衰老过程中大白鼠脾细胞的DNA单链断裂与重接能力的变化

 DNA被紫外线损伤后,由DNA切除修复酶切除嘧啶二聚体,随之以另一条正常的DNA链为模板修复合成DNA片段,最后由DNA连接酶将新合成的DNA片与原有的DNA链连接。本文用荧光法测定DNA修复过程中DNA单链的断裂及重接能力与衰老的关系。结果表明,不同年龄大鼠脾细胞均具有修复DNA单链断裂的能力,DNA单链断裂重接的能力与年龄有相关性,断乳鼠及青年鼠的脾细胞当保温至30min时,即开始了DNA链的重接,保温90min后则恢复到原有水平;而老年鼠脾细胞保温至90min时才开始DNA链的重接,保温150min,尚未恢复到原有水平。还发现,断乳鼠及老年鼠脾细胞的单链DNA含量高于青年鼠。     

DNA分析与基因组序列和植物系统学研究

从DNA杂交、RFLP分析、DNA的限制酶图谱分析等方面描述DNA分析技术在植物学研究中的应用,讨论了DNA分析技术与植物系统学的关系及分子数据的分析方法。并以高等植物为对象,从核DNA、叶绿体DNA和线粒体DNA三方面对植物分子系统学进行了论述。     

DNA损伤检测技术

检测DNA损伤的方法有很多,根据其原理大致可以分为3类：基于损伤DNA理化性质的改变检测DNA损伤、基于分子杂交检测DNA损伤以及基于DNA损伤后形成的产物检测DNA损伤。检测DNA损伤的方法目前还在不断快速发展、完善中。本文就DNA损伤的检测方法及其发展做一综述。     

酶学方法第68卷(重组DNA)

本书介绍研究遗传工程、分子生物学方面很重要的重组DNA的研究方法及最新技术。内容包括重组DNA技术,用于重组DNA研究的酶学,DNA的合成、分离与提纯,用于重组DNA无性繁殖的载体和宿主,DNA无性繁殖系的筛选,无性繁殖基因表达的检验与分析方法。     

鸡肠道菌群总DNA三种提取方法的比较

目的比较不同方法提取鸡肠道菌群总DNA的差异,为分子方法分析肠道菌群组成提供质量较高的DNA模板。方法采用反复冻融法、酶裂解法和试剂盒法（E.N.Z.A Stool DNA Kit）来提取鸡肠道菌群的总DNA,并根据DNA浓度及纯度、16S DNA扩增产物和ERIC-PCR产物所反映的片段多态性4个指标,对这3种方法提取的DNA质量进行比较。结果3种方法均能提取DNA,所得DNA都可以用于16S DNA的扩增,但后2种方法所得DNA的ERIC-PCR结果能反映出更高的菌群多样性。结论试剂盒法和酶裂解法所提取的DNA质量好,适合用于肠道菌群的分子生态研究。     

一种同时提取水稻土壤中细胞外和细胞内形态DNA的方法

采用灭菌的水稻田土壤为基质,分别投加细菌基因组DNA和细菌活体,应用该方法提取细胞内和细胞外DNA。结果表明,DNA提取效率平均在75.4%-82.3%,DNA纯度OD260/280在1.75-1.85之间。用细菌16S rDNA通用引物PCR表明,DNA纯度能满足PCR要求,细胞内DNA与细胞外DNA互不污染。     

真核生物DNA甲基化的演化

DNA甲基化是最早发现的修饰途径之一,它能引起DNA构象、DNA稳定性及DNA与蛋白质相互作用方式的改变,从而控制基因表达。科学家通过一种可披露DNA甲基化模式的测序技术,分析了5种植物、5种真菌和7种动物基因组中DNA甲基化的情况,结果显示,与通过有性繁殖的陆地植物及动物（它们的DNA广泛存在甲基化）不同,可无性生殖的单细胞动物和真菌很少或没有DNA甲基化。     

从DNA修复机理看细胞癌变的发生机制

DNA损伤是引起基因突变,导致细胞恶性转化的重要原因．DNA损伤的修复过程非常复杂,是与细胞周期调节、DNA复制和DNA转录等生命活动紧密相连的．首先DNA修复需要细胞周期停滞,避免DNA损伤进入子代细胞．其次,参与DNA转录的某些基因产物参与DNA损伤的识别,有利于转录链的优先修复．最后,DNA修复系统NER、MMR参与损伤修复．上述DNA修复过程任何环节的异常,都将造成DNA修复功能减弱,导致某些功能基因突变,从而导致细胞的恶性转化．     

电脉冲和布吡卡因增强A型肉毒毒素DNA核酸疫苗的免疫效果

目的：考查DNA疫苗注射免疫后电脉冲和布吡卡因佐剂化DNA疫苗递送方式对A型肉毒毒素DNA核酸疫苗免疫效果的影响。方法：A型肉毒毒素DNA复制子疫苗和传统DNA疫苗肌肉注射免疫小鼠后电脉冲和布吡卡因佐剂化DNA后再肌肉注射免疫小鼠;检测免疫小鼠的抗体和细胞水平,并分析抗体亚类。结果：电脉冲和布吡卡因这二种递送方式均增强DNA复制子疫苗和传统DNA疫苗的体液免疫和细胞免疫效果;电脉冲提高DNA疫苗免疫效果更为明显,并且电脉冲和布吡卡因组合这种递送方式增强DNA疫苗体液免疫和细胞免疫水平最高;与传统DNA疫苗相比,A型肉毒毒素DNA复制子疫苗在这些递送方式下均诱导产生了更好的特异性体液免疫和细胞免疫应答,并且这些递送方式没有改变DNA疫苗的Th1/Th2免疫应答特性,即DNA复制子疫苗诱导产生Th1/Th2混合免疫应答但偏向于Th2途经,而传统DNA疫苗则完全偏向于Th2途经。结论：电脉冲和布吡卡因增强DNA复制子疫苗和传统DNA疫苗的免疫效果,是提高DNA疫苗免疫原性的良好策略。     

电离辐射诱导DNA—PKcs缺失小鼠T细胞特异的V（D）J重组恢复

NA依赖的蛋白激酶 (DNA PK)是一种DNA活化的核丝氨酸苏氨酸蛋白激酶。DNA PK由一种与DNA末端结合的调节亚单位异构二聚体Ku蛋白和DNA PK催化亚单位 (DNA PKcs)组成。DNA PK在DNA暴露于电离辐射后诱导的双链损伤修复中起主要作用。为了更好地了解与DNA PKcs缺失相关的DNA修复缺陷的本质。建立了DNA PKcs-/ -小鼠胚胎成纤维细胞株和裸鼠模型 ,调查这些突变的细胞和小鼠对DNA损害的反应。DNA PKcs-/ -细胞对电离辐射超敏感 ,在克隆形成实验中显示较低的生成率。同样 ,DNA PKcs-/ -小鼠也显示极大的放射敏感性 ,新生DNA PKcs-/ -小鼠用亚致死剂量电离辐射处理恢复T细胞受体 (TCR) β重组和T细胞成熟。然而 ,放射辐射并不恢复B细胞发育。DNA PKcs-/ -小鼠最终发生胸腺淋巴瘤。这些结果提示DNA双链断裂 (DSB)修复 ,V(D)J重组和淋巴瘤发生之间的相互关系。提供一种体内模型以阐明DNADSB修复调节、V(D)J重组和淋巴瘤发生分子机制三者之间的关键通路     

Restriction enzyme cleavage of fluorescently labeled DNA fragments--analysis of the method and its usage in examination of digestion completeness

Restriction enzymes have proven to be among the most valuable tools in molecular biology. In this work, we demonstrate that the cleavage of fluorescently labeled, PCR-amplified DNA can be used as a simple and highly sensitive technique for detection of sequences present in a percentage as low as 0.6% in a DNA pool. Due to the fact that fluorescent labeling of DNA fragments enables such sensitive detection and quantification of restriction enzyme cleavage, the method was further exploited in monitoring of the enzymatic digestion completeness and in determination of factors that influence restriction enzyme effectiveness. We analyzed the activity of six restriction endonucleases; the percentage of uncleaved DNA fragments predominantly ranged between 2.0 and 2.5 and the highest value was 8.00%. We conclude that, since the enzymatic digestion completeness may not always be assured, each assay based on restriction enzyme cleavage that is intended to be used in investigations of heterogeneity in a DNA pool should be constructed so that the presence of cleaved sequences is the indication of pool nonuniformity. When the presence of uncleaved sequences indicates pool heterogeneity, the results could be misleading due to possible incompleteness of enzymatic cleavage.     

Whole genome methylation scanning based on phi29 polymerase amplification

Identifying differences in DNA methylation is critical to understanding how epigenetics influences gene expression during processes such as development. Here, we propose a method that employs a single, methylation-sensitive restriction endonuclease of choice, to produce discrete pools of methylated and unmethylated DNA from the same sample. A pool of restriction fragments representing unmethylated regions of the genome is first obtained by digestion with a methylation-sensitive endonuclease. The restriction-digested DNA is then concatamerized in the presence of stuffer-adaptor DNA, which prevents interference from originally unmethylated DNA by blocking the ends of the restriction fragments. The concatamerized DNA is amplified by phi29 polymerase to remove methylation marks, and again digested with the same endonuclease to produce a pool of DNA fragments representing methylated portions of the genome. The two pools of DNA fragments thus obtained can be analyzed by end-sequencing or hybridization to a genomic array. In this report we detail a proof of concept experiment that demonstrates the feasibility of our method.     

Toward automated nucleic acid enzyme selection.

Methods for automation of nucleic acid selections are being developed. The selection of aptamers has been successfully automated using a Biomek 2000 workstation. Several binding species with nanomolar affinities were isolated from diverse populations. Automation of a deoxyribozyme ligase selection is in progress. The process requires eleven times more robotic manipulations than an aptamer selection. The random sequence pool contained a 5' iodine residue and the ligation substrate contained a 3' phosphorothioate. Initially, a manual deoxyribozyme ligase selection was performed. Thirteen rounds of selection yielded ligators with a 400-fold increase in activity over the initial pool. Several difficulties were encountered during the automation of DNA catalyst selection, including effectively washing bead-bound DNA, pipetting 50% glycerol solutions, purifying single strand DNA, and monitoring the progress of the selection as it is performed. Nonetheless, automated selection experiments for deoxyribozyme ligases were carried out starting from either a naive pool or round eight of the manually selected pool. In both instances, the first round of selection revealed an increase in ligase activity. However, this activity was lost in subsequent rounds. A possible cause could be mispriming during the unmonitored PCR reactions. Potential solutions include pool redesign, fewer PCR cycles, and integration of a fluorescence microtiter plate reader to allow robotic 'observation' of the selections as they progress.     

The scintillometric evaluation of DNA repair synthesis can be distorted by changes of thymidine pool radioactivity

The induction of DNA repair synthesis by UV radiation and methylmethane sulphonate (MMS) in mammalian cell lines of human (EUE, HeLa, FT, KB) and hamster (CHO, BHK) origin has been evaluated by means of autoradiography and the scintillometric procedure which implied the use of hydroxyurea (HU) to suppress DNA replication.While with UV radiation both methods produce concordant positive results, in the case of MMS the evidence of DNA repair synthesis obtained from the autoradiograms is occasionally accompanied by a lack of increase of DNA radioactivity in the treated cultures, as detected by scintillation counting. In such instances MMS is shown to reverse the enhancement of pool radioactivity in the cultures incubated with HU and even to reduce the radioactivity of thymidine pool below control values. By normalizing DNA radioactivities on the basis of pool variations, the discrepancy between autoradiography and scintillation counting is solved.The chromatographic analysis of thymidine pool components justifies the normalization procedure as it demonstrates that also in cultures treated with MMS or MMS + HU pool variations closely parallel the variations of thymidine triphosphate (dTTP) level.The normalization of DNA radioactivities based on the overall pool radioactivities gives an improved evaluation of the actual rate of DNA synthesis. It can be recommended for screening studies of DNA repair inducers because it allows one to correct false negative results without producing false positive data. Compared with the dTTP levels, overall pool radioactivities used as normalizing factors still produce an underestimate of DNA repair when high doses of MMS are applied to hamster cell cultures.     

Bacteriophage T4 head morphogenesis. VII. Terminal stages of head maturation.

Several aspects of the terminal stages of T4 head maturation were investigated using ts and am mutants blocked at single steps of the assembly pathway. We had previously found that cells infected with mutants of gene 13, e.g., tsN38 and amE609, accumulated both stable (10 to 20%)- and fragile (80%)-filled head precursors (Hamilton and Luftig, 1972). Here we showed the following for such gene 13-defective, mutant-infected cells. (i) Using thin-section analysis the pool of phage precursor structures observed under nonpermissive conditions was one-third of that observed when the cells were cultured under permissive conditions. (ii) In order for complete conversion of the precursors into viable phage to occur, there were apparent requirements of metabolic energy, protein, and DNA synthesis. (iii) The intracellular DNA pool under nonpermissive conditions exhibited a 50% distribution between 63S (mature size) and 200 S (concatenate size) DNA, with the latter DNA serving as a precursor pool. Further, this DNA pool when spread onto a protein monolayer exhibited a dispersed array of DNA, strands around a core, which was less dense than that found for the greater than 1,000S DNA concatenate isolated from gene 49-defective infected cells. (iv) When precuations were taken to stabilize the head precursors, such as lysis of the cells into glutaraldehyde, there was a 30% increase in the yield of 1,200S filled heads. Correlating these results and previous results concerning gene 49-defective unfilled heads, we propose that there are several forms of gene 13 fragile head precursors which serve as intermediates between gene 49 unfilled heads and gene 13 stable filled heads. We cannot, however, rule out the possibility that all gene 13-defective heads represent a single class of unstable particles, which decay slowly. In either case, we have shown that gene 13-defective particles are unstable to some degree inside the cell and are highly unstable outside the cell; yet all particles can still be efficiently converted to phage in vivo.     

A DNA solution of SAT problem by a modified sticker model

Among various DNA computing algorithms, it is very common to create an initial data pool that covers correct and incorrect answers at first place followed by a series of selection process to destroy the incorrect ones. The surviving DNA sequences are read as the solutions to the problem. However, algorithms based on such a brute force search will be limited to the problem size. That is, as the number of parameters in the studied problem grows, eventually the algorithm becomes impossible owing to the tremendous initial data pool size. In this theoretical work, we modify a well-known sticker model to design an algorithm that does not require an initial data pool for SAT problem. We propose to build solution sequences in parts to satisfy one clause in a step, and eventually solve the whole Boolean formula after a number of steps. Accordingly, the size of data pool grows from one sort of molecule to the number of solution assignments. The proposed algorithm is expected to provide a solution to SAT problem and become practical as the problem size scales up.     

Changes of deoxyribonucleoside triphosphate pools induced by hydroxyurea and their relation to DNA synthesis

Hydroxyurea inactivates ribonucleotide reductase from mammalian cells and thereby depletes them of the deoxynucleoside triphosphates required for DNA replication. In cultures of exponentially growing 3T6 cells, with 60-70% of the cells in S-phase, 3 mM hydroxyurea rapidly stopped ribonucleotide reduction and DNA synthesis (incorporation of labeled thymidine). The pool of deoxyadenosine triphosphate (dATP) decreased in size primarily, but also the pools of the triphosphates of deoxyguanosine and deoxycytidine (dCTP) were depleted. Paradoxically, the pool of thymidine triphosphate increased. After addition of hydroxyurea this pool was fed by a net influx and phosphorylation of deoxyuridine from the medium and by deamination of intracellular dCTP. An influx of deoxycytidine from the medium contributed to the maintenance of intracellular dCTP. 10 min after addition of hydroxyurea, DNA synthesis appeared to be completely blocked even though the dATP pool was only moderately decreased. As possible explanations for this discrepancy, we discuss compartmentation of pools and/or vulnerability of newly formed DNA strands to nuclease action and pyrophosphorolysis.     

Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

Molecular approaches that target the total DNA pool recovered from permanently anoxic marine ecosystems have revealed an extraordinary diversity of prokaryotes and unicellular eukaryotes. However, the presence of gene sequences contained within the extracellular DNA pool is still largely neglected. We have investigated the preservation, origin and genetic imprint of extracellular DNA recovered from permanently anoxic deep-sea sediments of the Black Sea. Despite high DNase activities, huge amounts of total extracellular DNA were found in both the surface and subsurface sediment layers, suggesting reduced availability of the extracellular DNA pool to nuclease degradation. The reduced degradation of the total extracellular DNA was confirmed by its low decay rate and the high accumulation in the deeper sediment layers. The copy numbers of 16S and 18S rDNA contained within the extracellular DNA pool in both the surface and subsurface sediment layers was very high, indicating that permanently anoxic sediments of the deep Black Sea are hot spots of preserved extracellular gene sequences. The extracellular DNA recovered from these sediment layers also contained highly diversified 18S rDNA sequences. These were not only representative of the major protistan lineages, but also of new very divergent lineages, branching as independent clades at the base of the tree. Our findings indicate that the extracellular DNA pool is a major archive of present/past eukaryotic gene sequences, and they highlight the importance of integrating molecular cell-oriented approaches with molecular analyses of the extracellular DNA pool, for a better assessment of microbial diversity and temporal changes in marine benthic ecosystems.     

Deoxynucleoside triphosphate pool changes and UV-induced depression of DNA synthesis

It has been reported that changes in deoxynucleotide pool levels following exposure to UV might lead to an overestimation of the UV-induced depression in DNA synthesis as analyzed by incorporation of 3H-thymidine (1). We attempted to determine the importance of such pool effects in two ways. First, we examined the grain density along DNA fiber autoradiographs obtained from CHO AA8, and CHO UV-5 cells exposed or sham exposed to UV. Exposure to UV did not alter the grain density immediately or 5 hours after exposure to UV in these cell lines. Second, we examined the kinetics of incorporation of 3H-dTTP in permeabilized AA8 cells under conditions of increased dCTP or increased exogenous dTTP levels. The extent of the depression of 3H-dTTP was identical under all incubation conditions.