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.     

外消旋化合物生物催化去对称化研究进展

手性化合物外消旋体的生物催化去对称化是目前生物与有机合成领域的重点、难点和热点,也是制备光学纯手性化合物的重要途径.我们将近年来发展起来的手性化合物生物催化去对称化的方法归纳为立体转化去对称化法、线性去对称化法、循环去对称化法、对映体收敛去对称化法和一步去对称化法5大类,对这些方法的原理、特点及其应用进展分别进行介绍,...     

DNA的电化学研究

本文对ＤＮＡ与电极的相互作用，ＤＮＡ的电化学反应，ＤＮＡ与其它分子相互作用的电化学研究和ＤＮＡ的电化学分析等方面的研究进展作了归纳和评述。     

基于DNA酶催化的卟啉金属化检测锌

利用G-四链体DNA（T30695）催化Zn²⁺插入到中卟啉IX（MPIX）中，引起荧光偏移的特点，建立了检测Zn²⁺的方法。在40μmol/L MPIX、0.6μmol/L Pb²⁺、5μmol/L T30695和1%Triton的最优实验条件下，该方法在Zn²⁺浓度为0.5～5μmol/L范围内呈现良好的线性关系，相关系数R²=0.95，检出限为73.5 nmol/L。离子选择性实验表明该方法对Zn²⁺具有较好的选择性，用于实际样品测定，回收率在94.7%～100.4%之间。     

Optical Separation of Racemic Phenyl-alanine,and Structure of Complex Consisting of R-Phenylalanine and R-Mandelic Acid

1INTRODUCTIONTheformationofco-crystalsofadiastereo-mericmolecularcomplexisaneffectivemethodforseparatingracemicmixtureintoitsenantiomers[1,2].Asasequeltotheinvestigationonseparatingtheracemicmandelicacidbyachiralalanineinthelaboratory[3],inthepresentworkt…     

对映体制备性分离方法的进展

旋光性化合物越来越引起人们的关注。外消旋体拆分法是获得单一手性化合物的重要途径。本文综述了近年来制备性对映体拆分中发展比较快的手性固定相液相色谱法和膜拆分法。     

基于DNA四面体纳米结构探针的电化学生物传感器检测DNA甲基化

该文以DNA四面体纳米结构探针(TSP)为捕获探针,将辣根过氧化物酶标记的IgG抗体结合在纳米金颗粒表面(AuNPs-IgG-HRP)作为信号分子,构建了一种新型DNA甲基化电化学传感器。利用一步热变性法组装成TSP后,通过Au—S键固定在修饰纳米金颗粒的金电极表面,经过靶标DNA杂交、5-甲基胞嘧啶(5-mc)抗体及AuNPs-IgG-HRP结合后,用差分脉冲伏安法(DPV)进行检测。采用循环伏安法(CV)和电化学阻抗谱(EIS)对修饰电极的构建过程进行电化学表征。探究了杂交时间、5-mc抗体浓度、IgG-HRP加入体积、氢醌(HQ)和过氧化氢(H₂O₂)浓度对传感器的影响。在最佳条件下,该传感器对甲基化DNA的线性响应范围为1.0×10^-15～1.0×10^-10 mol/L,检出限(S/N=3)为4.4×10^-16 mol/L。该传感器具有良好的选择性和稳定性,为DNA甲基化检测提供了新方法。     

三菲咯啉合铁手性配合物键合DNA的立体选择性

应用光谱法研究了手性金属配合物［Ｆｅ（ｐｈｅｎ）３］＾２＋与小牛胸腺ＤＮＡ的作用，确定了△型异构体对Ｂ型右手螺旋ＤＮＡ有优先键合的立体选择性。     

DNA电化学生物传感器在重金属快速检测中的研究进展

DNA电化学生物传感器是一类以DNA为敏感元件或检测对象,将核酸分子特异性识别过程中产生的信号通过换能器转化为电信号,从而实现对目标物定性或定量检测的传感器,具有响应速度快、操作简单、选择性好、灵敏度高、检测成本低等优点,实现了多领域中重金属、真菌毒素、核酸等的快速实时检测.介绍了 DNA电化学生物传感器的组装单元、电...     

Mirror-image carbohydrates: synthesis of the unnatural enantiomer of a blood group trisaccharide

Methyl D-glucoside and d-glucose pentaacetate are transformed, respectively, into methyl alpha-O-glucuronide 3 and hydroxymethyl beta-C-glucuronide 9, which undergo decarboxylative elimination efficiently to produce 4-deoxypentenoside 4 and L-glucal 10. These unsaturated pyranosides provide an expeditious entry into mirror-image oligosaccharides, as demonstrated in the synthesis of the unnatural enantiomer of the H-type II blood group determinant trisaccharide (D-Fuc-(alpha1-->2)-L-Gal-(beta1-->4)-L-GlcNAc-beta-OMe). This work illustrates that D-glucose, a common starting material in the synthesis of naturally occurring carbohydrates, can also be used to prepare their mirror-image analogues.     

镜像配基筛选:克服“酶屏障”的多肽、寡核苷酸药物研发技术

生物体内存在的酶屏障是功能性多肽和寡核苷酸成药的重要瓶颈.以镜像噬菌体展示技术(mirror-image phage display)和镜像适配体筛选技术(Spiegelmer technology)为代表的镜像配基筛选技术能有效地克服这一屏障,获得对靶点具有特异识别能力且在生理条件下高度稳定的D型多肽和L型寡核苷酸配基,有望成为多肽或寡核苷酸类特异性药物研发的有利工具.本文主要综述镜像配基筛选技术的原理及其在药学领域的研究进展.     

Mirror-image packing in enantiomer discrimination molecular basis for the enantioselectivity of B.cepacia lipase toward 2-methyl-3-phenyl-1-propanol

Synthetic chemists often exploit the high enantioselectivity of lipases to prepare pure enantiomers of primary alcohols, but the molecular basis for this enantioselectivity is unknown. The crystal structures of two phosphonate transition-state analogs bound to Burkholderia cepacia lipase reveal this molecular basis for a typical primary alcohol: 2-methyl-3-phenyl-1-propanol. The enantiomeric alcohol moieties adopt surprisingly similar orientations, with only subtle differences that make it difficult to predict how to alter enantioselectivity. These structures, along with a survey of previous structures of enzyme bound enantiomers, reveal that binding of enantiomers does not involve an exchange of two substituent positions as most researchers assumed. Instead, the enantiomers adopt mirror-image packing, where three of the four substituents at the stereocenter lie in similar positions. The fourth substituent, hydrogen, points in opposite directions.     

Ligating DNA with DNA

Cloning DNA typically involves the joining of target DNAs with vector constructs by enzymatic ligation. A commonly used enzyme for this reaction is bacteriophage T4 DNA ligase, which requires ATP as the energy source to catalyze the otherwise unfavorable formation of a phosphodiester bond. Using in vitro selection, we have isolated a DNA sequence that catalyzes the ligation of DNA in the absence of protein enzymes. We have used the action of two catalytic DNAs, an ATP-dependent self-adenylating deoxyribozyme (AppDNA) and a self-ligating deoxyribozyme, to create a ligation system that covalently joins oligonucleotides via the formation of a 3',5'-phosphodiester linkage. The two-step process is conducted in separate reaction vessels wherein the products of deoxyribozyme adenylation are purified before their use as substrates for deoxyribozyme ligation. The final ligation step of the deoxyribozyme-catalyzed sequence of reactions mimics the final step of the T4 DNA ligase reaction. The initial rate constant (k(obs)) of the optimized deoxyribozyme ligase was found to be 1 x 10(-)(4) min(-)(1). Under these conditions, the ligase deoxyribozyme promotes DNA ligation at least 10(5)-fold faster than that generated by a simple DNA template. The self-ligating deoxyribozyme has also been reconfigured to generate a trans-acting construct that joins separate DNA oligonucleotides of defined sequence. However, the sequence requirements of the AppDNA and that of the 3' terminus of the deoxyribozyme ligase limit the range of sequences that can be ligated.     

DNA polymerase-catalyzed DNA network growth

The distinct base pairing property of DNA is an advantageous phenomenon that has been exploited in the usage of DNA as scaffold for directed self-organization to form nanometer-sized objects in a desirable fashion. Herein we report the construction of three-dimensional DNA-based networks that can be generated and amplified by the DNA polymerase chain reaction (PCR). The approach is flexible allowing tuning of the meshes of the network by variation of the size of the template. Additionally, further diversification can be introduced by employment of chemically modified nucleotides in PCR allowing the introduction of functionalities and reporter moieties.     

DNA loops and semicatenated DNA junctions

Background  

Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized.     

Electrontransfer through DNA and metal-containing DNA

DNA is currently explored as a new material for functional, molecular nano-architectures. In this respect, one major question is to transform DNA into a conducting material which has the potential for self-assembly into electronically active networks. The article covers recent insight into how DNA transports positive (holes) and negative (excess electrons) charges. It was found that holes move through DNA over significant distances using a G- and to a lesser extent also A-based hopping mechanism. EPR studies and recent investigations with model systems show that excess electrons can also hop through the duplex. The second part of the article describes how DNA is currently modified, particularly coated with metals, in order to increase the conductivity.     

Manipulating DNA writhe through varying DNA sequences

It is demonstrated that the shapes and magnitudes of DNA writhe can be precisely manipulated solely through maneuvering the nucleotide sequence of DNA and without the assistance of topoisomerases.     

New DNA Technology and the DNA Biosensor

Abstract

Recently there has been an increasing demand to produce systems for the detection of specific DNA sequences that are amenable to non-specialised laboratories. This demand has led to many innovative and novel approaches to DNA analysis which may collectively be termed ′new DNA technology′. Here, we review these advances in relation to their applicability for the production of a DNA biosensor. The present state of the art is described and future possibilities are considered.     

QUANTITATION OF DNA DAMAGE IN NON-RADIOACTIVE DNA

Three principal methods have been developed for measuring femtomoles of damage in nanogram quantities of non-radioactive DNA. Lesions which can be quantified include single and double strand breaks, alkali labile sites including apurinic and apyrimidinic sites, and pyrimidine dimers. The first in vitro method measures the conversion of supercoiled DNA to relaxed or linear molecules, and can detect up to four lesions per molecule. The second in vitro method (supercoil depletion) assesses the fraction of intact linear molecules of homogeneous length, and allows detection of 8 lesions/molecule. The third method, measurement of molecular length distributions of DNAs of heterogeneous length, reveals the extent of DNA damage and repair in vivo or in vitro.