Crystal structure of T4 endonuclease VII resolving a Holliday junction

Holliday proposed a four-way DNA junction as an intermediate in homologous recombination, and such Holliday junctions have since been identified as a central component in DNA recombination and repair. Phage T4 endonuclease VII (endo VII) was the first enzyme shown to resolve Holliday junctions into duplex DNAs by introducing symmetrical nicks in equivalent strands. Several Holliday junction resolvases have since been characterized, but an atomic structure of a resolvase complex with a Holliday junction remained elusive. Here we report the crystal structure of an inactive T4 endo VII(N62D) complexed with an immobile four-way junction with alternating arm lengths of 10 and 14 base pairs. The junction is a hybrid of the conventional square-planar and stacked-X conformation. Endo VII protrudes into the junction point from the minor groove side, opening it to a 14 A x 32 A parallelogram. This interaction interrupts the coaxial stacking, yet every base pair surrounding the junction remains intact. Additional interactions involve the positively charged protein and DNA phosphate backbones. Each scissile phosphate that is two base pairs from the crossover interacts with a Mg2+ ion in the active site. The similar overall shape and surface charge potential of the Holliday junction resolvases endo VII, RuvC, Ydc2, Hjc and RecU, despite having different folds, active site composition and DNA sequence preference, suggest a conserved binding mode for Holliday junctions.     

星形共聚高分子微相分离的DPD模拟

用耗散粒子动力学(DPD)模拟方法研究了两种不同类型四臂星形两嵌段共聚物(A)4(B)4和(AB)4的微相分离,得到了体心立方球状、六方圆柱、层状、多孔层状和双连续螺旋状等几种稳定的介观结构以及一些过渡态结构。结果表明:其微相分离行为在总体上与线性和环状两嵌段共聚高分子相类似,而(A)4(B)4比(AB)4更容易发生相分离。介观层次上的计算机模拟可以作为对理论研究的一种补充,从而能够提供更为详细的信息。     

Synthesis from DNA of a molecule with the connectivity of a cube

A principal goal of biotechnology is the assembly of novel biomaterials for analytical, industrial and therapeutic purposes. The advent of stable immobile nucleic acid branched junctions makes DNA a good candidate for building frameworks to which proteins or other functional molecules can be attached and thereby juxtaposed. The addition of single-stranded 'sticky' ends to branched DNA molecules converts them into macromolecular valence clusters that can be ligated together. The edges of these frameworks are double-helical DNA, and the vertices correspond to the branch points of junctions. Here, we report the construction from DNA of a covalently closed cube-like molecular complex containing twelve equal-length double-helical edges arranged about eight vertices. Each of the six 'faces' of the object is a single-stranded cyclic molecule, doubly catenated to four neighbouring strands, and each vertex is connected by an edge to three others. Each edge contains a unique restriction site for analytical purposes. This is the first construction of a closed polyhedral object from DNA.     

异径四通管液压胀形工艺分析及过程仿真

将相似理论与正交试验设计引入计算机仿真方案的制定中,并使用大型通用非线性有限元软件MARC/AutoForge对异径四通管的液压胀形工艺过程进行了仿真,得到了最佳工艺参数.     

润滑表面膜在线电测技术研究

为了在线研究摩擦副中表面膜的变化,提出采用摩擦副间的动态接触电阻定性地表征表面膜状态的测试技术．测量电路包括四臂电桥测电阻,信号放大、光耦隔离等模块．针对往复运动的特点,提出了可揭示表面膜状态的数据处理方法,并在自制的缸套／活塞环摩擦试验机上进行润滑条件下表面膜形成和损伤的试验研究．研究表明：采用接触电阻法可在线观测表面膜的形成、损伤及恢复等表面膜变化比较显著的过程．     

利用Fabry-Perot谐振腔和介质谐振天线实现约瑟夫森结阵列的自辐射

本文提出了一种利用Fabry-Perot谐振腔和介质谐振天线,同时集成偶极天线阵实现约瑟夫森结阵列自辐射的方法.在介质基片上制作集成偶极天线阵的双晶约瑟夫森结阵列,并将其嵌入到Fabry-Perot谐振腔内.将基片作为一介质谐振天线,使其与Fabry-Perot谐振腔谐振在同一频率下,从而通过高频电磁耦合机制实现结之间以及结与外部微波电路之间的耦合.文中分别进行了数值仿真和实验研究.对一个包含166个双晶约瑟夫森结的结阵列进行了液氮温度时的测试,在片外（off-chip）检测到了75.2GHz,10pW的辐射信号,与仿真结果吻合.该方法为基于约瑟夫森效应的太赫兹（THz）源提供了一种可能.     

Sequence of retrovirus provirus resembles that of bacterial transposable elements

The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified lambda phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell-virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.     

新型四臂巡检机器人结构设计及转向越障研究

针对巡检机器人工作任务的需求和高压输电线路障碍物的特点,提出一种由三轴复合转动关节和双轴复合转动关节串联三个杆件组成的新型四臂巡检机器人,机器人可以通过各个关节之间的配合来实现转向越障中的重力平衡.分析了机器人转向越障的重力平衡条件和转向越障的步态,并利用Adams仿真软件对转向越障整体过程进行仿真分析,最后进行了样机的实验.通过对仿真结果和样机实验的分析表明,该巡检机器人具有转向越障的能力,并能够在转向越障中保证重力平衡.     

单分子二极管整流特性的第一性原理计算

在分子电子学领域中, 设计分子的结构可以实现特定的功能. 单分子二极管的整流行为是极具吸引力的器件功能之一. 研究了对称分子和非对称分子结的电子输运, 分别对应为四苯基和二嘧啶基二苯基单分子结, 二者均是共价结合到两金属电极. 与其同源对称嵌段相比, 非对称二嵌段分子表现出明显的整流行为, 且电子输运方向是从二苯基流向二嘧啶基. 利用密度泛函理论(density functional theory, DFT)和非平衡格林函数(non-equilibrium Green's function, NEGF)结合的第一性原理方法研究了单分子结的电子结构及其量子输运. 电流-电压 ($I$-$V$)曲线的非对称性可以用非对称分子二嵌段在偏压下由于电子态的局域性带来的非平衡效应进行解释. 本理论计算定性上符合其他小组的实验结果, 且尝试了不同的末端接触. 结果发现, 实验中的扫描隧道显微镜(scanning tunneling microscope, STM)针尖接触结构会一定程度地抵消非对称分子的整流效应, 而 STM 针尖接触结构的结果分析也符合之前的理论预测.     

DNA bending at adenine . thymine tracts

Intrinsic bending of DNA molecules results from local structural polymorphism in regions of homopolymeric dA . dT which are at least 4 base pairs long; the A . T tracts must be repeated in phase with the helix screw. Bending, in the direction of base-pair tilt rather than roll, occurs at the junctions between the A . T tract and adjacent B-DNA, with a larger angle at the 3' than at the 5' end of the A tract.     

Formation and branch migration of Holliday junctions mediated by eukaryotic recombinases

Holliday junctions (HJs) are key intermediates in homologous recombination and are especially important for the production of crossover recombinants. Bacterial RecA family proteins promote the formation and branch migration of HJs in vitro by catalysing a reciprocal DNA-strand exchange reaction between two duplex DNA molecules, one of which contains a single-stranded DNA region that is essential for initial nucleoprotein filament formation. This activity has been reported only for prokaryotic RecA family recombinases, although eukaryotic homologues are also essential for HJ production in vivo. Here we show that fission yeast (Rhp51) and human (hRad51) RecA homologues promote duplex-duplex DNA-strand exchange in vitro. As with RecA, a HJ is formed between the two duplex DNA molecules, and reciprocal strand exchange proceeds through branch migration of the HJ. In contrast to RecA, however, strand exchange mediated by eukaryotic recombinases proceeds in the 3'-->5' direction relative to the single-stranded DNA region of the substrate DNA. The opposite polarity of Rhp51 makes it especially suitable for the repair of DNA double-strand breaks, whose repair is initiated at the processed ends of breaks that have protruding 3' termini.     

杂交狼尾草分子标记分析DNA快速提取方法

以杂交狼尾草叶片为材料,用0.05 mol NaOH溶液在沸水浴中加热处理10 min,进而用pH3.0的TE溶液进行中和获得DNA提取液,并用该DNA提取液为模板进行RAPD-PCR和SSR-PCR扩增.结果显示:用该方法提取的DNA与常规CTAB法提取的DNA质量相当,可用于以PCR技术为基础的DNA分子标记分析与96孔板技术相结合,可以实现DNA高通量提取.     

鼠痘病毒PCR检测方法的建立及在鼠源性生物制品检定中的应用

目的建立小鼠鼠痘病毒PCR检测方法,并应用于鼠源性生物制品的检测。方法根据鼠痘病毒基因组序列中保守的crmD片段设计一对引物,建立鼠痘病毒PCR检测方法;人工感染20只小鼠,对其肝、脾、肾、脚掌及血液采用该方法进行检测;提取鼠源性生物制品中DNA,采用该方法检测其是否存在鼠痘病毒。结果该方法可以检测到稀释至10-5感染鼠痘病毒的细胞,在BHK21细胞和牛痘病毒中均未扩增出相应片段;该方法可检测出人工感染小鼠不同组织中病毒DNA;在鼠源性生物制品中未检测出鼠痘病毒DNA。结论该方法具有良好的特异性和敏感性,可以应用于染病动物组织及鼠源性生物制品中鼠痘病毒的检测。     

单周控制四桥臂三相四线制有源电力滤波器

提出一种基于单周控制的四桥臂三相四线制有源滤波器.该控制方法不需要检测三相负载电流和三相电源电压,不需要使用任何乘法器,可以大大简化谐波检测电路和电流跟踪控制电路.整个控制电路由4个带复位积分器、几个触发器、比较器和一些模拟器件组成,控制电路简单、可靠、无延佑迟.主电路开关频率恒定,容易实现.在对四桥臂变换器的三相四线制有源滤波器进行分析、建模的基础上,进行了仿真研究,仿真结果表明单周控制三相四线制有源滤波器能有效地补偿系统谐波、零序和无功电流,而且响应快、补偿性能好.     

一种适用于昆虫微量DNA模板制备的方法

随着分子生物学在昆虫领域中运用 ,昆虫 DNA的提取是有技术运用的前提 ,具有其重要的地位。但是由于一些昆虫体形较小 ,采用传统的酚 :氯仿抽提法不适用于微量 DNA模板的制备 ,而某些生物公司的试剂合相对而言价格较高。本文介绍一种适用于普通昆虫实验室贮藏及运用的微量 DNA模板制备方法。     

过氧化草酸酯化学发光检测DNA荧光探针

根据过氧化草酸酯与双氧水作用产生的高能中间体激发荧光物质发光的原理,研究了利用过氧化草酸酯TCPO-H2O2化学发光体系测定Cy5标记的DNA探针的新方法,探讨了溶剂、酸度、催化剂及发光溶液浓度对化学发光信号的影响,确立了最佳分析条件.其线性范围为8.4×10-9~2.8×10-6mol/L,检出限(3σ)为2.8×10-9mol/L.据此建立了操作简便、灵敏度高的测定Cy5标记的DNA探针的新方法.     

Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.

The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered structure attracts high-mobility-group domain (HMG) and other proteins. This binding of HMG-domain proteins to cisplatin-modified DNA has been postulated to mediate the antitumour properties of the drug. Many HMG-domain proteins recognize altered DNA structures such as four-way junctions and cisplatin-modified DNA, but until now the molecular basis for this recognition was unknown. Here we describe mutagenesis, hydroxyl-radical footprinting and X-ray studies that elucidate the structure of a 1:1 cisplatin-modified DNA/HMG-domain complex. Domain A of the structure-specific HMG-domain protein HMG1 binds to the widened minor groove of a 16-base-pair DNA duplex containing a site-specific cis-[Pt(NH3)2[d(GpG)-N7(1),-N7(2)]] adduct. The DNA is strongly kinked at a hydrophobic notch created at the platinum-DNA crosslink and protein binding extends exclusively to the 3' side of the platinated strand. A phenylalanine residue at position 37 intercalates into a hydrophobic notch created at the platinum crosslinked d(GpG) site and binding of the domain is dramatically reduced in a mutant in which alanine is substituted for phenylalanine at this position.     

Acid etching process for fabrication of Bi2Sr2CaCu2O8＋x stack

We adopted a new method, acid etching process, to fabricate the intrinsic Josephson junctions based on the Bi2Sr2CaCu2O8 x single crystals. By soaking the crystals into the dilute hydrochloric acid, we fabricated a junction stack successfully, and meantime made the surrounding area insulated. A certain concentration of hydrochloric acid was used to maintain the roughness of the modified layer. The cur-rent-voltage characteristic was achieved through the four terminal measurement. We could control the junctions' number by changing the concentration and the soaking time. We also found that the thick-ness of the stack was equal to the average height of the insulation layer. Such a simple, convenient and controllable fabrication method with a high yield might widen the applications of the intrinsic Joseph-son junctions.     

53BP1 facilitates long-range DNA end-joining during V(D)J recombination

Variable, diversity and joining (V(D)J) recombination and class-switch recombination use overlapping but distinct non-homologous end joining pathways to repair DNA double-strand-break intermediates. 53BP1 is a DNA-damage-response protein that is rapidly recruited to sites of chromosomal double-strand breaks, where it seems to function in a subset of ataxia telangiectasia mutated (ATM) kinase-, H2A histone family member X (H2AX, also known as H2AFX)- and mediator of DNA damage checkpoint 1 (MDC1)-dependent events. A 53BP1-dependent end-joining pathway has been described that is dispensable for V(D)J recombination but essential for class-switch recombination. Here we report a previously unrecognized defect in the joining phase of V(D)J recombination in 53BP1-deficient lymphocytes that is distinct from that found in classical non-homologous-end-joining-, H2ax-, Mdc1- and Atm-deficient mice. Absence of 53BP1 leads to impairment of distal V-DJ joining with extensive degradation of unrepaired coding ends and episomal signal joint reintegration at V(D)J junctions. This results in apoptosis, loss of T-cell receptor alpha locus integrity and lymphopenia. Further impairment of the apoptotic checkpoint causes propagation of lymphocytes that have antigen receptor breaks. These data suggest a more general role for 53BP1 in maintaining genomic stability during long-range joining of DNA breaks.