蓟马基因组DNA提取方法的改进

在昆虫分子生物学的研究中,从昆虫样品中有效地获得总DNA是分子实验成功的前提。但是,常规提取方法由于不能保留昆虫所有的形态特征,这对于体形较小的珍稀标本是不适用的。文中通过对改进的盐析法和STE法与KAc法的对比,发现盐析法和STE法提取的DNA质量明显优于KAc法,并且能够通过针刺从单头蓟马中成功提取DNA而不影响形态鉴定。2种提取方法的优点是单头蓟马在提取过DNA以后,虫体仍然可用以做成永久玻片进行形态鉴定。提取的DNA经实验证明,可以顺利的进行mtDNA-COI和rDNA-ITS2基因序列引物的扩增。     

短序十大功劳基因组总DNA提取方法研究

以短序大功劳嫩叶为材料,采用CTAB法、CTAB改良法1、CTAB改良法2、SDS法和试剂盒法五种方法提取短序十大功劳基因组总DNA,用分光光度计和琼脂糖凝胶电泳方法检测所得总DNA的纯度和得率,用ISSR-PCR扩增的方法检测所得总DNA的质量。结果表明,五种方法均能从短序大功劳叶片中提取到基因组DNA,但不同方法提取得的基因组DNA的纯度、浓度和得率存在明显的差异。CTAB改良法2和试剂盒法提取的DNA纯度高,可直接用于下游分子生物学实验,CTAB法、CTAB改良法1和SDS法提取的总DNA质量较差,不利于下游的分子生物学实验;五种方法提取的总DNA的得率在10.836~451.709μg/g之间,呈CTAB法>SDS法>CTAB改良法1>CTAB改良法2>试剂盒法的现象。此实验获得的结果可以为短序十大功劳分子生物学研究提供基础。     

一种适用于昆虫痕量DNA模板制备的方法

近年来分子生物学技术在昆虫学各领域中得到了广泛地运用 ,从昆虫样品中有效地获得DNA模板是实验成功的前提。但是由于许多昆虫体形微小 ,许多研究需要取单个个体的样品 ,用传统的酚∶氯仿抽提法难以从痕量样品中获得总DNA ,而某些生物公司的试剂盒相对而言价格昂贵。该文介绍一种快速简便、广泛适用于不同种类昆虫、各种不同保存方法保存的昆虫样品和标本的微量DNA模板制备方法     

细菌基因组DNA提取方法概述

细菌基因组DNA提取是分子生物学研究的基础,DNA提取的质量和效率可直接影响后续实验结果的准确性和精确性。综述并比较了近10年细菌DNA提取的几种方法,分析不同方法的提取效率,以期为分子生物学研究提供更可靠的基础。     

从棉铃虫体中提取总RNA的一种有效方法

昆虫组织细胞中含有大量的RNA酶 ,在提取其RNA时 ,防止RNA酶的降解 ,是保证所得RNA片段完整的关键。目前提取动物组织细胞总RNA的方法主要采用“异硫氰酸胍 酚 氯仿抽提”一步法操作 ,但从昆虫组织细胞中提取RNA尚无明确的方法。本实验根据昆虫组织细胞中RNA的分子结合其它蛋白等次生物质的特性不同 ,适当的调整该方法 ,从棉铃虫中提取到了完整、无降解、纯度高的RNA ,适用于Northern杂交和cDNA合成等分子生物学操作     

SDS-CTAB结合法提取棉花总DNA

根据以往提取棉花总DNA的经验 ,并参考了几种相关的植物总DNA提取方法 ,得到一种更适合棉花 (GossypiumL .)总DNA提取的方法。该提取方法综合了SDS法与CTAB法的优点 ,使获得的棉花总DNA纯度高 ,得率大 ,完整性较好 ,可用于PCR检测 ,Southern杂交 ,RAPD ,染色体步移等分子生物学操作。     

从动物组织提取高纯度总RNA方法的改进及应用

从动物组织中提取总RNA是现代分子生物学研究中经常使用的重要实验技术,按常规方法获得的总RNA产品中常伴有大分子量染色体DNA污染。为此,我们摸索出了保证RNA制品纯度、质量和产量的DNA酶消化最佳反应条件。利用改良后的方法提取了小鼠脏器组织总RNA,进行了新基因mPC-1在小鼠脏器中表达的组织分布研究。     

不同保藏处理的昆虫标本DNA提取及其随机扩增多态DNA反应

实验利用CTAB法对柳二十斑叶甲Chrysomelavigintipunctata (Scopoli)、异色瓢虫HarmoniaaxyridisPollas、七星瓢虫Coc cinellaseptempunctataLinnaeus、小地老虎Agrotisypsilon (Rottemberg)、红蜻CrocothemisserviliaDrury、无齿稻蝗OxyaabentataWil lemse和中华稻蝗Oxyachinensis (Thunberg)等 7种昆虫进行了基因组DNA提取。从自然干燥标本、烘干标本及酒精浸泡标本获得的DNA均可用于RAPD PCR反应 ,且烘干标本、酒精浸泡标本提取效果优于自然干燥标本。这种提取方法简便易行 ,容易掌握 ,且耗资小于其它分子生物学方法。     

大青杨基因组DNA的提纯及鉴定

由于各种林木在组织结构和化学成分上的差异,核酸的提取方法将不尽相同。高质量的DNA是林木分子生物学研究的关键因素。探索一种科学的、合适的DNA提取方法尤为重要。本文对大青杨基因组DNA的提取方法进行了优化。通过电泳检测、紫外分析、限制性内切酶消化和随机引物PCR扩增鉴定所获得的基因组DNA,证明其完全可以满足分子生物学实验的要求。     

梨不同DNA提取方法的效果研究

以7个梨品种为实验材料,比较分析了SDS法、CTAB法、SDSCTAB法、改良的CTAB法、高盐低pH值法、分步离心法对梨总DNA提取的效果。结果表明:利用以上6种方法提取的梨总DNA在纯度和量上有很大的差别。所得到的平均DNA量从大到小依次为:分步离心法、SDS法、SDSCTAB法、改良的CTAB法、CTAB法、高盐低pH值法。DNA提取纯度依次为分步离心法、SDSCTAB法、改良的CTAB法、高盐低pH值法、CTAB法、SDS法。RAPD和自交不亲和基因(S基因)特异性引物扩增实验结果都比较理想,但分步离心法和SDSCTAB法提取的DNA双酶切效果较好。分步离心法提取的梨总DNA更适用于后续的分子生物学实验操作。     

Direct Isolation of High-Quality Low Molecular Weight RNA of Pear Peel from the Extraction Mixture Containing Nucleic Acid

Low molecular weight RNA (LMW RNA) is generally obtained either from the total RNA or from total nucleic acids solution. Many steps and chemical reagents are involved in traditional methods for LMW RNA isolation where degradation of LMW RNA often occurs, especially for plant materials with high levels of secondary catabolites. In this study, an efficient method was developed to directly isolate pure LMW RNA from pear peel, a material rich in polyphenolics that is covered with a layer of wax. The method was based on polyethylene glycol (PEG) precipitation combining CTAB buffer which is often used to isolate RNA from polysaccharide-rich and polyphenolics-rich materials. The entire procedure could be completed within 6 h and many samples could be processed at the same time. Few and common chemicals are used with this method. Hence, it could be used as an ordinary method in the laboratory. The developed method was further tested by isolating LMW RNA from Arabidopsis. Using the isolated LMW RNA samples, microRNAs were successfully detected and characterized.     

Positional cloning without a genome map: using 'Targeted RFLP Subtraction' to isolate dense markers tightly linked to the regA locus of Volvox carteri.

The ability to isolate genes defined by mutant phenotypes has fueled the rapid progress in understanding basic biological mechanisms and the causes of inherited diseases. Positional cloning, a commonly used method for isolating genes corresponding to mutations, is most efficiently applied to the small number of model organisms for which high resolution genetic maps exist. We demonstrate a new and generally applicable positional cloning method that obviates the need for a genetic map. The technique is based on Restriction Fragment Length Polymorphism (RFLP) Subtraction, a method that isolates RFLP markers spanning an entire genome. The new method, Targeted RFLP Subtraction (TRS), isolates markers from a specific region by combining RFLP Subtraction with a phenotypic pooling strategy. We used TRS to directly isolate dense markers tightly linked to the regA gene of the eukaryotic green alga Volvox. As a generally applicable method for saturating a small targeted region with DNA markers, TRS should facilitate gene isolation from diverse organisms and accelerate the process of physically mapping specific regions in preparation for sequence analysis.     

Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies

Circular yeast artificial chromosomes (YACs) provide significant advantages for cloning and manipulating large segments of genomic DNA in Saccharomyces cerevisiae. However, it has been difficult to exploit these advantages, because circular YACs are difficult to isolate and purify. Here we describe a method for purification of large circular YACs that is more reliable compared with previously described protocols. This method has been used to purify YACs up to 600 kb in size. The purified YAC DNA is suitable for restriction enzyme digestion, DNA sequencing and functional studies. For example, YACs carrying full-size genes can be purified from yeast and used for transfection into mammalian cells or for the construction of a synthetic genome that can be used to produce a synthetic cell. This method for isolating high-quality YAC DNA in microgram quantities should be valuable for functional and synthetic genomic studies. The entire protocol takes ～3 d to complete.     

Simultaneous purification of chloroplast and mitochondrial DNA without isolation of intact organelles from green carrot tissue and suspension cultures

We report here the simultaneous purification of chloroplast (cpDNA) and mitochondrial DNA (mtDNA) from green tissue and suspension cultures of carrot without organelle isolation. This method is based on isolating total nucleic acids from frozen tissue and separating the nuclear, chloroplast and mitochondrial fractions using sequential isopycnic sedimentation in two gradients of cesium chloride containing bisbenzamide. From 10 g of mature carrot leaves, 10 to 30μg of organelle DNA was consistently recovered from mature carrot leaves, while 30 to 50 μg was recovered from suspension cells. The method can be used to isolate chloroplast and mitochondrial DNAs from single plants without sacrificing the individual.     

Using partial genomic fosmid libraries for sequencing complete organellar genomes

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However; for some organisms, it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.     

Genome walking of large fragments: an improved method

The PCR-based genome walking method has been commonly used to isolate upstream regions from known cDNA sequences. The limitation of this technique is based on the location of the restriction site upstream to the gene-specific primer in the genome; hence, different restriction enzymes have to be used to isolate larger upstream fragments. In this paper, we present the advantageous use of partial and size-selected DNA as templates for genome walking, in isolating larger upstream fragments. We have successfully tested this approach to isolate larger upstream fragments using the FailSafe PCR System. Use of partial digestion and size selection can provide better chances in obtaining larger flanking regions of known DNA sequence, when compared to use of total digested DNA.     

Producing a P1 bacteriophage library from pine: isolation and cloning of very high molecular weight DNA.

We have generated a genomic P1 bacteriophage library using Monterey pine (Pinus radiata) DNA. We first developed a method for isolating from pine tissue the very high molecular weight DNA necessary for the preparation of libraries requiring large inserts. The method involves protoplasting the cells, isolating nuclei and lysis in a high concentration of detergent. Fragments of greater than two megabases in size are produced in solution. Modifications introduced to the protocol for library preparation and for P1 plasmid isolation are described.     

Isolation of high-molecular-weight plant DNA for DNA damage quantitation: relative effects of solar 297 nm UVB and 365 nm radiation

Quantitation of UV-induced DNA damages in nanogram quantities of non-radiactive DNA from irradiated plants by gel electrophoresis requires a prompt, efficient, high-yield method of isolating DNA yielding high-molecular-weight, enzymatically digestible DNA. To meet these criteria we devised a high-yield method for isolating from plant tissue, DNA whose single-strand molecular length is greater than about 170 kb. Leaf tissue is embedded in agarose plugs, digested with Proteinase K in the presence of detergent, and treated with phenylmethylsulfonyl fluoride (PMSF). The agarose plugs are then soaked with buffer appropriate to the desired enzyme treatment. Evaluation of the DNA on neutral and alkaline gels indicates its high molecular length and low frequency of single-strand breaks. The DNA can be digested with damage-specific and other endonucleases. The method is especially suitable for DNA damage quantitation, as tissue processing is carried out immediately after harvesting (allowing DNA lesion measurement at precisely known times after irradiation), and many samples can be easily handled at once. It should also be useful for molecular analysis of large numbers of plant samples available only in small quantities. We here use this method to quantitate DNA damage induced by 297 and 365 nm radiation, and calculate the relative damaging effects of these wavebands in today's solar spectrum.     

General method for cloning amplified DNA by differential screening with genomic probes.

Mutant Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate, a potent and specific inhibitor of aspartate transcarbamylase, have amplified the gene coding for the multifunctional protein (CAD) that includes this activity. The average amount of DNA amplified is approximately 500 kilobases per gene copy, about 20 times the length of the CAD gene itself. A differential screening method which uses genomic DNAs as probes was developed to isolate recombinant phage containing fragments of amplified DNA. One probe was prepared by reassociating fragments of total genomic DNA from 165-28, a mutant cell line with 190 times the wild-type complement of CAD genes, until all of the sequences repeated about 200 times were annealed and then isolating the double-stranded DNA with hydroxyapatite.This DNA was highly enriched in sequences from the entire amplified region, whereas the same sequences were very rare in DNA prepared similarly from wild-type cells. After both DNAs were labeled by nick translation, highly repeated sequences were removed by hybridization to immobilized total genomic DNA from wild-type cells. A library of cloned DNA fragments from mutant 165-28 was screened with both probes, and nine independent fragments containing about 165 kilobases of amplified DNA, including the CAD gene, have been isolated so far. These cloned DNAs can be used to study the structure of the amplified region, to evaluate the nature of the amplification event, and to investigate gene expression from the amplified DNA. For example, one amplified fragment included a gene coding for a 3.8-kilobase, cytoplasmic, polyadenylated RNA which was overproduced greatly in cells resistant to N-(phosphonacetyl)-L-aspartate. The method for cloning amplified DNA is general and can be used to evaluate the possible involvement of gene amplification in phenomena such as drug resistance, transformation, or differentiation. DNA fragments corresponding to any region amplified about 10-fold or more can be cloned, even if no function for the region is known. The method for removing highly repetitive sequences from genomic DNA probes should also be of general use.