DNA电性能测定方法以及DNA分子器件的研究进展

DNA分子不仅能够定义生命机体的基因代码，而且在生命科学领域以外，尤其是纳米技术领域中发挥着重要的作用．关于DNA分子的导电性，目前存在争议．文中在大量文献的基础上，试图对DNA分子导电性的研究现状和测定方法进行较详尽的评述，并对电荷在DNA内的可能迁移机制做简要的介绍．此外，基于DNA分子或以DNA分子为模板的分子器件是当前国际的一个研究热点，文中对DNA分子器件的研究现状进行了总结，并对其应用前景进行了预测．     

非特异性PCR产物的分离和扩增

在PCR（polymerase chain reaction)扩增产物的非特异性电泳带位置上及弥散状背景的一定间隔位置上，分别以切胶分离相应分子量的DNA分子作为模板，用产生这些非特异性DNA分子的一种引物在通用PCR条件下进行PCR扩增，仅在切胶的相应位置出现DNA分子量同样大小的电泳条带。阐述了这种模板DNA分子形成和出现非特异性电泳带与弥散状背景之间的关系。     

DNA的生物催化功能

近年来，发现不少结构特殊的DNA分子具有多种生物催化功能，这些DNA分子被称为脱氧核酶或酶性DNA，它们在用作RNA或DNA工具酶、基因分析和诊断手段以及基因治疗药物等方面的潜力引人注目，综述了这些DNA分子的种类、性质和应用方面的最新研究进展。     

基于DNA链置换反应的编码器逻辑运算模型研究

作为自组装DNA计算领域中一门新技术,DNA链置换反应在分子计算领域得到了广泛的应用.基于自组装DNA计算原理,设计了对应不同逻辑门的DNA分子电路.基于DNA链置换反应机理构建了编码器逻辑电路的分子计算模型.当输入DNA分子信号链时,将不同分子浓度比的DNA分子逻辑门电路混合,借助分子间的特异性杂交反应及分子间链置换反应,最终可输出信号链分子.Visual DSD仿真结果表明了本文设计的编码器逻辑计算模型的可行性与准确性.为拓展分子逻辑电路的应用做出有益的探索.     

DNA分子标记在猫科动物系统发生关系研究中的应用

DNA分子标记的广泛应用,使得系统进化、生物地理、群体遗传及人类学等领域的研究得到前所未有的发展.猫科动物分子系统发育关系的重建是目前猫科动物DNA研究的主要方向,进而可以从DNA分子水平上研究猫科动物的进化过程及系统发育关系的本质.本文对DNA分子标记在猫科动物分子系统学中的部分研究成果做了概括.     

DNA计算研究的新进展

DNA计算(DNA computing)是伴随着分子生物学的兴起和发展而出现的．作为一种全新的算法，DNA计算显示了其进行复杂运算的可行性．该文介绍DNA计算的机理，探讨了目前DNA计算的研究进展，并介绍了表面固定的生物计算和由输入DNA分子同时提供数据和燃料的生物分子自动机．     

分子生态学与生物多样性研究

讨论了分子生态学的概念、研究方法及发展状况，其中，DNA水平和蛋白质水平的研究方法是分子生态学的重要研究方法．最后，系统论述了分子生态学在生物多样性研究中的应用现状，并对其应用前景作了展望。     

DNA粘接计算模型及其应用

DNA计算是应用分子生物技术进行计算的新方法。应用形式语言及自动机理论技术研究DNA计算理论,有利于推动理论计算科学的发展。本文根据DNA分子的结构及特点给出了DNA分子的形式化描述,介绍了DNA粘接计算模型的文法结构和计算能力,并应用DNA计算方法求解3-SAT问题。     

DNA大分子上一种新的硫修饰

DNA分子硫修饰的发现，为生物学研究打开了又一扇大门。“DNA大分子上一种新的硫修饰”的论文，首次揭开了细菌DNA大分子上掺入硫元素的一种崭新的修饰系统的面纱，上海交通大学教授邓子新和他的课题组为这一成果做出巨大贡献。[编者按]     

DNA分子标记在水稻遗传育种中的应用

综述了近年来DNA分子标记在水稻分子遗传图谱的构建、遗传资源保存和遗传多样性分析、基因的标记及克隆、比较基因组学研究、分子标记辅助育种等方面研究的应用及存在的问题，展望了其应用前景。     

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components is reviewed. It has been found that acetone is the only effective sensitizer for the study of the triplet excited states of DNA components. The transient absorption spectrum of guanyl radical cation resulting from the interaction of triplet acetone and DNA was observed directly, and the original evidence for selective damage of DNA by excited photosensitizer was obtained for the first time, which offered a new pathway for obtaining the main transient species of selective damage of DNA by photonucleases and illustrating initial oxidation mechanism of DNA via electron transfer.     

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components

Progress in dynamic study on the triplet excited states and radical ions of DNA and its components is reviewed. It has been found that acetone is the only effective sensitizer for the study of the triplet excited states of DNA components. The transient absorption spectrum of guanyl radical cation resulting from the interaction of triplet acetone and DNA was observed directly, and the original evidence for selective damage of DNA by excited photosensitizer was obtained for -the first time, which offered a new pathway for obtaining the main transient species of selective damage of DNA by photonucleases and illustrating initial oxidation mechanism of DNA via electron transfer.     

Base stacking controls excited-state dynamics in A.T DNA

Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50-150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.     

基于分子信标的逻辑门的计算模型

基于DNA计算的布尔电路的模拟是DNA计算研究中的一个非常具有应用前景的潜在的研究方向。利用分子信标和三链核酸分子的高度特异性及稳定性,提出了一个逻辑与、逻辑或门的DNA计算模型。基于分子信标的二种状态,将逻辑门的信息处理过程分为计算和输出二个子过程,从而使得这种基于DNA分子的逻辑门具有重复可用性,为构建基于DNA分子的大规模集成电路奠定了基础。     

量子的半保留克隆

目的提出一种使得量子可以完全克隆的机制——量子半保留克隆机制。方法比较量子的克隆机制与DNA的半保留机制,研究量子的半保留克隆机制。结果通过各种条件的对比研究,获得量子的半保留克隆机制。结论存在任意一个未知的、具有空间对称的量子态,不需要正交条件,其可以在量子克隆机作用下以任意一个基矢为模板,按照空间同步的或者空间异步的方式,克隆出另外一个基矢;在空间的对称操作下产生分离,形成了两个与初始量子态完全等价的量子态;两个量子态各半保留了其初始量子态的基矢。     

Mechanism of DNA translocation in a replicative hexameric helicase

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral 'staircase' that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.     

DNA-programmable nanoparticle crystallization

It was first shown more than ten years ago that DNA oligonucleotides can be attached to gold nanoparticles rationally to direct the formation of larger assemblies. Since then, oligonucleotide-functionalized nanoparticles have been developed into powerful diagnostic tools for nucleic acids and proteins, and into intracellular probes and gene regulators. In contrast, the conceptually simple yet powerful idea that functionalized nanoparticles might serve as basic building blocks that can be rationally assembled through programmable base-pairing interactions into highly ordered macroscopic materials remains poorly developed. So far, the approach has mainly resulted in polymerization, with modest control over the placement of, the periodicity in, and the distance between particles within the assembled material. That is, most of the materials obtained thus far are best classified as amorphous polymers, although a few examples of colloidal crystal formation exist. Here, we demonstrate that DNA can be used to control the crystallization of nanoparticle-oligonucleotide conjugates to the extent that different DNA sequences guide the assembly of the same type of inorganic nanoparticle into different crystalline states. We show that the choice of DNA sequences attached to the nanoparticle building blocks, the DNA linking molecules and the absence or presence of a non-bonding single-base flexor can be adjusted so that gold nanoparticles assemble into micrometre-sized face-centred-cubic or body-centred-cubic crystal structures. Our findings thus clearly demonstrate that synthetically programmable colloidal crystallization is possible, and that a single-component system can be directed to form different structures.     

产冷活性淀粉酶嗜冷菌的分离和纯化

文章主要对产冷活性淀粉酶的冷适应微生物进行分离和纯化。通过对菌株的分离和提取基因组DNA进行PCR扩增得到其16S rRNA基因后连接于T-载体再转入大肠杆菌JM109中，筛选阳性克隆转化子进行培养，最后提取质粒进行琼脂糖凝胶电泳检测。     

Protein activity regulation by conformational entropy

How the interplay between protein structure and internal dynamics regulates protein function is poorly understood. Often, ligand binding, post-translational modifications and mutations modify protein activity in a manner that is not possible to rationalize solely on the basis of structural data. It is likely that changes in the internal motions of proteins have a major role in regulating protein activity, but the nature of their contributions remains elusive, especially in quantitative terms. Here we show that changes in conformational entropy can determine whether protein-ligand interactions will occur, even among protein complexes with identical binding interfaces. We have used NMR spectroscopy to determine the changes in structure and internal dynamics that are elicited by the binding of DNA to several variants of the catabolite activator protein (CAP) that differentially populate the inactive and active DNA-binding domain states. We found that the CAP variants have markedly different affinities for DNA, despite the CAP?DNA-binding interfaces being essentially identical in the various complexes. Combined with thermodynamic data, the results show that conformational entropy changes can inhibit the binding of CAP variants that are structurally poised for optimal DNA binding or can stimulate the binding activity of CAP variants that only transiently populate the DNA-binding-domain active state. Collectively, the data show how changes in fast internal dynamics (conformational entropy) and slow internal dynamics (energetically excited conformational states) can regulate binding activity in a way that cannot be predicted on the basis of the protein's ground-state structure.