DNA序列特征的统计分析

介绍了近年来在多种学科领域对DNA碱基序列的研究中发展起来的定量分析符号序列的方法,归纳了将碱基与数字对应起来的规则和进行统计分析的方法．并给予一定的评价。DNA分子包涵了丰富的化学信息和生物信息,对于DNA序列的统计分析显得非常重要。将DNA序列表达成数字信号通常有从一维到四维4种不同维数空间的映射方式,其相应的统计方法有均方根涨落、熵近似方法、傅立叶变换和小波变换等,各种方法从多个角度多个层次来分析揭示了DNA序列的结构规律。     

中药色谱指纹图谱的小波变换及分形表达方法

提出一种基于小波变换的色谱指纹图谱分形表达方法。该法运用小波变换将色谱谱线分解至不同分辨尺度，然后计算各尺度分量的分形维数，用色谱的小波基分形参量替代色谱指纹图谱的采样值。仿真实验结果表明，色谱小波基分形参量对谱峰保留时间漂移具有较好的抗干扰能力。以当归和川芎两种中药材的品种及道地性鉴别分类问题为实例，比较研究色谱采样值与小波基分形参量，k-近邻法的交叉验证计算结果表明，小波基分形参量的分类效果优于色谱采样值。     

基于近红外光谱技术的内燃机油鉴别研究

针对常规近红外光谱技术测试内燃机油时光谱信号响应低,对大分子基团分辨率不高,以及光谱信息与其结构组成之间存在非线性关系等难点,提出了一种基于电压为外扰方式的内燃机油二维近红外光谱测试技术,介绍了近红外光谱具有分形的特征.运用小波变换将近红外光谱分解至不同分辨尺度,然后计算各尺度分量的分形维数(盒维数),用近红外光谱的小波基分形参量替代近红外光谱的采样值.计算结果表明,在不同小波基和不同分解尺度下,内燃机油近红外光谱具有不同的盒维数,得到了近红外光谱在分形意义下的特征信息.以美孚、埃索和壳牌3种内燃机油品种鉴别分类问题为实例,比较研究了近红外光谱采样值与小波基分形参量,K近邻法的交互验证计算结果表明,小波基分形参量的分类效果优于近红外光谱采样值.采用近红外光谱技术测试内燃机油的结构组成信息是可行的.     

基于小波变换模极大法的聚乙烯催化剂表面分形分析

运用分形和小波相结合的方法研究负载型聚乙烯催化剂(简称催化剂)表面形态. 采用小波变换模极大(WTMM)法提取了催化剂表面多尺度边缘(细节)图像, 用分形和多重分形方法研究了各尺度边缘图像中边缘点的分布情况, 并用基于小波变换模极大的多重分形谱法讨论了催化剂边缘点奇异强度的分布状况. 研究结果表明, 催化剂的较小尺度边缘图像的分维和多重分形谱可以与催化剂的表面形态和活性进行较好的关联; 高活性催化剂的基于WTMM的多重分形谱的奇异强度跨度更宽, 拥有较多具有较高奇异强度的奇异点. 基于小波和分形对催化剂表面形态的研究, 发挥了小波和分形各自的优点, 为研究物体表面形态提供了思路.     

基于富G序列的无标记荧光传感器检测单链核酸

具有特定构象的富G序列（如G-四链体和G-三链体）与荧光染料相互作用可有效增强其荧光信号强度，被广泛应用于构建无标记荧光生物传感。本研究以硫磺素T(Thioflavin T, ThT)为荧光染料，构建了两种基于富G序列的无标记荧光传感器，用于检测阿尔兹海默病标志物β-淀粉样蛋白（β-Amyloid protein, Aβ）的基因序列。实验结果表明，分子发夹茎长为4个碱基时，富G序列以G-三链体的结构存在，以此构建的G-三链体传感器的输出信号随Aβ基因浓度增加而降低，线性检测范围为1～100 nmol/L，检出限为0.3 nmol/L(S/N=3)。分子发夹茎长为8个碱基且5′端添加碱基AATT时，其与Aβ基因结合后，富G序列多以G-四链体结构存在，以此构建的G-四链体传感器的输出信号随Aβ基因浓度增加而增强，线性检测范围为0.1～100 nmol/L，检出限为0.04 nmol/L (S/N=3)。两种传感器制备过程相似但检测原理不同，为富G序列的深入研究与应用提供了参考，同时为单链核酸的无标记荧光检测提供了新的思路。     

五级谢尔尔宾斯基基三角形形的制备

正分形结构是指不同尺度下具有自相似特性的一类几何结构,由Mandelbrot首先提出~1。分形结构广泛存在于自然界内,例如冬季的雪花、大陆的海岸线等,无不包含着分形的特征。分形研究对于自然科学、工程学以及美学都具有重要意义。尤其在纳米尺度上,构建具有高度自相似的分形结构,对于纳米技术的发展具有一定价值。     

二次电子衬度曲线法研究PVC/MBS共混物断面的分形特征

利用二次电子衬度曲线法测定了聚氯乙烯甲基丙烯酸甲酯丁二烯苯乙烯共聚物(PVCMBS)共混物冲击断面的形貌特征及对应的分形维数值.结果表明,材料的断口或微观结构并不是严格的分形结构,这种自相似性仅存在于一定尺码范围内,不同断面形貌特征所对应的分形维数测量值不同,随着MBS用量增加,PVCMBS共混物缺口冲击强度随满足自相似原理的形貌特征所对应的分形维数值增大而增大.本文从理论上讨论了材料断裂韧性与分形维数的关系.     

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。     

d(C4)相关序列形成四分子i-Motif结构的电喷雾质谱研究

设计了与富含胞嘧啶(C)的DNA序列d(C4)相关的DNA序列d(C4), d(TC4), d(AC4), d(T2C4), d(A2C4), d(C4T), d(C4A)和d(TC4T); 采用电喷雾质谱测定发现这些序列形成四分子非共价复合物离子, 根据离子的相对丰度可确定形成四链i-motif结构的数量和可能性; 同时考察了腺嘌呤(A)和胸腺嘧啶(T)在d(C4)序列的5'和3'端对其形成四分子i-motif结构的影响. 结果表明, 在d(C4)的5'端增加A碱基或T碱基更易形成四分子复合物; 5'端含T碱基比含A碱基更利于形成四分子复合物; 而在d(C4)序列中增加2个A碱基或T碱基比增加相应的单个碱基形成了更高丰度的四分子离子峰.     

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。     

Characterizing Long—range Correlation Properties in Nucleotide Sequences

Using continuous wavelet transform as the analytical tool,the fractal characteristic of nucleotide sequences was studied.The fractal dimension of the exon and intron sequences for different species was calculated.We use the Mexican hat wavelet function as the mother wavelet and Hurst exponent describe the long-range correlation.It is found that the Hurst exponent of intron sequence is larger than of exon sequence for the same gene.     

Prediction of protein secondary structure based on continuous wavelet transform

In this paper, continuous wavelet transform (CWT) is used to extract the number and the relevant positions of the α-helices and short peptides connecting α-helices and β-strands (connecting peptides) from the amino acid sequences of proteins. The amino acid sequence is first mapped into hydrophobicity sequence, and then transformed into CWT value of sequence domain in appropriate scale via CWT. The number and the relevant positions of the α-helices and connecting peptides can be extracted easily and accurately according to the minima of wavelet coefficient in corresponding CWT plot of hydrophobic value sequences with appropriate scale. The analytical results demonstrate that α-helices and connecting peptides can be predicted conveniently and rapidly when this method is used in the processing of 100 non-homologous sequences. However, this method is not suitable for predicting the length of α-helices and connecting peptides.     

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。     

Fractal analysis of polyethylene catalysts surface morphologies based on wavelet transform modulus maxima method

Surface morphologies of supported polyethylene (PE) catalysts are investigated by an approach combining fractal with wavelet. The multiscale edge (detail) pictures of catalyst surface are extracted by wavelet transform modulus maxima (WTMM) method. And, the distribution of edge points on the edge image at every scale is studied with fractal and multifractal method. Furthermore, the singularity intensity distribution of edge points in the PE catalyst is analyzed by multifractal spectrum based on WTMM. The results reveal that the fractal dimension values and multifractal spectrums of edge images at small scales have a good relation with the activity and surface morphology of PE catalyst. Meanwhile the catalyst exhibiting the higher activity shows the wider singular strength span of multifractal spectrum based on WTMM, as well as the more edge points with the higher singular intensity. The research on catalyst surface morphology with hybrid fractal and wavelet method exerts the superiorities of wavelet and fractal theories and offers a thought for studying solid surfaces morphologies. Supported by the Chinese Petroleum & Chemical Corporation Development Department (Grant No. x504024)     

The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage

Tandem repeats of short DNA sequences are commonly found in human DNA. These simple sequence repeats or microsatellites are highly polymorphic in the human genome. Since the anti-tumour agent cisplatin preferentially forms DNA adducts at runs of consecutive guanine nucleotides (poly(G)), the position and frequency of occurrence of poly(G) sequences in the updated human genome was investigated. There are more runs of consecutive guanines than would be expected by random chance. This especially true for poly(G) sequences longer than approximately n = 9. A plot of poly(G) length against log(observed/expected) frequency produced a straight line for n > 9. A similar observation was also found for poly(A) DNA sequence repeats. This data implied that the increase in observed/expected frequency is directly related to length of DNA repeat. It was proposed that long runs of consecutive guanine nucleotides could be a sensitive sensor of cellular DNA damage since a number of DNA damaging agents cause lesions at poly(G) sequences.     

LONG-RANGE CORRELATIONS IN DNA SEQUENCES USING TWO-DIMENSIONAL DNA WALKS

The characterization of long-range correlations and fractal properties of DNA sequences has proved to be a difficult though rewarding task mainly due to the mosaic character of DNA consisting of many patches of various lengths with different nucleotide constitutions. In this paper we investigate statistical correlations among different positions in DNA sequences using the two-dimensional DNA walk. The root-mean-square fluctuation F(l) is described by a power law. The autocorrelation function C(l), which is used to measure the linear dependence and periodicity, exists a power law of C(l) -τμ. We also calculate the mean-square distance ＜R2(l)＞ along the DNA chain, and it may be expressed as ＜R2(l)＞ - l r with 2 ＞γ＞ 1. Our investigations can provide some insights into long-range correlations in DNA sequences.     

Similarity analysis of DNA sequences based on the weighted pseudo-entropy

A DNA primary sequence is a string consisting of letters on an alphabet Ω = {a, c, g, t}. Based on all of the 2-combinations of the set Ω, here the repetition is allowed, we transform a DNA primary sequence into a special sequence over a set with cardinality 10. With the 10-letter sequence, we associate 10 nonnegative numerical sequences and then derive a 10-component vector by means of a weighted pseudo-entropy, which can reflect the information on elements of a sequence and, especially, the order relation among them. The new quantitative characterization of DNA sequences is sensitive to substitution of the string elements. The examination of the relationship among β-globin genes of 15 species illustrates the utility of the proposed approach.     

A novel 2-D graphical representation of DNA sequences of low degeneracy

Some 2-D and 3-D graphical representations of DNA sequences have been given by Nandy, Leong and Mogenthaler, and Randic et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a novel graphical representation of DNA sequences by taking four special vectors in 2-D space to represent the four nucleic acid bases in DNA sequences, so that a DNA sequence is denoted on a plane by a successive vector sequence, which is also a directed walk on the plane. It is showed that the novel graphical representation of DNA sequences has lower degeneracy and less overlapping.     

A 2D graphical representation of DNA sequence based on dual nucleotides and its application

From the perspective of the neighboring dual nucleotides, we introduce a novel 2D graphical representation of DNA sequences based on the magic circle, which correspond to 16 dual nucleotides. So, we can reduce a DNA sequence into a plot set in two‐dimensional space and get a two‐component vector relatively to the introduced covariance matrix. The utility of our approach can be illustrated by the examination of similarities/dissimilarities among the complete coding sequences of β‐globin gene belonging to 11 species. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009