DNA单链二级结构预测与单链构象多态性分析的一致性研究

单链构象多态性(SSCP)分析是一种简便,快速检测DNA突变的方法,它在基因突变检测、遗传分析、进化研究等领域有着广泛的应用价值.但是这种方法的突变检出率随DNA序列不同而变化,一般只能达到70%～80%.这主要是有的碱基突变对单链DNA的构象影响较小,不能通过SSCP检测出来.将计算机对DNA二级结构的预测结果和实验结果作了对比,发现二者有很高的一致性.这一结果表明计算机的DNA单链二级结构预测分析可用于PCR-SSCP分析的辅助设计,提高SSCP的突变检出率.     

用毛细管电泳技术检测DNA点突变

毛细管电泳(ＣＥ)是90年代初发展起来的新技术,具有分辨率高、重现性好、灵敏度高、快速和易于实现自动化的特点。后来又发展了激光诱导荧光检测器(ＬＩＦ),大大提高了分析灵敏度,对微量样品如单细胞分析等,具有很大的优势。通常,利用ＣＥ技术可以在20ｍｉｎ内分析完成几千个碱基的ＤＮＡ片段。ＣＥ可以应用于ＤＮＡ点突变的检测,目前在ＰＣＲ基础上利用ＣＥ技术对ＤＮＡ已知点突变及未知点突变的检测发展十分迅速。1.已知点突变的检测1.1　扩增抗拒突变系统ＰＣＲ(ＡＲＭＳＰＣＲ)和短串联重复ＰＣＲ(ＳＴＲＰＣＲ)　　ＡＲＭＳＰＣＲ和Ｓ…     

害虫抗药性分子检测技术

PCR-限制性内切酶法(PCR—REN)、等位特异性PCR技术(PASA)、单链构型多态性分析(SSCP)和微测序法(minisequencing)等技术被应用于害虫靶标抗性的位点突变检测中,并已有成功的先例。然而,对代谢抗性的分子检测研究较少涉及,作者对此进行了分析和展望。     

毛细管电泳-单链构象多态分析检测胃癌中p16基因突变

目的:建立快速高效检测胃癌患者胃癌组织及癌旁正常组织中p16基因突变的方法。方法:采用PCR扩增p16基因第二外显子易发生突变片段,扩增样品纯化后经95℃变性;以毛细管电泳(CE)分析法结合单链构象多态性(SSCP)对60例胃癌患者p16基因突变情况进行分析。结果:分析结果表明只有3例低分化腺癌患者存在基因突变,测序表明p16基因第二外显子碱基序列AGAC发生碱基A丢失。结论:p16基因突变可能导致胃癌的发生,但不起主导作用;CE-SSCP分析方法具有快速、灵敏、准确的特点,可用于胃癌组织中p16基因的突变分析。     

在两个X连锁显性腓骨肌萎缩症家系中发现同一GJB1基因突变Glu208Lys

在两个X连锁显性腓骨肌萎缩症(Charcot-Marie-Tooth disease, CMT) 家系中进行了GJB1基因的突变分析。提取基因组DNA, PCR(polymerase chain reaction)反应扩增GJB1基因编码序列, 进行单链构象多态性(single strand conformational polymorphism, SSCP)分析, 对有差异SSCP带型的PCR产物进行测序, 结果在两家系中发现同一GJB1基因c.622G→A (Glu208Lys)突变。所发现的突变位点在国内尚未报道。     

宫颈癌患者核糖核酸酶抑制因子基因突变的分析

目的通过对宫颈癌患者血液核糖核酸酶抑制因子(ribonuclease inhibitor,RI)基因RNH的突变分析,探讨RNH基因与肿瘤生长的关系。方法针对RNH全基因序列设计21对引物,PCR扩增后采用SSCP对突变进行检测。结果正常人和宫颈癌患者均扩增出相应的21个条带,未发现异常;经过SSCP分析未发现所收集的18例宫颈癌患者血液中的RNH基因有突变发生。结论尚不能肯定RNH基因的突变是否与肿瘤无关,也不能肯定其他肿瘤没有发生突变。需缩小检测片段进一步实验。     

结核分枝杆菌katG基因突变的研究

探讨编码过氧化氢-过氧化物酶的katG基因突变与结核分枝杆菌异烟肼(INH)耐药性的相关关系。根据结核分枝杆菌GenBank中的katG序列,自行设计特异性寡聚核苷酸引物,采用聚合酶链反应-单链构象多态性(PCR-SSCP)分析和直接测序法(DS)分析结核分枝杆菌中katG基因突变情况。以HR37Rv标准株为对照。所有23株敏感菌均未有SSCP结果异常;35株耐药菌中,有2株(5．7％)katG基因扩增阴性,且发生在高度耐药菌中。进一步分析发现,SSCP法突变检出23株(65．7％),测序法突变检出24株(68．6％),符合率为95．8％(23／24)。参照测序法对耐药菌突变序列的分析结果,PCR—SSCP敏感、特异,可快速检测结核分枝杆菌katG耐药基因突变,有利于耐药结核分枝杆菌耐药性的快速检测。     

非同位素PCR-SSCP方法的初步临床应用

单链构象多态性检测法 (PCR-SSCP)是近年发展起来的一项检测人类基因组 突变的新技术。然而,在该技术中需要使用放射性同位素标记的核苷酸或引物,从而限制 了其广泛临床研究及诊断方面的应用。本文报告一种改进的PCR-SSCP方法, 该方法不用 同位素标记引物,而直接在溴乙啶染色的聚丙烯酰胺凝胶上显示SSCP。用该方法对55例 平滑肌肉瘤p53基因第7外显子突变的检测表明,38%的瘤组织DNA存在异常的SSCP。其中10例有HaeⅢ和MspⅠ酶切位点的突变(18%), 19例有突变型p53蛋白的过度表达(9例同时有异常SSCP改变)。而p53质粒D NA,平滑肌瘤及Alzheimer病患者基因组DNA无p53基因第7外显子扩增片段的异常SSCP改变。同时,还使用该方法对临床诊断的20例Alzheimer病患者和8例健康对照进行了β-淀粉样蛋白前体基因第16和17外显子的扩增及分析,均未发现有异常SSCP改变及EcoRⅠ,BclⅠ酶切位点的突变。本研究结果提示,该非同位素PCR-SSCP方法可靠、敏感、简便、快速,具有潜在的推广价值。     

单链构象多态性（SSCP）及其在昆虫学中的应用

单链构象多态性（SSCP）能够快速、灵敏地检测基因的点突变,其应用范围日益扩大。本文重点综述了其在昆虫学研究中的作用。 bstract:Single-strand conformation polymorphism (SSCP) can detect point mutation quickly and sensitively and its scope of application is enlarged everyday.In this paper,its important roles in entomology are summarized.     

应用膜反向斑点杂交技术快速检测结核分支杆菌耐乙胺丁醇基因型的研究

应用膜反向斑点杂交技术快速检测结核分支杆菌对乙胺丁醇（EMB）耐药性。设计与合成用于检测结核分支杆菌耐EMB基因embB的寡核苷酸探针,点于硝酸纤维素膜上,与结核分支杆菌临床分离株生物素标记的聚合酶链反应（PCR）产物进行反向斑点杂交,并与PCR单链构象多态性（PCRSSCP）和PCR直接测序（PCRDS）结果比较。对81株结核分支杆菌临床分离株进行分析,31株EMB敏感株中,26株embB基因的SSCP图谱、膜反向斑点杂交结果与标准株(H37Rv)完全相同;其余5株SSCP图谱出现泳动变位,其中3株E1b杂交阳性,PCRDS分析为embB基因306位密码子ATG→GTG突变;2株E1d杂交阳性,PCRDS分析为embB基因306位密码子ATG→ATA突变。50株耐EMB菌株中,24株PCRSSCP 图谱与标准菌株相同,E1杂交阳性;26株PCRSSCP图谱出现泳动变位,其中18株E1b杂交阳性,2株E1c杂交阳性,5株E1d杂交阳性,1株E1e杂交阳性,未发现E1f杂交阳性,与PCRSSCP、PCRDS分析结果一致。突变检出率为52%。 膜反向斑点杂交技术可能成为检测部分结核分支杆菌乙胺丁醇耐药基因型简便、快速的方法。     

High-throughput single-strand conformation polymorphism analysis by capillary electrophoresis

Mutation detection plays a great role in genetic and medical research and clinical diagnosis of inherited diseases and particular cancers. Single-strand conformation polymorphism (SSCP) analysis is one of the most popular methods for detection of mutations. Recently, automated capillary electrophoresis (CE) systems have been used in SSCP analysis instead of conventional slab gel electrophoresis. SSCP analysis in combination with CE is a rapid, simple, sensitive and high-throughput mutation screening tool, and has been successfully applied for mutation detection involving human tumor suppressor genes, oncogenes and disease-causing genes. The new technique has a great potential for mutation screening of large numbers of samples in clinical diagnosis. This review discusses basic issues about the methodology of SSCP analysis based on CE and summarizes several key applications.     

Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection

SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large number of DNA samples is screened for specific mutations. Here we describe a novel combined SSCP/duplex analysis adapted to the modern capillary electrophoresis (CE) system, which takes advantage of multicolor labeling of DNA fragments and laser-induced fluorescence detection. In developing this method, we first established the optimum conditions for homoduplex and heteroduplex analysis by CE. These were determined based on comprehensive analysis of representative Tamra-500 markers and BRCA1 fragments at different concentrations of sieving polymer and temperatures in the presence or absence of glycerol. The intrinsic features of DNA duplex structures are discussed in detail to explain differences in the migration rates between various types of duplexes. When combined SSCP/duplex analysis was carried out in single conditions, those found to be optimal for analysis of duplexes, all 31 BRCA1 and BRCA2 mutations, polymorphisms and variants tested were detected. It is worth noting that the panel of analyzed sequence variants was enriched in base substitutions, which are usually more difficult to detect. The sensitivity of mutation detection in the SSCP portion alone was 90%, and that in the duplex portion was 81% in the single conditions of electrophoresis. As is also shown here, the proposed combined SSCP/duplex analysis by CE has the potential of being applied to the analysis of pooled genomic DNA samples, and to multiplex analysis of amplicons from different gene fragments. These modifications may further reduce the costs of analysis, making the method attractive for large scale application in SNP scanning and screening.     

Detection of point mutations in DNA using capillary electrophoresis in a polymer network

The use of capillary electrophoresis (CE) in a polymer network for single-strand conformation polymorphism (SSCP) is investigated. SSCP is a method to detect DNA point mutations, essential in the diagnosis of several diseases. The PCR (polymerase chain reaction) amplified p53 gene, a tumour suppressor gene known to be frequently mutated in malignant cells, was subjected to CE analysis. Two single-strand DNA fragments of 372 bp in length differing in only one nucleotide could be separated. We conclude that SSCP using CE in a polymer network is a powerful method for the detection of point mutations in DNA sequences.     

Optimized sample preparation for tandem capillary electrophoresis single-stranded conformational polymorphism/ heteroduplex analysis

Here we describe DNA sample preparation methods that allow the rapid, simultaneous generation of both single-stranded conformational polymorphism (SSCP) and heteroduplex DNA elements from a single sample in a single tube, which are suitable for direct injection into a capillary electrophoresis (CE) instrument with excellent sensitivity of genetic mutation detection. The p53 gene was used as a model DNA region for this study, which was performed on a high-throughput MegaBACE 96-capillary array electrophoresis instrument. We found that, contrary to the practice common in slab-gel SSCP analysis, denaturants such as formamide are incompatible with this novel technique because they result in homo- and heteroduplex peak broadening in CE (possibly as a result of incomplete dsDNA re-hybridization) that reduces the peak resolution and hence the sensitivity of mutation detection. We also have found that PCR buffers, which are typically used to suspend samples for slab-gel heteroduplex analysis (HA), but which are less suitable for CE because of the presence of extra salt that reduces the efficiency of electrokinetic injection, may be substituted with a 10 mM Tris-HCI buffer (pH 8.5). The use of this Tris-HCl buffer for sample preparation provides both a high sensitivity of mutation detection by tandem SSCP/HA and high efficiency ofelectrokinetic injection by CE. In a related study (published elsewhere), we have applied this optimized protocol to the screening of a set of 32 mutant DNA samples from p53 exons 7 and 8 and recorded 100% sensitivity of mutation detection for tandem CE-SSCP/HA, whereas each individual method yielded lower sensitivity on its own (93% for SSCP and 75% for HA).     

Single-strand conformation polymorphism analysis by capillary and microchip electrophoresis: a fast, simple method for detection of common mutations in BRCA1 and BRCA2

As a result of intensive studies on hereditary breast and ovarian cancers, two breast cancer susceptibility genes, BRCA1 and BRCA2, have been identified. In each gene, a small number of specific mutations have been found at relatively high frequency in certain ethnic populations. The mutations, 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2, have been identified as common mutations in the Ashkenazi Jewish population, with a combined frequency of 2.0 to 2.5%. Women who have one of the above three common mutations are at a high risk of developing breast or ovarian cancer. Consequently, accurate and cost-effective detection of these three mutations may have important implications for risk assessment in susceptible women and men. In this report, we describe a fast and simple capillary electrophoresis (CE)-based method using a polymer network for screening the three common mutations in BRCA1 and BRCA2. Fluorescent dye-labeled primers (6-FAM-tagged) were used to amplify three DNA fragments of 258, 296, and 201 bp for detection of the 185delAG, 5382insC, and 6174delT mutations, respectively. After the PCR products were denatured, a single-strand conformation polymorphism (SSCP) profile could be obtained for each mutation in less than 10 min by CE in a polymer network. We demonstrate the potential provided by translating this assay to the microchip format where the SSCP analysis is complete in 120 s, representing only a fraction of the reduction in analysis time that can be achieved with microchip technology. The speed and simplicity of the SSCP methodology for detection of these mutations make it attractive for use in the clinical diagnostic laboratory.     

Analysis of major histocompatibility complex class II gene in water voles using capillary electrophoresis‐single stranded conformation polymorphism

Analysis of a single strand conformation polymorphism (SSCP) using capillary electrophoresis (CE) is a novel method to study polymorphism of DNA sequences in large scale population studies. We optimized CE‐SSCP analysis to study the major histocompatibility complex (MHC) class II alpha gene (DQA) polymorphism. Short‐chain linear polyacrylamide (6%) as sieving matrix, TrisCl (pH 8.5) as buffer for sample dilution, and 27 °C, 9 kV as electrophoresis parameters were suitable for sufficient resolution of all alleles. We found that almost 25% of clones contained a PCR (polymerase chain reaction) artefact and strict criteria have to be applied when using cloning and sequencing to analyse the allelic diversity of MHC genes.     

SSCP analysis of Mhc class IIB genes in the threespine stickleback

Due to its universality, speed, sensitivity, precision and reproducibility, PCR followed by fluorescence SSCP analysis represents an attractive tool for the characterization of Mhc class II B genotypes and the estimation of DNA sequence variability of Mhc genes in natural stickleback Gasterosteus aculeatus populations.     

Analysis of ellagic acid in pomegranate rinds by capillary electrophoresis and high-performance liquid chromatography

Two novel methods for the analysis of ellagic acid in pomegranate (Punica granatum) rinds are proposed. Capillary electrophoresis (CE) was performed in a bare fused-silica capillary using a buffer solution of tri(hydroxymethyl)aminomethane:potassium dihydrogen phosphate (pH 8.4) with an applied voltage of 20 kV and UV detection at 254 nm. HPLC analysis was performed with a Zobax SB C(18) column and a mobile phase consisting of methanol:ethyl acetate:potassium dihydrogen phosphate: phosphoric acid at a flow rate of 1.0 mL/min. Under optimised conditions, the HPLC retention and the CE migration times for ellagic acid were 10.32 and 12.23 min, respectively. Calibration curves of peak area vs. concentration gave correlation coefficients of 0.9999 for HPLC and 0.9990 for CE. The detection limits for HPLC and CE were 2.8 and 2.2 microg/mL, respectively. Average recoveries were 98.32 +/- 1.2% for HPLC and 96.52 +/- 2.8% for CE. Both methods were shown to be suitable for the determination of ellagic acid in pomegranate rinds extraction; however, the CE method required less solvent and gave better column efficiency, whilst the HPLC provided superior precision.     

Electrochemiluminescence detection with integrated indium tin oxide electrode on electrophoretic microchip for direct bioanalysis of lincomycin in the urine

In this article, an antibiotic, lincomycin was determined in the urine sample by microchip capillary electrophoresis (CE) with integrated indium tin oxide (ITO) working electrode based on electrochemiluminescence (ECL) detection. This microchip CE-ECL system can be used for the rapid analysis of lincomycin within 40s. Under the optimized conditions, the linear range was obtained from 5 to 100 microM with correlation coefficient of 0.998. The limit of detection (LOD) of 3.1 microM was obtained for lincomycin in the standard solution. We also applied this method to analyzing lincomycin in the urine matrix. The limit of detection of 9.0 microM was obtained. This method can determine lincomycin in the urine sample without pretreatment, which demonstrated that it is a promising method of detection of lincomycin in clinical and pharmaceutical area.