problems. In our proposed procedure, it is suggested that it is possible to solve more complicated problems with more variables by this model.     

间歇式活性污泥法处理生活污水的试验研究

对间歇式活性污泥法对城市生活污水进行了试验研究.在试验中探讨了生物脱氮除磷的规律及对处理效果的影响.结果表明:在总停留时间控制在4.5～5.5 h,污泥负荷为0.14～0.26 kgBOD5/(kgMLSSd),进水BOD594.7～135.0 mg/l,CODcr186～266.7 mg/l,NH4-N15.0～25.4 mg/l,TP5.6～7.1 mg/l条件下,达到了既去除有机物又能脱氮除磷的效果.出水BOD5浓度在6.63～17.05 mg/l,去除率达85%～93%;出水CODcr浓度在22.32～48.0 mg/l,去除率达82%～88%;出水NH4-N浓度在2.83～9.83 mg/l,去除率达53%～87%,出水TP浓度在0.1～0.45 mg/l,去除率达85%～99%.     

背包问题的三链DNA计算模型

背包问题是组合优化中很重要的NP问题。因为三链DNA的特殊结构在参与反应时可以减少计算模型的错解率,且在生化反应中利用磁珠分离法对解进行分离较方便准确,文章利用三链模型求解0-1背包问题和完全背包问题。首先将背包问题的约束条件进行分解,再将物品质量编码为DNA片段,链接反应后,利用凝胶电泳技术和三链模型检测所包含的物品组合,得到满足约束条件的物品组合,再利用此方法检测价值最大的组合,即问题的解。其他的背包问题也可用此方法来解决。     

Molecular logic computing model based on self-assembly of DNA nanoparticles

In this paper, a logic computing model was constructed using a DNA nanoparticle, combined with color change technology of DNA/Au nanoparticle conjugates, and DNA computing. Several important technologies are utilized in this molecular computing model: DNA self-assembly, DNA/Au nanoparticle conjugation, and the color change resulting from Au nanoparticle aggregation. The simple logic computing model was realized by a color change, resulting from changing of DNA self-assembly. Based on this computing model, a set of operations computing model was also established, by which a simple logic problem was solved. To enlarge the applications of this logic nanocomputing system, a molecular detection method was developed for H1N1 virus gene detection.     

光谱法研究阿米卡星与DNA的相互作用

在pH 6.O的Tris-HC1介质中,以溴化乙锭为荧光探针,研究了阿米卡星与小牛胸腺DNA之间的相互作用.采用荧光光谱、吸收光谱、Scatchard方程、圆二色谱、黏度等手段,对作用机理进行了研究,结果表明阿米卡星与小牛胸腺DNA之间的作用方式为混合方式,嵌入与沟槽作用是两种主要作用方式.求得25℃时的结合常数为2.2×104L·mo1-1.     

光谱法研究头孢曲松钠与DNA的相互作用

在pH 7.4的Tris-HCl介质中,以溴化乙锭为荧光探针,研究了头孢曲松钠与小牛胸腺DNA之间的相互作用.采用荧光光谱、吸收光谱、Scatcllard方程、圆二色谱、热变性等手段,对作用机理进行了研究,结果表明头孢曲松钠与小牛胸腺DNA之间的作用方式为混合方式,嵌入与沟槽作用是两种主要作用方式.求得25℃时的结合常数为6.3×104L·mol-1.