用墨西哥帽小波研究DNA序列的分形特征

结合小波分析和分形理论，采用分数布朗运动(FBM)建立数学模型，研究脱氧 核糖核酸(DNA)序列的自相似性。用DNA walk的方式将DNA序列表达成为一个数字信 号，通过不同小波变换的尺度对应不同特征长度的碱基，选择墨西哥帽小波为母小 波，进行实验考察，结果发现小波系数的图形在许多尺度看上去很相似，大尺度对 应较多的碱基(小波变换尺度为2^7时，对应512个碱基)，能看到概貌；小尺度对应 较少的碱基(小波变换尺度为2^3时，对应32个碱基)，可看到细节。这表明其DNA序 列中存在分形结构，可以用分维数来作为定量描述。这种算法为进一步研究与基因 序列自相似结构有关的基因进化信息提供一种选择的途径。     

二维DNA晶体的程序化设计与自组装的研究进展

按照Watson-Crick的碱基配对原则，在理论上能够人工设计与合成DNA碱基序列并自组装成任何一维和二维结构的DNA晶体。DNA分子这种底端向上(bottom-up)的自组装模式为我们提供了一种精确合成纳米材料的方法。本文将从程序化设计、合成刚性的DNA分子瓦(DNA tile)、分子瓦自组装成二维DNA晶体以及二维DNA晶体作为模板在纳米技术中的应用等方面展开，简述这一新奇的并且有着潜在应用前景的研究领域的最新进展。     

化学与酶促相结合合成并克隆核糖体失活蛋白Gelonin基因

利用已知Gelonin的氨基酸序，逆向推算出整个基因的碱基序列，根据E.coli的密码子偏爱性和后续基因克隆的需要，通过沉默突变设计相应的酶切位点和碱基序列，将整个基因分为四段，每个片段约175－220pb，每一个片段中的互补链从5′末端用化学合成100－120的碱基单链，其中两个链的3′末端有20个互补碱基。利用T4DNA聚合酶酶促添补成双链DNA，用分子克隆技术，分别构建重组子，然后再构建成含整个Gelonin基因的表达载体pET-gel进行表面，经诱导后，获得了一个28000的重组蛋白，并主要以可溶形式存在。     

采用纳米金和双链探针比色检测单碱基突变

将链置换的高度特异性与纳米金凝聚变色的光学特性相结合,设计了一种新型的单碱基突变比色检测方法。本方法直接采用纳米金作为比色报告基团,以两个末端均带有巯基的双链DNA为特异捕获探针,利用互补序列和单碱基突变序列对双链探针置换能力的差异,实现了对单碱基突变的检测。本检测方法直观、快速、简便、成本低,pmol级的样品无需仪器就可以观察到颜色的变化。     

Pb2+与Co(phen)33+及DNA间的相互作用及其分析测定的研究

DNA电化学传感器是近几年发展起来的一类新型的生物传感器[1]。它不仅可以用来识别和检测特定碱基序列的DNA[2],还可以用来研究DNA的损伤及与药物的作用机理[3]。与同位素标记等方法相比,该类传感器具有识别能力强、简单、快速和灵敏度高等特点[4]。随着人类基因组计划和流行性     

高灵敏纳米金比色芯片检测乙型肝炎病毒DNA及其变异

构建了新型纳米金比色芯片,利用Taq DNA连接酶的连接特异性,将其与乙型肝炎病毒DNA( HBV-DNA)靶序列完全互补杂交的捕获探针(固定在芯片上)和纳米金修饰的探针连接成一条链,从而将纳米金颗粒固定到芯片点阵上,再通过银染反应放大,形成裸眼可见的显色信息.通过点阵的位置及灰度,即可判断HBV-DNA靶序列的单碱基突变,并得出相对定量信息.本实验对不同浓度的HBV-DNA靶序列进行了检测.结果显示:此技术对单碱基突变有很强的特异性识别能力,并且具有较高的灵敏度(约10 pmol/L),在10～100 pmol/L浓度范围内表现出较好的线性关系.该技术检测时间短(＜1 h)、操作简单、不需要特殊的检测设备,具有很好的临床应用前景.     

溴化乙锭标记DNA电化学探针的研究

以乙基-(3-二甲基丙基)碳化二亚胺盐酸盐(EDC)为偶联活化剂,将电化学活性物质溴化乙锭(Ethidiumbromide,EB)成功地标记在人工合成的含有21个碱基的寡聚DNA片段上,制备成EB标记DNA探针;用电化学方法将待测样品DNA片段固定在石墨电极表面,在一定的温度、pH值和离子强度条件下与EB标记DNA探针进行杂交反应,从而对靶序列DNA片段进行识别和测定.此外,还讨论了该探针的电化学性质、荧光光谱、待测DNA片段在石墨电极表面的电化学固定、DNA链碱基长度对EB标记DNA电化学探针的影响以及探针的选择性、重现性和寿命,结果令人满意.     

盐酸小檗碱与DNA作用的序列特异性研究

基于分子吸收和发射测量,研究了盐酸小檗碱与特定序列DNA间的相互作用.结果发现双链DNA中含有不配对 G 碱基时,其与盐酸小檗碱作用后产生的光谱特征将明显不同于完全互补的双链DNA.该特征可被用于检测1个错配碱基的双链DNA.利用 Hyperchem Professional 软件包计算了4种寡聚核苷酸的电荷分布情况,并在此基础上进一步探讨了盐酸小檗碱与寡聚核苷酸之间的作用机理.     

寡聚酰胺为探针的电化学DNA生物传感器

DNA分子中的碱基对可以长程传递电荷, DNA分子中的碱基π堆积结构为电荷的长程传递提供了良好的通道. 电荷在DNA分子中的传递受碱基序列的影响, 利用这种性质可以构建DNA碱基错配检测的电化学传感器. 寡聚酰胺能和DNA以小沟绑定方式高亲和力地结合, 并且具有序列识别功能, 本文以带有硝基官能团的寡聚酰胺分子为电化学探针, 设计了电化学DNA生物传感器. 结果显示, 寡聚酰胺与DNA修饰电极作用后, 电化学响应显著增强, 并且可以作为检测DNA碱基错配的电化学探针分子.     

基于纳米金比色检测NOS1AP基因单碱基突变

基于单、双链DNA与纳米金颗粒间的不同静电作用, 建立了一种基于颜色反应检测NOS1AP基因单碱基突变的方法. 根据NOS1AP基因的单碱基多态位点设计检测探针、互补靶序列及带有单碱基突变序列寡核苷酸DNA. 室温下, 检测探针分别与互补序列、单碱基突变序列在缓冲液中进行杂交, 再分别加入纳米金溶液以及NaCl溶液. 用肉眼可以观察到纳米金溶液在两种不同杂交溶液中产生明显不同的颜色变化. 这种变化可通过紫外-可见分光光度计测定纳米金溶液的紫外吸收峰值的变化来证实. 实验结果表明, 纳米金溶液在一定浓度NaCl存在的条件下, 对互补双链NOS1AP DNA及单碱基突变NOS1AP DNA呈现出不同的颜色反应及紫外吸收光谱的改变. 此方法可望用于相关疾病的医学诊断及单碱基突变的检测.     

Computational analyses of high-throughput protein-protein interaction data

Protein-protein interactions play important roles in nearly all events that take place in a cell. High-throughput experimental techniques enable the study of protein-protein interactions at the proteome scale through systematic identification of physical interactions among all proteins in an organism. High-throughput protein-protein interaction data, with ever-increasing volume, are becoming the foundation for new biological discoveries. A great challenge to bioinformatics is to manage, analyze, and model these data. In this review, we describe several databases that store, query, and visualize protein-protein interaction data. Comparison between experimental techniques shows that each high-throughput technique such as yeast two-hybrid assay or protein complex identification through mass spectrometry has its limitations in detecting certain types of interactions and they are complementary to each other. In silico methods using protein/DNA sequences, domain and structure information to predict protein-protein interaction can expand the scope of experimental data and increase the confidence of certain protein-protein interaction pairs. Protein-protein interaction data correlate with other types of data, including protein function, subcellular location, and gene expression profile. Highly connected proteins are more likely to be essential based on the analyses of the global architecture of large-scale interaction network in yeast. Use of protein-protein interaction networks, preferably in conjunction with other types of data, allows assignment of cellular functions to novel proteins and derivation of new biological pathways. As demonstrated in our study on the yeast signal transduction pathway for amino acid transport, integration of high-throughput data with traditional biology resources can transform the protein-protein interaction data from noisy information into knowledge of cellular mechanisms.     

DNA中编码序列的分形特征研究

随着基因组数据库的日益增大，如何从这庞大的数据库中提取有用的信息已成为全世界科学家迫在眉睫的难题。本文运用网格维数分别刻画了60个人类基因序列编码区的分形特征。研究结果表明：在同一个基因中，外显子的维数一般要大于整个蛋白质编码序列的维数，并通过对比随机序列的网格维数，证实了这一结论。结合分形理论及功率谱研究可以得出，具有较少外显子的基因，外显子中包含有较多的遗传信息，而对于较多外显子的基因则相反，遗传信息可能储存于内含子中。这些结论对内含子功能以及DNA序列的复杂性的研究具有一定的理论意义和实用价值。     

人类Y染色体回文序列中的重复序列与碱基关联

利用信息论和统计学的方法并结合生物学的特征研究人类Y染色体回文序列的互信息、“n字”熵、条件熵,定量分析了回文序列的长程关联和短程关联,发现其中既存在长程关联也存在短程关联,并且它们主要是由序列中的重复序列引起的．研究表明重复序列含量越高碱基之间的关联越强．     

Linear regression model of DNA sequences and its application

We constructed six new models to analyze the DNA sequences. First, we regarded a DNA primary sequence as a random process in t and gave three ways to define nucleotides' random distribution functions. We extracted some parameters from the linear model and analyzed the changes of the nucleotides' distributions. In order to facilitate the comparison of DNA sequences, we proposed two ways to measure their similarities. Finally, we compared the six models by analyzing the similarities of the DNA primary sequences presented in Table 1 and selected the optimal one.     

A novel graphical representation of protein sequences and its application

On the basis of information on the evolution of the 20 amino acids and their physiochemical characteristics, we propose a new two-dimensional (2D) graphical representation of protein sequences in this article. By this representation method, we use 2D data to represent three-dimensional information constructed by the amino acids' evolution index, the class information of amino acid based on physiochemical characteristics, and the order of the amino acids appearing in the protein sequences. Then, using discrete Fourier transform, the sequence signals with different lengths can be transformed to the frequency domain, in which the sequences are with the same length. A new method is used to analyze the protein sequence similarity and to predict the protein structural class. The experiments indicate that our method is effective and useful.     

Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements

Recent comparative studies of the human and mouse genomes have revealed sets of conserved nongenic sequences (CNGs) and sets of ultraconserved elements (UCEs). Both sets of sequences, which exhibit extremely high levels of conservation, extend over hundreds of bases and have no known function. Since there is no detectable sequence homology between paralogous CNGs or UCEs in either of the species, an alignment-free technique is needed for their analysis. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers, including information on stability, the minimum energy conformation, and flexibility. We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences.     

Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes

New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive detection of transgenic maize at percentages lower than 1%.