Preparative Scale,High Resolution Purification of Low Molecular Weight DNA Fragments

Abstract

A commercially available continuous electro elution system has been used to separate and purify low molecular weight DNA fragments from polyacrylamide gels. This method has several advantages over previously reported methods for the recovery of DNA fragments from polyacrylamide gels. This technique, which gives very high recovery rates (80–95%), can be carried out on a relatively large scale and in a way that is not labour intensive. Data are presented for the purification of DNA fragments with molecular weights in the range 1–4 ± 10 (200–700 base-pairs), although the method is also applicable to larger molecular weight DNA fragments, RNAs and proteins.     

具有原核基因启动子活性的蓖麻蚕染色体DNA片段

利用大肠杆菌启动子克隆载体pHE5,研究了蓖麻蚕染色体的Hind Ⅲ酶解片段在大肠杆菌中作为四环素抗性基因启动子的功能作用。蓖麻蚕染色体的Hind Ⅲ片段与pHE5重组,在大约10~6个重组子中获得953株启动子重组体。测定了这些含有重组质粒的菌株抗四环素能力,其中有4株在平板上抗四环素水平超过225微克/毫升。对其中pARP201的插入片段进行了限制性图谱分析和启动子活性区域的缺失定位,证明了pARP-DB(由pARP201衍生而来)中的约0.5kb的外源插入片段具有完整的原核启动子功能。我们分析了这段DNA的部分核苷酸顺序,发现它与原核基因启动子极其相似。     

Ds因子在烟草染色体插入位点旁邻顺序的克隆

用ＮｅｓｔｅｄＰＣＲ 方法从含Ｄｓ 因子的转基因烟草ＤＮＡ 中克隆了Ｄｓ 因子在烟草染色体插入位点的９ 个旁邻ＤＮＡ 片段,以这些片段作探针,和野生型烟草的ＤＮＡ 进行Ｓｏｕｔｈｅｒｎ 杂交,以检测这些片段在烟草基因组中的拷贝数,结果表明它们都属于烟草染色体上的低拷贝ＤＮＡ。另外,对这些ＤＮＡ 片段进行核苷酸序列测定,并将它们的顺序与Ｇｅｎｂａｎｋ 数据库中已有的核苷酸序列相比较,其中长度为１２８ 核苷酸的片段１ 和荷兰芹的４ＣＬ２ 基因的一个区段有５７ ．８ ％ 同源性,而另一长度为１６９ 核苷酸的片段３ 和百合中的反转座子的一个区段有６０ ．９ ％ 的同源性。这都表明Ｄｓ 因子在异源植物烟草中插入染色体单拷贝基因的机率很高,这对转座子标签法克隆基因是非常有利的。     

Efficiency and Stability of High Molecular Weight DNA Transformation: an Analysis in Tomato

The efficiency of the binary bacterial artificial chromosome (BIBAC) vector for Agrobacterium-mediated stable transfer of high molecular weight DNA into plants was tested in tomato. Several variables affecting transformation efficiency were examined including insert size, Agrobacterium genetic background, and the presence of additional copies of the virG, virE1 and virE2 genes. It was found that a helper plasmid containing extra copies of virG was an absolute requirement for obtaining tomato transformants with the BIBAC. MOG101 with the virG helper plasmid was found to be the most efficient strain for transfer of high molecular weight DNA (150kb). Selected high molecular weight DNA transformants were advanced several generations (up to the R4) to assess T-DNA stability. This analysis showed that the T-DNA was stably maintained and inherited through several meioses regardless of whether it was in the hemizygous or homozygous state. Expression of a selectable marker gene within the T-DNA was also examined through several generations and no gene silencing was observed. Thus, the BIBAC is a useful system for transfer of large DNA fragments into the plant genome.     

烟草曲茎病毒卫星DNA在不同寄主中的分子变异比较

近年来对一些单组分菜豆金色花叶病毒属病毒(begomoviruses)的研究发现,这类单组分begomoviruses伴随着一种新型卫星分子-DNAβ。对我国云南省发生的双生病毒的研究表明,云南begomoviruses普遍伴随DNAβ分子,DNAβ分子与致病性紧密相关,且begomoviruses与其伴随的卫星DNA的是共进化的。为了弄清卫星DNAβ是否存在类似于卫星RNA的高度变异,将烟草曲茎病毒(Tobacco curly shoot virus,TbCSV)及其伴随卫星DNAβ的侵染性克隆共同接种本氏烟(Nicotiana benthamiana)和心叶烟(N．glutinosa),对TbCSV卫星DNAβ在不同寄主中的分子变异进行了比较。     

植物大片段 DNA 的研究进展

植物大片段 DNA 的研究成为了基因组学研究的一个重要方面．对它的研究得益于容纳大片段 DNA 片段载体的发展．对构建植物大片段 DNA 的载体、植物大片段 DNA 的提取方法、植物大片段 DNA 的主要应用领域的最新进展进行了介绍．     

3-氨基苯酰胺对氧化应激诱导的HeLa细胞端粒DNA链断裂重连接作用的影响

端粒是位于真核细胞染色体末端的DNA-蛋白质复合体,在维持染色体稳定上起着重要的作用,并且与细胞的衰老和凋亡有着密切的关系.在各种DNA损伤中,单链断裂(single-strand breaks, SSBs)是最常见的类型之一,既可直接通过内源活性氧或离子化辐射产生,也可间接地在DNA代谢或碱基切除修复期间产生.已知多聚(ADP-核糖)聚合酶［poly(ADPribose) polymerase, PARP］在SSBs修复中起着极为重要的作用.本实验观察了PARP抑制剂3-氨基苯酰胺(3-aminobenzamide, 3-AB)对氧化应激诱导的HeLa细胞端粒DNA链断裂重连接的效应以及对过氧化氢(H2O2)抑制HeLa细胞增殖的影响.结果表明3-AB能够显著地抑制氧化应激诱导的HeLa细胞端粒DNA链断裂后的重连接作用,并能增强H2O2对HeLa细胞增殖的抑制作用,提示PARP参与了端粒DNA链断裂损伤的修复过程.     

High Molecular Weight Protease in Rumen Ciliate Protozoa

Mixed rumen ciliate protozoa (mainly Entodiniinae) from goats have two kinds of protease; one has a pH optimum of 3.0, the other is active at neutral or alkaline pH. The protease active at neutral or alkaline pH was partially purified from the supernatant after centrifugation of sonicated mixed rumen ciliate protozoa. The supernatant was chromatographed on Bio-Gel A-1.5m and a partially purified protease was obtained. This protease had a molecular weight of more than 400,000. When the sonicated protozoa were heated at 55°C for 15min, the active peak from the Bio-Gel A-1.5m column was shifted to a lower molecular weight, 27,000. The high molecular weight protease was strongly activated by high temprature and SDS, and inhibited by E-64 c. The protease degraded many proteins including those found in rumen bacteria. These findings suggest that rumen ciliate protozoa have high molecular weight protease that plays a role in the digestion of feed and bacterial protein.     

High Molecular Weight Mucin-like Glycoprotein in Bovine Milk

We purified an enzyme hydrolyzing 2-sulfo-α-L-fucopyranose pyridylaminated 2-sulfo-α-L-fucopyranosyl-(1→2)-fucose from the acetone powder of the digestive tract of a sea urchin. The enzyme was purified 307-fold with an overall recovery of 1.63% by ammonium sulfate precipitation, cation exchange chromatography, and gel filtration chromatography. The enzyme is useful for the structural analysis of sulfated fucan.     

The absence of Arabidopsis-type telomeres in Cestrum and closely related genera Vestia and Sessea (Solanaceae): first evidence from eudicots

Using slot-blot and fluorescent in situ hybridization (FISH), we found no evidence for the presence of the Arabidopsis-type telomeric sequence (TTTAGGG)n at the chromosome termini in any of the Cestrum species we investigated. Probing for the human-type telomere (TTAGGG)n also revealed no signal. However, polymerase chain reaction experiments indicated that there are short lengths of the sequence TTTAGGG dispersed in the genome but that these sequences are almost certainly too short to act as functional telomeres even if they were at the chromosome termini. An analysis of related genera Vestia and Sessea indicates that they too lack the Arabidopsis-type telomere, and the sequences were lost in the common ancestor of these genera. We found that the Cestrum species investigated had particularly large mean chromosome sizes. We discuss whether this is a consequence of alternative telomere end maintenance systems.     

High Humidity and Heat Stress Causes Dissociation of Endoplasmic Reticulum in Tobacco Pollen

High humidity (95 % RH) and temperature (38/45 °C) stress for 4h applied to pollen grains of Nicotiana tabacum did not affect pollen viability, assessed on the basis of the fluorochromatic reaction test, but affected in vitro germination; pollen grains treated at 38 °C showed marked delay in germination, while those treated at 45 °C failed to germinate in vitro. The major ultrastructural effect of the stress was on RER. Stacks of RER, characteristically present in fresh pollen, were largely dissociated in the stressed pollen. The extent of dissociation of RER was greater in pollen samples stressed at 45 °C than at 38 °C. The generative cell did not show any obvious change in the stressed pollen. RER was restored in pollen grains which showed germination following culture; but not in those which failed to germinate. Apart from affecting other RER-related functions the dissociation of RER is likely to result in the destruction of long-lived mRNA and thus affect the ability of pollen grains to initiate protein synthesis needed for germination.     

In VivoAddition of Telomeric Repeats to Foreign DNA Generates Extrachromosomal DNAs in the Taxol-Producing FungusPestalotiopsis microspora

Transformation of the taxol-producing filamentous fungusPestalotiopsis microsporawith a plasmid containing the bacterial hygromycin resistance gene fused toAspergillusregulatory sequences resulted in thein vivoformation of extrachromosomal DNAs with telomeric repeats in the majority of transformants. Repeats of the telomeric sequence 5′-TTAGGG-3′ were appended to nontelomeric transforming DNA termini. No fungal sequences other than telomeric repeats were detected in extrachromosomal DNAs. Transformants contained three to six different sizes or conformational forms of extrachromosomal DNAs. The DNAs showed no change in size or internal structure during 6 months of growth with selection, but were lost after 20 days of growth without selection. Transformation of wild-typeP. microsporawith a PCR-amplified extrachromosomal DNA having terminal telomeric repeats produced up to 50-fold more transformants than the original transformation vector. The addition of telomeric repeats to foreign DNA is unusual among fungi and may have important adaptive or developmental implications.     

DNA分子标记在药用植物中的应用

对DNA分子标记技术在药用植物鉴定、中药质量标准化、遗传图谱构建和近缘物种进化关系等方面的研究进展进行了综述,并展望了分子标记技术在药用植物研究中的发展前景。     

Molecular phylogeny of Dipterocarpaceae in Indonesia based on chloroplast DNA

In order to construct a molecular phylogeny of Indonesian Dipterocarpoideae (Dipterocarpaceae), PCR-RFLP of the chloroplast regions rbcL, petB, psbA, psaA, and trnL-F was performed with seven restriction enzymes in 129 samples including 58 species from nine genera. In the strict consensus tree with Monotes kerstingii as outgroup Indonesian Dipterocarpaceae were divided into two major clades. One clade (bootstrap value=71) consisted of Upuna, Cotylelobium, Anisoptera, Vatica, Dipterocarpus (tribe Dipterocarpeae, bootstrap value=83) and Dryobalanops (tribe Shoreae, bootstrap value=99) in a basal position. The second clade consisted of Hopea, Parashorea, and Shorea (tribe Shoreae) with 95% bootstrap support. Tribe Dipterocarpeae is monophyletic, tribe Shoreae is polyphyletic since Dryobalanops is sister to tribe Dipterocarpeae. In the neighbour-joining tree the sister group position of Dryobalanops to tribe Dipterocarpeae is not supported by the bootstrap analysis. Alternatively, we used Upuna borneensis as outgroup. The effect of outgroup selection on tree topology, taxonomic classification and the interpretation of character evolution is discussed.     

微生物发酵法生产高分子量透明质酸的研究进展

透明质酸是一种线性大分子黏多糖,分子量定义其流变性能,影响生理反应,并决定合适的用途。传统研究通过优化发酵提高透明质酸的产量已取得显著成效,近年来,研究重点逐渐转向如何提高透明质酸产品的分子量。目前,高分子量透明质酸具有良好的黏弹性、保湿性、黏附性,在医药中的应用是中、低分子量透明质酸不可替代的。概述了透明质酸分子量的调控机制,以及利用微生物发酵法生产高分子量透明质酸的研究进展,并对其发展方向进行了展望。     

植物钾营养高效分子遗传机制

钾是植物生长发育所必需的矿质营养元素之一。不同种类植物的钾营养效率存在差异,已有证据表明这种差异是受遗传基因控制的。植物细胞依靠细胞膜上的各种钾转运体和通道蛋白吸收和转运钾离子,这些膜蛋白的活性调控是植物钾营养效率调控的关键和基础。本文对植物钾营养高效性状分子遗传机制以及相关基因的分子功能和调控机制的研究进展进行了简要评述,并讨论了改善作物钾营养高效性状的可能途径。     

上槽泄露导致双向电泳凝胶高分子量区域垂直拖尾

本文探讨了电泳系统上槽泄露引起双向电泳凝胶蛋白点纵向拖尾问 题.上槽泄露导致上槽SDS损耗,电流增大以及局部温度升高从而导致双向 电泳凝胶高分子量区域蛋白点纵向拖尾.上槽泄露与上槽设计存在不足,使 用者不适当操作以及上槽维护不良有关.对Ettan DALT six电泳系统而言, 一旦出现上槽泄漏问题,建议更换改良后的新版上槽.电泳过程中应避免上 槽泄露,SDS的不足或损耗,电流过大和电泳液温度过高.     

Molecular Dynamics Simulation in Solvent of the Estrogen Receptor Protein DNA Binding Domain in Complex with a Non-Consensus Estrogen Response Element DNA Sequence

Abstract

We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the estrogen receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nucleotide base pairs. This ERE nucleotide sequence occurs naturally upstream of the Xenopus laevis Vitelligenin AI gene. The ER DBD is encoded by three exons. Namely, exons 2 and 3 which encode the two zinc binding motifs and a sequence of exon 4 which encodes a predicted alpha helix. We generated a computer model of the ER DBD using atomic coordinates derived from the average of 30 nuclear magnetic resonance (NMR) spectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinations and no coordinates were reported. This disordered region includes 10 amino acids of a predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in DNA binding and are also believed to function as a nuclear translocation signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino acids encoded in exon 4 and attached this helix to the carboxyl end of the ER DBD at the exon 3/4 splice junction site. We docked the ER DBD model within the DNA major groove halfsites of the 29 base pair non-consensus ERE and flanking nucleotides. We constructed a solvated model with the ER DBD/ERE complex surrounded by a ten Angstrom water layer and conducted molecular dynamics simulations. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the ER DBD DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the ERE DNA right major groove halfsite. Amino acids of the ER DBD exon 4 encoded predicted alpha helix formed direct and water mediated H-bonds with base and backbone sites of their cognate codon-anticodon nucleotides within the minor grooves flanking the ERE DNA major groove halfsites. These interactions together induced bending of the DNA into the protein.     

小麦高分子量麦谷蛋白亚基的遗传变异与小麦加工品质改良

高分子量麦谷蛋白亚基（HMW-GS）是小麦胚乳中一种具有多态性的蛋白质组分,在面团中它们可以通过相互之间或与低分子量麦谷蛋白亚基（LMw-Gs）之间形成二硫键来组成麦谷蛋白多聚体。由于其在小麦面粉加工所需的粘性和弹力方面具有极其重要的作用,过去几十年间在小麦加工品质相关蛋白研究方面的工作大多数集中在高分子量麦谷蛋白亚基上。近几年在高分子量麦谷蛋白亚基及其编码基因的鉴定、基因的遗传变异以及不同变异在小麦加工品质中的作用方面进行了大量研究。本文对近几年在HMW-GS领域的研究进展进行综述并且重点讨论HMW-GS的变异及其对小麦品质育种的重要意义。