一种简便、高效、经济的从凝胶中回收DNA的方法

目的:尝试一种简便、高效的从凝胶中回收DNA的方法。方法:在Eppendorf管的管底用注射器扎孔,将一小团用Eppendorf管融化后拉成的细丝放入管中,把含有DNA的凝胶放在细丝上,离心,收集从管底流出的液体,经酚氯仿抽提后用乙醇沉淀DNA。结果:经过简单的离心即可近乎100%地回收凝胶中的DNA。结论:使用该方法从琼脂糖凝胶回收DNA,操作简单,回收率高,无其他试剂污染。     

一种从琼脂糖凝胶上回收DNA的高效、快捷、经济的方法

目前在国内分子生物学实验室所采用的多种从琼脂糖凝胶上回收DNA的方法普遍存在着各种问题。本文介绍一种新的从琼脂糖凝胶上分离和提取DNA简易装置。实验表明用这种装置回收DNA具有高效、快捷和经济的优点,非常适合在国内实验室普及推广。     

一种高效、快速从凝胶中回收DNA的方法

目的:介绍了一种从普通琼脂糖电泳中回收DNA的简便、快捷、高效且廉价的方法.方法:利用0.5 mL离心管、1.5mL离心管、尼龙膜做成的一个小装置.把含有DNA的凝胶放在膜上,离心,收集从管底流出来的液体,用乙醇沉淀DNA.结果:最终回收率为60%左右,回收率大约为市售试剂盒的90%,接近市售DNA回收试剂盒.结论:该方法操作简单,回收率高,无其他试剂污染.     

琼脂糖凝胶中DNA片段的挤压回收法

为了简化琼脂糖凝胶中DNA片段的回收,该文报道一种新的挤压回收法。将含有DNA片段的凝胶块放在折叠的封口膜之间,然后用一小塑料平板将凝胶块中的DNA溶液用力挤出,用移液枪把所有挤压出的DNA溶液放入effendorf管中,然后用常规的苯酚抽提法进行纯化。DNA回收率达到40-60%(w/w)。该方法简单而有效,且回收的DNA能够直接应用于酶切、连接及PCR等各种分子生物学操作。     

回收琼脂糖凝胶中DNA的简便方法

多年来国内分子生物学实验室所采用的几种从琼脂糖凝胶中回收DNA的方法不同程度地存在着各种问题。现介绍一种新的从琼脂糖凝胶上分离和提取DNA的简易方法,采用实验室常用的吸附柱中的吸附膜对DNA进行拦截、纯化和回收。实验证明这种方法回收DNA具有简便快捷、成本低和效率高等优点,是一种切实可行的方法。     

简便实用的琼脂糖凝胶回收DNA片段方法

介绍一种简便实用的DNA片段回收方法,与以前所报道的DEAE-纤维素膜电泳法、透析袋电洗脱法、低融点琼脂糖凝胶法、凝胶冻融法等相比,所需器材简单、操作简便、回收率高、成本低。回收的DNA片段在进一步克隆和测序中表现出较好的效果,是一种适合于科研和教学的实验方法。     

一种从琼脂糖凝胶中同步回收DNA和琼脂糖的方法

介绍一种从琼脂糖凝胶同步回收DNA和琼脂糖的方法。利用0.25 mol/L异硫氰酸胍溶液(p H 8.0)溶解含有目的 DNA片段的的凝胶条,胶条溶解后,静置冰上10 min再加入预冷的异丙醇,琼脂糖呈颗粒状析出,通过离心即可初步分离DNA和琼脂糖。上清液用异丙醇沉淀回收DNA片段,利用50%PEG溶液沉淀琼脂糖。分别对0.2 kb、1 kb和10 kb长度的DNA片段进行回收,回收率分别为19.44%、36.40%、13.49%,回收的DNA纯度高,电泳条带清晰。琼脂糖均回收率为62.52%,回收琼脂糖脱水后的状态为白色颗粒。该方法切实可行,回收成本低廉,回收的DNA和琼脂糖可用于后续实验。     

DNA甲基化的研究进展

甲基化修饰是脊椎动物DNA唯一的自然修饰方式,动物基因组甲基化与基因表达密切相关.DNA甲基化通过与反式作用因子相互作用或通过改变染色质结构而影响表达,在细胞分化、发育、X染色体失活、基因组印记及肿瘤发生发展中起重要作用.     

一种从琼脂糖凝胶中回收DNA片段的简单电洗脱装置

我们设计了一种简单电洗脱装置,从琼脂糖胶中回收ＤＮＡ。该装置由两个带旋盖的小管、两块透析膜和一个凝胶屏障组成。在电场作用下,ＤＮＡ从凝胶中迁移出来,通过凝胶屏障进入由凝胶屏障和透析膜组成的回收小仓。用微量吸样器收集ＤＮＡ,乙醇沉淀和清洗。该法ＤＮＡ的回收率约８５％;回收的ＤＮＡ可用于基因工程常规实验。     

一种快速、简单的琼脂糖凝胶DNA片段分离法

该方法利用Ｎａｌ溶解凝胶,硅胶颗粒吸附ＤＮＡ片段便之分离。有快速、不影响后续酶反应、高回收率等特点,可用于基因工程中酶切片段、ＰＣＲ产物的分离纯化。     

High-Speed Conversion of Cytosine to Uracil in Bisulfite Genomic Sequencing Analysis of DNA Methylation

Bisulfite genomic sequencing is a widely used technique foranalyzing cytosine-methylation of DNA. By treating DNA withbisulfite, cytosine residues are deaminated to uracil, whileleaving 5-methylcytosine largely intact. Subsequent PCR andnucleotide sequence analysis permit unequivocal determinationof the methylation status at cytosine residues. A major caveatassociated with the currently practiced procedure is that ittakes 16–20 hr for completion of the conversion of cytosineto uracil. Here we report that a complete deamination of cytosineto uracil can be achieved in shorter periods by using a highlyconcentrated bisulfite solution at an elevated temperature.Time course experiments demonstrated that treating DNA with9 M bisulfite for 20 min at 90°C or 40 min at 70°C allcytosine residues in the DNA were converted to uracil. Underthese conditions, the majority of 5-methylcytosines remainedintact. When a high molecular weight DNA derived from a cellline (containing a number of genes whose methylation statuswas known) was treated with bisulfite under the above conditionsand amplified and sequenced, the results obtained were consistentwith those reported in the literature. Although some degradationof DNA occurred during this process, the amount of treated DNArequired for the amplification was nearly equal to that requiredfor the conventional bisulfite genomic sequencing procedure.The increased speed of DNA methylation analysis with this novelprocedure is expected to advance various aspects of DNA sciences.     

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol.     

An Integrated Workflow for DNA Methylation Analysis

The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our “Next-Gen Sequence” websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.     

Methylation status of Sillago japonica satellite DNA examined by bisulfite modification

A member of Sillago japonica satellite DNA contained internal subrepeats in its 174 bp unit. S. Japonica genomic DNA isolated from liver tissue was subjected to bisulfite modification, and the DNA sequences of about 40 bp flanked by both subrepeats were amplified by polymerase chain reaction (PCR). This protocol, combination of bisulfite reaction and PCR, converts cytosines in the genomic DNA to thymines in the amplified DNA, whereas 5-methylcytosines in the genomic DNA remain as cytosines. Sequence analysis of the amplified DNA fragments revealed that most of the cytosine residues at CpG were methylated in this region.     

从琼脂糖电泳凝胶中回收DNA的几种简便方法

介绍两类从普通琼脂糖电泳凝胶中回收ＤＮＡ的简便、快捷、高效且廉价的方法．第一类为电泳洗脱法．方法ａ：利用１．５ｍＬ微量离心管、ｌｍＬ吸头、尼龙网膜和透析膜做成的一个小装置,快速有效回ＤＮＡ,最终回收率为７０％左右．方法ｂ：不用ＤＥＡＥ－纤维素膜,而用透析膜在凝胶中作出横隔挡在ＤＮＡ条带前,最终回收率为５０％左右;第二类为冰冻融解法,最终回收率也在５０％左右．如果联合使用冰冻融解法和电泳洗脱法,回收率可进一步提高至９０％．     

Improved PCR-BSP Assay for Multiplex Methylation Pattern Analysis in Minimal Amount of DNA

Cell-specific DNA methylation pattern detection is of great importance for the tumorigenesis and differentiation studies. Comparatively, large amounts of DNA were needed for traditional methods of DNA methylation pattern detection, and therefore, more sensitive method for high throughput analysis with a limited amount of DNA is needed. With Mouse 3T3 cells, we developed new multiplex-nested PCR technologies for bisulfite-assisted genomic sequencing PCR (BSP) methylation pattern detection method. Primers step add-in method and templates precipitation methods efficiently increase the throughput of the assay, and the nested PCR method also increased the sensitivity. The optimized assay could successfully detect 15 sequences of methylation pattern with a minimal amount of DNA (500–1,000 cells of genome DNA).     

An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA from Arabidopsis Embryo

DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.     

应用亚硫酸氢盐修饰后PCR联合TA克隆测序对E-cadherin启动子区甲基化水平的检测

E-cadherin是一种细胞粘附因子,通过增强细胞之间的粘附而起到抑制肿瘤转移的作用.Ecadherin基因启动子区的高甲基化是导致其在众多肿瘤细胞中表达下调甚至缺失的主要原因之一.本实验首先抽提SGC-7901细胞(胃腺癌细胞)、A549细胞(肺腺癌细胞)、MCF-7细胞(乳腺癌细胞)等3个肿瘤细胞株的全基因组DNA,然后对抽提的DNA进行亚硫酸氢盐修饰和纯化回收,根据修饰后的DNA序列设计引物并对其进行PCR扩增.然后将PCR扩增产物与pUC-T TA载体连接并转化入感受态大肠杆菌DH5α中进行培养,对筛选出的含有阳性重组子的菌落进行测序.测序结果显示,3个肿瘤细胞株的E-cadherin基因启动子区的CpG岛都呈现了高度的甲基化,亚硫酸氢盐的修饰效率达到了99.2%.综上研究表明,亚硫酸氢盐修饰后PCR(BSP)联合TA克隆测序可以对肿瘤细胞某基因启动子区CpG岛的甲基化水平进行精确量化,研究所使用的3个肿瘤细胞株均可作为研究肿瘤细胞E-cadherin基因甲基化的细胞模型.