Mechanochemical analysis of DNA gyrase using rotor bead tracking

DNA gyrase is a molecular machine that uses the energy of ATP hydrolysis to introduce essential negative supercoils into DNA. The directionality of supercoiling is ensured by chiral wrapping of the DNA around a specialized domain of the enzyme before strand passage. Here we observe the activity of gyrase in real time by tracking the rotation of a submicrometre bead attached to the side of a stretched DNA molecule. In the presence of gyrase and ATP, we observe bursts of rotation corresponding to the processive, stepwise introduction of negative supercoils in strict multiples of two. Changes in DNA tension have no detectable effect on supercoiling velocity, but the enzyme becomes markedly less processive as tension is increased over a range of only a few tenths of piconewtons. This behaviour is quantitatively explained by a simple mechanochemical model in which processivity depends on a kinetic competition between dissociation and rapid, tension-sensitive DNA wrapping. In a high-resolution variant of our assay, we directly detect rotational pauses corresponding to two kinetic substeps: an ATP-independent step at the end of the reaction cycle, and an ATP-binding step in the middle of the cycle, subsequent to DNA wrapping.     

毕赤酵母FLD1启动子元件的克隆与测序

为了应用毕赤酵母表达某些食用蛋白或同时表达多个异源蛋白,本文以毕赤酵母GS115基因组DNA为模板,采用prime5.9程序设计了一对不等长引物,经多轮直接多聚酶链式反应,扩增获得了大小为597bp目标DNA片段;再经限制性内切酶和双脱氧末端终止法分析,其DNA片段排列顺序与EMBL发表的FLD1启动子的序列完全一致。     

Effect of novobiocin on initiation of DNA replication in Bacillus subtilis.

The initiation of DNA replication of small replicons in vitro involves conformational changes in the whole DNA molecule or in the region near to the replication origin. One striking finding has been the role of DNA gyrase (that is, the necessity for supercoiled structure) in the initial stage of ColE1 replication in vitro. However, little is known about the effect of gyrase on the initiation of replication of bacterial chromosomes in vivo. We have constructed a map of cleavage sites of restriction enzymes at the region of the origin of replication of the Bacillus subtilis chromosome (accompanying paper). This has now enabled us to examine the effect of novobiocin, a selective inhibitor of DNA gyrase, on the replication of the specific chromosomal segments near the origin and to seek a possible role for the gyrase in the initiation of chromosomal replication. We have found that only a limited segment of the chromosome at the origin region was replicated in the presence of novobiocin. This effect allowed us to locate the site of the origin of replication to within a DNA fragment of molecular weight 3.4 x 10(6).     

Visualization of protein RecR in Escherichia coli by fluorescent labelling

RecR protein, a functional equivalent of Rad52 in eukaryotes, plays a critical role in the RecF pathway of homologous recombination in Escherichia coli. By constructing and expressing the recR-yfp hybrid gene, the distribution of the RecR-YFP fusion protein was visualized in E. coli by fluorescent microscopy. Our results showed that RecR proteins can be localized predominantly in the nucleoid region of E. coli. By measuring the UV resistance of a recR mutant carrying the recR-yfp gene in the plasmid, the expressed RecR-YFP was found to be functional in improving the UV resistance of the recR deficiency strain.     

Bombyx mori bidensovirus: The type species of the new genus Bidensovirus in the new family Bidnaviridae

Bombyx mori bidensovirus （BmBDV）, which had been assigned to Densovirinae in Parvoviridae previously, replicates mainly in silkworm midgut columnar cells and causes the fatal flacheric disease. In contrast to parvovirus, this virus possesses two single-stranded DNA genome segments and encodes a putative protein-primed DNA polymerase. The accumulating evidence sug- gests that it has unique characteristics different to parvovirus and adopts its own mechanisms for replication. So far, little is known about the replication mechanisms of BmBDV. In this review, we focus on the pathology associated with this virus and the viral biology such as viral genome structure, viral genes, and viral replication and expression strategies.     

Bioactivity and constituents of several common seaweeds

Bioactivity and constituents of 8 common seaweeds from Dalian intertidal zone of northern Yellow Sea were investigated. In the anti-methicillin-resistant Staphylococcus aureus (MRSA) test, Symphyocladia latiuscula and Enteromorpha intestinalis showed obvious activities with MICs much lower than 1.0 mg·mL-1 . In the DNA damage repair test (DDRT), Chondrus ocellatu showed selective inhibitory activity against the DNA repair-defective E. coli strain vs. the wild-type E. coli strain; while Sym. latiuscula, Enteromorpha intestinalis and Sar. kjellmanianum showed significant anti-E. coli activity with MICs of 64-128 g·mL-1 . In the anti-Pyricularia oryzae test, Sym. latiuscula and Rh. confervoides strongly inhibited the germination of the spores of P. oryzae on agar plate. In the brine shrimp larvicidal test, Sym. latiuscula, Rh. confervoides and Sar. kjellmanianum exhibited potent toxicity against brine shrimp larvae, with LC50 much lower than 1 mg·mL-1 . The HPTLC analysis revealed their diversified secondary metabolites. The HPLC-DAD-MS analysis of the strongest species Sym. latiuscula and database searching showed that it can produce quite diversified metabolites, including halogenated ones, some of which may be new natural products. The results demonstrated the potentials of these seaweeds in the development of new antibiotics, antitumor drugs, agricultural fungicides and pesticides.     

Development of a propulsion system for a biomimetic thruster

We studied theoretically and experimentally a biomimetic propulsion system inspired by the motility mechanisms of bacteria such as E. coli. Our goal was to investigate the effect of the ??complex?? filament of Rhizobium Meliloti bacteria on thrust force. The complex filament is a helically perturbed filament, similar to a plain filament threaded through a small helix. The propulsive performance of this system was estimated by modeling the dynamics of helical wave motion in viscous fluid. The model consists of a helical filament which is axially rotated at angular velocity ??. Resistive force theory (RFT) was applied to this model to calculate the thrust force and required torque. The Buckingham PI theorem (non-dimensional analysis) was also used to analyze the theoretical results. The procedure for making a complex filament with various pitch angles ?? _s from a small helix and plain filament is explained in detail. To validate the theoretical results for helical wave propulsion and compare the characteristics of complex and plain filaments together, an experiment was performed to measure the thrust forces in silicone oil. The experimental results agreed with the theoretical values predicted by RFT. The thrust forces of complex filaments depended on the shape of small helix winding. The maximum thrust force was achieved at a small helix pitch angle of ?? _s = 45°. In addition, we found that the thrust force generated by a complex filament had a value about 10% higher than that of a plain filament with the same equivalent diameter d _e .     

Single-molecule analysis of DNA uncoiling by a type II topoisomerase

Type II DNA topoisomerases are ubiquitous ATP-dependent enzymes capable of transporting a DNA through a transient double-strand break in a second DNA segment. This enables them to untangle DNA and relax the interwound supercoils (plectonemes) that arise in twisted DNA. In vivo, they are responsible for untangling replicated chromosomes and their absence at mitosis or meiosis ultimately causes cell death. Here we describe a micromanipulation experiment in which we follow in real time a single Drosophila melanogaster topoisomerase II acting on a linear DNA molecule which is mechanically stretched and supercoiled. By monitoring the DNA's extension in the presence of ATP, we directly observe the relaxation of two supercoils during a single catalytic turnover. By controlling the force pulling on the molecule, we determine the variation of the reaction rate with the applied stress. Finally, in the absence of ATP, we observe the damping of a DNA crossover by a single topoisomerase on at least two different timescales (configurations). These results show that single molecule experiments are a powerful new tool for the study of topoisomerases.     

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity

T7 DNA polymerase catalyses DNA replication in vitro at rates of more than 100 bases per second and has a 3'-->5' exonuclease (nucleotide removing) activity at a separate active site. This enzyme possesses a 'right hand' shape which is common to most polymerases with fingers, palm and thumb domains. The rate-limiting step for replication is thought to involve a conformational change between an 'open fingers' state in which the active site samples nucleotides, and a 'closed' state in which nucleotide incorporation occurs. DNA polymerase must function as a molecular motor converting chemical energy into mechanical force as it moves over the template. Here we show, using a single-molecule assay based on the differential elasticity of single-stranded and double-stranded DNA, that mechanical force is generated during the rate-limiting step and that the motor can work against a maximum template tension of approximately 34 pN. Estimates of the mechanical and entropic work done by the enzyme show that T7 DNA polymerase organizes two template bases in the polymerization site during each catalytic cycle. We also find a force-induced 100-fold increase in exonucleolysis above 40 pN.     

The stress response factor RpoS is required for the natural transformation of Escherichia coli

The natural transformation of Escherichia coli is a novel and recently developed system that has significance for genetic studies and the biological safety of genetic engineering. However, the mechanisms of transformation, including development of competence and DNA uptake, are not thoroughly understood. In this study, we demonstrated the effect of the general stress response regulator RpoS, which has been associated with E. coli transformation, on natural transformation performed in an “open system”. We find that RpoS is required for natural transformation but not to artificial transformation and RpoS mainly affect transformation in the liquid culture prior to plating. In the liquid culture, RpoS over-expression promotes natural transformation in early exponential phase and static incubation accumulates RpoS and promotes transformation to a limited extent. These findings provide detailed understanding of RpoS function on natural transformation.     

卟啉衍生物TMPyP4与单链DNA的结合机理研究

通过圆二色谱、稳态吸收光谱、稳态荧光光谱和皮秒时间分辩荧光光谱研究了meso-四(4-(N-甲基吡啶基))卟啉(TMPyP4)与端粒DNA5′-TTAGGG-3′(S6)的结合机理.稳态光谱实验结果表明,在没有金属离子的Tris-HCl缓冲溶液中,S6DNA以单链的形式存在,TMPyP4与单链DNA的结合常数为1.51×106(mol/L)-1,饱和结合数为1.2.通过时间分辨荧光光谱对二者相互作用的机理进行了进一步研究,推测了TMPyP4与单链S6DNA之间的结合模式.     

粘结层中的Co对热障涂层界面结合因子的影响

用固体与分子经验电子理论(EET)和改进的TFD理论的结合,计算了热障涂层不同粘结层Co含量下的陶瓷层/粘结层界面的界面结合因子,结果表明:含Co界面的最小电子密度差Δρmin比不含Co时小,Co有利于缓解界面的应力;加Co后使该界面电子密度保持连续的原子状态组数σ′比不加Co至少增加一个数量级,Co有利于使界面稳定,且从σ_equal和σ_super可知这种稳定性不会由于应力的升高受到破坏;当粘结层的表面为(110)时,加Co后电子密度ρ总是提高,有利于提高界面的结合力;当粘结层的表面为(100)和 (111)时,界面的结合力不受Co含量影响。所以,Ni基粘结层中的Co可改善热障涂层的陶瓷层/粘结层的界面结合。     

The bacteriophage straight phi29 portal motor can package DNA against a large internal force

As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage straight phi29 packages its 6.6-microm long, double-stranded DNA into a 42 x 54 nm capsid by means of a portal complex that hydrolyses ATP. This process is remarkable because entropic, electrostatic and bending energies of the DNA must be overcome to package the DNA to near-crystalline density. Here we use optical tweezers to pull on single DNA molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 pN on average, making it one of the strongest molecular motors reported to date. Movements of over 5 microm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to approximately 50 pN owing to DNA confinement. Our data suggest that this force may be available for initiating the ejection of the DNA from the capsid during infection.     

派罗宁GS双峰双波长光度法测定核酸

 采用光度法研究了派罗宁GS与核酸的结合反应,结果表明在pH 6.0左右的介质中,派罗宁GS与核酸在室温下能迅速结合形成紫红色复合物,该复合物在570 nm处有正吸收峰,在540 nm处有负吸收峰.据此,建立了1个测定核酸的双峰双波长光度分析新方法.用该方法测定小牛胸腺DNA(ctDNA)、鱼精子DNA(fsDNA)、酵母RNA(yt RNA)及热变性ctDNA(Dct DNA)的检出限均低于0.011μg/mL.方法简单、快速,试剂及反应体系稳定、选择性好、准确度高,用于4个合成试样的分析,回收率为96.1%~103.0%.     

Synthesis of Schiff bases of naphtha[1,2-d]thiazol-2-amine and metal complexes of 2-(2′-hydroxy)benzylideneaminonaphthothiazole as potential antimicrobial agents

Objective: A series of 2-benzylideneaminonaphthothiazoles were designed and synthesized incorporating the lipophilic naphthalene ring to render them more capable of penetrating various biomembranes. Methods: Schiff bases were synthesized by the reaction of naphtha[1,2-d]thiazol-2-amine with various substituted aromatic aldehydes. 2-(2′-Hydroxy)benzylideneaminonaphthothiazole was converted to its Co(II), Ni(II) and Cu(II) metal complexes upon treatment with metal salts in ethanol. All the compounds were evaluated for their antibacterial activities by paper disc diffusion method with Gram positive Staphylococcus aureus and Staphylococcus epidermidis and Gram negative Escherichia coli and Pseudomonas aeruginosa bacteria. The minimum inhibitory concentrations of all the Schiff bases and metal complexes were determined by agar streak dilution method. Results: All the compounds moderately inhibited the growth of Gram positive and Gram negative bacteria. In the present study among all Schiff bases 2-(2′-hydroxy)benzylideneaminonaphthothiazole showed maximum inhibitory activity and among metal complexes Cu(II) metal complex was found to be most potent. Conclusion: The results obtained validate the hypothesis that Schiff bases having substitution with halogens, hydroxyl group and nitro group at phenyl ring are required for the antibacterial activity while methoxy group at different positions in the aromatic ring has minimal role in the inhibitory activity. The results also indicated that the metal complexes are better antibacterial agents as compared to the Schiff bases.     

The Escherichia coli O157:H7 DNA detection on a gold nanoparticle-enhanced piezoelectric biosensor

This paper presents development of a quartz crystal microbalance （QCM） biosensor for real-time detection of E. coil O157：H7 DNA based on nanogold particles amplification. Many inner Au nanoparticles were immobilized onto the thioled surface of the Au electrode, then more specific thiolated sin- gle-stranded DNA （ssDNA） probes could be fixed through Au-SH bonding. The hybridization was induced by exposing the ssDNA probe to the complementary target DNA of E. coli O157：H7 gene eaeA, then resulted in a mass change and corresponding frequency shifts （ △f ） of the QCM. The outer avidin-coated Au nanoparticles could combine with the target DNA to increase the mass. The electrochemical techniques, cyclic voltammetry （CV） and electrochemical impedance spectroscopy （EIS） were adopted to manifest and character each step. The target DNA corresponding to 2.0×10^3 colony forming unit （CFU）/mL E. coil O157：H7 cells can be detected by this biosensor, so it is practical to develop a sensitive and effective QCM biosensor for pathogenic bacteria detection based on specific DNA analysis. The piezoelectric biosensing system has potential for further applications, such as food safety and environment monitoring, and this approach lays the groundwork for incorporating the method into an integrated system for in-field bacteria detection.