超淬灭分子信标的合成与性能研究

合成并纯化了普通DNA引物、常规分子信标和超淬灭分子信标,利用基质辅助激光解析电离飞行时间质谱对产物进行解析,证明了其为目标产物.与cDNA杂交的结果表明,超淬灭分子信标的信背比达到40倍,比常规分子信标高出4倍,有望实现对样品的高灵敏检测.     

分子信标研究进展

分子信标是一种新型核酸探针,它在核酸检测中具有高特异性、高选择性和高灵敏度,取得了广泛的应用.该文主要介绍了分子信标的原理,一些新型的分子信标的结构及其优缺点和潜在的应用前景,并对分子信标的应用领域做了一个简单的介绍.     

DNA折纸术在0-1背包问题中的应用

DNA折纸术因其反应的可编程性、纳米可寻址性等优点被广泛地应用于DNA计算中。利用DNA折纸术和杂交链式反应构建0-1背包问题的计算模型。以四个变量的0-1背包问题为例,首先将九种发夹结构和一种分子信标锚定在DNA折纸基底上并加入足量的辅助链;其次通过加入不同的引发链可以触发不同路径上的杂交链式反应,并得到问题的所有可能解;最后,通过荧光信号的数量确定可行解,从而找到问题的最优解。该模型不受权重过大或过小的影响,在折纸基底上可等比例的缩放权重。用Visual DSD软件对该模型进行仿真,模型显示出良好的可行性。     

DNA自组装的可满足性问题模型

DNA自组装技术在DNA计算和纳米技术领域都发挥着极其重要的作用,许多小规模NP完全问题都可以通过自组装模型得以解决.文中以可满足问题为模型,通过构造范式中变量的特殊补链,使其与初始数据库中初始DNA链发生杂交反应,形成发夹结构,利用形成发夹结构的DNA链与没形成发夹结构的DNA链长度不同的特点,通过凝胶电泳将这些带发夹的DNA链提取出来;然后加入与这些特殊补链完全互补的DNA链,在一定温度下,通过碱基互补配对原则,发夹结构又将被重新打开.该模型充分利用了DNA分子间的自组装能力,在计算过程中只需要用到凝胶电泳操作,在一定程度上大大减少了因生物操作过多而引起的各种实验误差.     

分子信标用于平阳霉素切割DNA反应的实时监测

报道了一种实时监测平阳霉素(BLM A5)氧化切割DNA过程的荧光分析方法.利用分子信标核酸探针作为BLM A5底物和探针分子,通过检测BLM A5切割分子信标反应过程中荧光信号的变化,实现了对BLM A5在Fe2 和O2介导下切割DNA反应的实时监测.同时,考察了一些金属离子和抗肿瘤药物对BLM A5切割DNA反应的影响.在此基础上建立了一种快速、灵敏的BLM A5定量测定方法,线性响应范围为0.05～1.0 μmol/L.     

茎部可控核酸探针设计策略

分子探针是指利用分子工程技术获得的对某一特定对象具有特异性识别能力的功能分子。在传统生物分子探针中,蛋白质类识别分子（如抗体）的特异性和亲和力好,已广泛用于疾病的分子诊断和生命科学的研究中。核酸类识别单元如核酸适体、分子信标等,一般是通过碱基之间精确的氢键识别（杂交）来探测含有与该探针互补序列的核酸,     

分子信标荧光探针快速检测p21mRNA的新方法

1996年美国科学家首次设计并合成了一种新型荧光探针--分子信标(MB)[1],它是一种同时带有荧光基团和熄灭基团的发夹型单链DNA分子,能对目标DNA或RNA分子产生特异性的识别.由于具备了良好的检测性能,并且杂交以后无须分离多余的未杂交探针,MB在生物医学中得到了广泛的应用,如基因芯片的制备、痕量核酸的分离、活体细胞中mRNA的监测等[2].目前,检测mRNA的手段主要依靠RT-PCR,但是从反转录到PCR以及再次扩增是一个较麻烦的过程,实验成本高、周期长,也常出现假阳性和假阴性问题,影响了其准确性.     

柔性制造系统非阻塞监督控制器优化设计

针对一类含有并发执行装配过程的柔性制造系统G-systems,提出一种新的死锁预防策略保证该系统的非阻塞性,即在控制下,受控系统从任意可达状态都可以到达理想状态.首先对Petri网模型中基本信标实施控制,保证了基本信标的最大可控,然后通过线性规划算法求取所有从属信标满足可控性的条件,即获得基本信标的控制深度变量.与现有方法相比,该策略优点在于只需加入少量的控制库所,就可避免不必要的迭代过程;其次是提出控制器输出弧位置优化策略,得到了结构更为简单、许可行为更多的非阻塞Petri网控制器.     

Petri网的子类G–system网的死锁控制策略

由于柔性制造系统中的死锁问题与对应建模Petri网中信标密切相关, 如何准确和快捷地求解这样的信标, 对于基于信标可控的死锁控制策略设计而言, 是十分重要的. 本文提出了基于G-system网灵巧信标的迭代式求解与受控的死锁控制策略. 与目前求解导致死锁信标所采用的部分枚举方法相比, 该方法避免了先求解出最大的死标识信标, 进而从中提取极小信标的步骤, 提高了信标的计算效率. 同时, 通过添加适当的控制库所, 使得灵巧信标满足max'-controlled, 获取的活性受控G–system网系统的许可行为数目可以得到进一步的提升. 通过理论分析和算例验证, 表明了该死锁控制策略的正确性和有效性.     

基于粘贴和2-臂DNA模型的层次聚类算法

为了充分利用DNA分子在生物计算中的高度并行性和强大的存储能力,将DNA计算引入层次聚类实现对数据集的全局搜索。提出了粘贴模型与2-臂DNA分子相结合的混合模型求解最近邻层次聚类的DNA算法。针对二维数据空间,算法首先基于最小生成树思想产生图的边的所有组合链;其次筛选含n-1条边的链,基于边附着顶点,并选择包含全部顶点的复合链;再将复合链末尾连接相应边的权值片段,电泳出最短链;最后通过荧光分析法读解,得到最终的聚类结果。与已有文献同类算法对比表明,该算法在保持多项式操作时间下,更充分考虑连接边的长度,并将读解步骤数限定为常数步。     

Combinatorial algorithms for DNA sequence assembly

The trend toward very large DNA sequencing projects, such as those being undertaken as part of the Human Genome Program, necessitates the development of efficient and precise algorithms for assembling a long DNA sequence from the fragments obtained by shotgun sequencing or other methods. The sequence reconstruction problem that we take as our formulation of DNA sequence assembly is a variation of the shortest common superstring problem, complicated by the presence of sequencing errors and reverse complements of fragments. Since the simpler superstring problem is NP-hard, any efficient reconstruction procedure must resort to heuristics. In this paper, however, a four-phase approach based on rigorous design criteria is presented, and has been found to be very accurate in practice. Our method is robust in the sense that it can accommodate high sequencing error rates, and list a series of alternate solutions in the event that several appear equally good. Moreover, it uses a limited form of multiple sequence alignment to detect, and often correct, errors in the data. Our combined algorithm has successfully reconstructed nonrepetitive sequences of length 50,000 sampled at error rates of as high as 10%.This research was supported by the National Library of Medicine under Grant R01-LM4960, by a postdoctoral fellowship from the Program in Mathematics and Molecular Biology of the University of California at Berkeley under National Science Foundation Grant DMS-8720208, and by a fellowship from the Centre de recherches mathématiques of the Université de Montréal.     

Preparation of an electrochemical PNA biosensor for detection of target DNA sequence and single nucleotide mutation on p53 tumor suppressor gene corresponding oligonucleotide

Development of an electrochemical biosensor based on peptide nucleic acid (PNA) probe for detection of target DNA sequence and single nucleotide mutation in p53 tumor suppressor gene corresponding oligonucleotide using methylene blue (MB) as an electrochemical indicator is described. The interaction between MB and short sequence of p53, one of the most important tumor suppressor genes due to its dysfunction in the majority of human cancers, was studied by differential pulse voltammety (DPV). Probe modified electrode was prepared by self-assembled monolayer (SAM) formation of thiolated PNA molecules on the surface of gold electrode (GE). The hybridization of PNA probe with target DNA was performed in solution to form PNA-DNA hybrid on the surface of the GE. A significant increase in the reduction signal of MB was observed upon hybridization of the probe with the complementary DNA. The selectivity of the biosensor was studied using noncomplementary oligonucleotides. Furthermore, our results confirmed the ability of the sensor to detect single base mismatch in the sample oligonucleotide. The influence of probe concentration on the effective discrimination against noncomplementary sequence and point mutation was also investigated. Diagnostic performance of the biosensor is described and the detection limit is found 6.82 × 10⁻¹⁰ M. The electrochemical impedance spectroscopy was also employed to further investigate the sensor function.     

Structural dynamics of wild type and mutated forms of human L1 endonuclease and insights into its sequence specific nucleic acid binding mechanism: A molecular dynamics study

Biomolecular recognition of proteins and nucleic acids is mainly mediated by their structural features and the molecular dynamics simulations approach has been used to explore this recognition processes at the atomic level. L1-Endonuclease, an enzyme involved in L1 retrotransposition, cleaves the TA junction DNA (5′-TTTT/AA-3′) and expresses high specificity for target site recognition. The present study highlights the structural features of L1-endonuclease as well as DNA responsible for such specific recognition. Especially, the importance of βB6-B5 hairpin loop in DNA recognition has been elucidated by analyzing the dynamics of Thr192 mutated L1-endonuclease. In addition, simulations of the endonuclease complexed with DNA substrates (sequences having TA and CG junctions) revealed the specificity of L1 endonuclease towards TA junction. Molecular dynamics simulations revealed that the βB6-B5 hairpin loop protrudes well into the minor groove of DNA having TA junction and induces DNA bending such that the width of minor groove is increased. Such endonuclease induced bending of TA junction DNA sequence positions the scissile phosphodiester bond of DNA for cleavage. The innate property of minor groove widening in TA junction than in CG junction is utilized by the βB6-βB5 hairpin loop of endonuclease while recognizing the DNA sequences. The present study also highlights the role of Mg²⁺ cation in catalysis and attempts to explore the possible target site DNA cleavage mechanism.     

无线传感器网络节点定位的同心圆改进算法

定位技术是无线传感器网络的关键技术之一。同心圆定位方法是新近提出的一种精度较高的定位方法,未知节点根据锚节点广播的信息确定自己在以该锚节点为圆心的哪个圆环内,把若干包含自己的圆环的交集的质心估计为其位置。提出一种改进的同心圆定位方法,在原方法的基础上,利用相邻圆环内的未知节点间的通信减小包含未知节点的圆环的宽度,从而更精确地估计出了未知节点的位置。该方法只比原方法增加很少的能耗。同时仿真结果表明,该方法在理想环境和有干扰环境下其定位精度都明显高于原方法。     

Software Trapping: A Strategy for Finding Genes in Large Genomic Regions

We present an approach to the gene identification phase of positional cloning that combines sparse sampling of DNA sequences from large genomic regions with computational analysis. We call the method "software trapping." The goal is to find coding exons while avoiding massive DNA sequence determination and contig assembly. Instead, rapid sequence sampling is combined with exon screening software such as a newly developed package called XPOUND to identify coding sequences. We have tested the approach using a set of model genomic sequences with known intron/exon structures as well as with bona fide P1 genomic clones. The results suggest that the strategy is a useful complement to other methods for finding genes in poorly characterized regions of genomes.     

Specificity of damage recognition and catalysis of DNA repair

A common feature of DNA repair enzymes is their ability to recognize the damage independently of sequence in which they are found. The presence of a flipped out base inserted into the protein in several DNA-enzyme complexes suggests a contribution to enzyme specificity. Molecular simulations of damaged DNA indicate that the damage produces changes in DNA structure and changes the dynamics of DNA bending. The reduced bending force constant can be used by the enzyme to induce DNA bending and facilitate base flipping. We show that a thymine dimer (TD) containing DNA requires less energy to bend, lowering the barrier for base flipping. On the other hand, bending in DNA with U-G mismatch is affected only by a small amount and flipping is not enhanced significantly. T4 endonuclease V (endoV), which recognizes TD, utilizes the reduced barrier for flipping as a specific recognition element. In uracil DNA glycosylase (UDG), which recognizes U-G mismatches, base flipping is not enhanced and recognition is encoded in a highly specific binding pocket for the flipped base. Simulations of UDG and endoV in complex with damaged DNA provide insight into the essential elements of the catalytic mechanism. Calculations of pKas of active site residues in endoV and endoV-DNA complex show that the pKa, of the N-terminus is reduced from 8.01 to 6.52 while that of Glu-23 increases from 1.52 to 7.82. Thus, the key catalytic residues are in their neutral form. The simulations also show that Glu-23 is also H-bonded to O4' of the 5'-TD enhancing the nucleophilic attack on Cl and that Arg-26 enhances the hydrolysis by electrostatic stabilization but does not participate in proton transfer. In the enzyme-substrate complex of UDG, the role of electrostatic stabilization is played by His-268, whose pKa increases to 7.1 from 4.9 in the free enzyme. The pKa of Asp-145, the other important catalytic residue, remains around 4.2 in the free enzyme and in the complex. Thus, it can not act as a proton acceptor. In the complex the 3'-phosphate of uracil is stabilized next to Asp-145 by two bridging water molecules. Such a configuration activates one water molecule to act as a proton acceptor to produce a stabilizing hydronium ion and the other as a proton donor to produce the nucleophilic hydroxide. It appears that DNA glycosylases share commonalties in recognition of damage but differ in their catalytic mechanisms.     

Beacon+：面向E级超级计算机的轻量级端到端I/O性能监控与分析诊断系统

随着E级计算的屏障被打破,高性能计算已经迈入了新时代。为了满足日益增长的数据访问需求,新兴的技术和存储介质都被运用到了超级计算机中,这使得其架构变得日趋复杂,其性能异常和系统热点定位也变得十分困难。为此,设计并实现了一个面向E级超级计算机的轻量级端到端I/O性能监控与分析诊断系统——Beacon+。该系统无需修改应用代码/脚本即可对每个应用的数据访问过程进行全路径实时监控与分析。通过在线+离线的压缩方法和分布式缓存/存储等机制,Beacon+在保证系统本身高扩展性、低开销的同时还可以持续稳定地提供I/O诊断服务。以神威新一代超级计算机为部署平台,通过I/O标准测试应用和实际应用证明了Beacon+的低开销和高准确性,以及I/O诊断的高效性。     

A RGB image encryption algorithm based on DNA encoding and chaos map

In this paper, a RGB image encryption algorithm based on DNA encoding combined with chaotic map is proposed aiming at characteristics of RGB image. The algorithm firstly carries out DNA encoding for R, G, B components of RGB image; then realizes the addition of R, G, B by DNA addition and carries out complement operation by using the DNA sequence matrix controlled by Logistic; three gray images are got after decoding; finally gets the encrypted RGB images by reconstructing R, G, B components which use image pixels disturbed by Logistic chaotic sequence. Simulation result shows that the proposed algorithm has a large secret key space and strong secret key sensitivity. Meanwhile, it can resist exhaustive attack, statistical attack, and thus it is suitable for RGB image encryption.     

Beacon signals: what, why, how, and where?

Beacons are primarily radio, ultrasonic, optical, laser or other types of signals that indicate the proximity or location of a device or its readiness to perform a task. Beacon signals also carry several critical, constantly changing parameters, such as power-supply information, relative address, location, timestamp, signal strength, available bandwidth resources, temperature and pressure. Although transparent to the user community, beacon signals have made wireless systems more intelligent and human-like. They are an integral part of numerous scientific and commercial applications, ranging from mobile networks to search-and-rescue operations and location-tracking systems. Beacon signals help synchronize, coordinate and manage electronic resources using miniscule bandwidth. Researchers continue to improve their functionality by increasing signal coverage while optimizing energy consumption. Beacon signals' imperceptibility and usefulness in minimizing communication delays and interference are spurring exploratory efforts in many domains, ranging from the home to outer space     

DBN在蛋白质编码区识别问题中的应用研究

针对真核生物DNA序列中蛋白质编码区的识别问题,提出基于深度置信网络（Deep Belief Network,DBN）的组合模型。通过信号处理技术对真核生物的DNA序列进行数值转换,并结合统计学知识提取转换后DNA序列的数值特征;利用随机森林对所提取的特征变量降维;用深度置信网络模型对DNA序列分类判别;根据短时傅里叶变换（Short Time Fourier Transform,STFT）技术对外显子区准确定位。在三个标准测试集上比较组合模型与传统[Logistic]回归模型、贝叶斯判别模型的判别效果,结果显示,深度置信网络组合模型的准确率和特异度等指标都明显优于[Logistic]回归模型和贝叶斯判别模型。