A microfluidic device integrated with multichamber polymerase chain reaction and multichannel separation for genetic analysis

This work describes a microfluidic device integrated with multichamber polymerase chain reaction (PCR) and multichannel separation for parallel genetic analysis. The microdevice consists of three functional units: temperature control, multiple PCR (four chambers PCR), and multiple channel separation (four separation channels, each channel connected to a PCR chamber). Platinum (Pt)/titanium (Ti) microheater was used to ensure homogeneous temperature field, and Pt-chip sensor was used for temperature monitoring. The interface between chip-PCR and chip separation was simplified by connecting the PCR chamber with separation channel directly. After chip-PCR, PCR products were introduced into parallel separation channels for subsequent separation/detection by applying an electric field automatically. This microdevice was successfully applied for detection of pathogens including hepatitis B virus (HBV) and Mycobacterium tuberculosis (MTB), and genotyping of human leucocyte antigen (HLA)-B27 as well, demonstrating the feasibility of the integrated microdevice for parallel genetic analysis.     

Construction and Validation of Simple Magnetic Nanoparticle Detector Based on Giant Magnetoresistive Effect

The finding of giant magnetoresistive（GMR） effect develops a new field for the sensing application with magnetic nanoparticles（MNPs） labeling. A convenient GMR sensor was built with a permanent magnet to excite the MNPs in this work. The sensing element contained a Wheatstone bridge with the GMR material as one of its branches. The magnetic field from MNPs unbalanced the Wheatstone bridge. After being amplified, the output signals were recorded. The construction and optimization of the magnetoresistive sensing platform were discussed in detail. The detection of three kinds of MNPs validated the performance of the proposed GMR sensor. The sensor showed a fast response to the addition or removal of MNPs. Because of its simplicity, this kind of GMR sensor can be developed in a routine laboratory. The finding of this new GMR sensor will promote the development of the method of probing biomoleeules and the study on the biomolecular interaction after being labeled magnetically.     

血液乙肝病毒基因检测

全世界每年死于乙型肝炎病毒相关疾病的人数已达60万人,应用荧光定量PCR法检测能够提高乙肝病毒基因的检出率,正确掌握该技术方法能够更加有效地进行疾病诊断和预防工作。基于此,研究针对荧光定量PCR法检测乙肝病毒基因的方法进行探讨。     

Simultaneous and multiplex detection of exosomal microRNAs based on the asymmetric Au@Au@Ag probes with enhanced Raman signal

Simultaneous and quantitative detection of multiple exosomal micro RNAs(miRNAs) was successfully performed by a surface-enhanced Raman scattering(SERS) assay consisting of Raman probes and capture probes. In this design, the asymmetric core-shell structured Au@Au@Ag nanoparticles were first synthesized by layer-by-layer self-assembly method and modified with different Raman molecules and recognition sequences(poly A-DNA) to prepare the surface-enhanced Raman probes. Then, the streptavidinmodifie...     

Rapid and sensitive genotyping of dopamine D4 receptor tandem repeats by automated ultrathin-layer gel electrophoresis

Prior studies have revealed possible association between the presence of a seven repeat of the 48 bp variable number tandem repeat polymorphism of the human dopamine D4 receptor gene (DRD4) and some normal and pathological human traits, such as novelty seeking, hyperactivity disorders, and substance abuse. Some reports supported this finding whereas others did not. Incorrect genotyping could be one of the reasons for these controversial results, and might originate from preferential amplification of shorter polymerase chain reaction (PCR) products, resulting in the so-called allele dropout. In this paper we optimized the conditions for simultaneous amplification of shorter and longer amplicons of the 48 bp repeat region of the DRD4 gene in order to avoid the loss of the longer allele and consequent incorrect genotyping, using very low DNA template concentrations and partial replacement of 2'-deoxyguanosine-5'-triphosphate (dGTP) by 2'-deoxyinosine-5'-triphosphate (dITP). The optimized PCR method in combination with high throughput automated ultrathin-layer gel electrophoresis was suitable for rapid genotyping from less than a nanogram DNA using noninvasive sampling (buccal epithelial cells). All detected genotypes are presented, including such rear heterozygotes as the 2 x and 8 x 48 bp repeats in the same sample, showing the reliability of our novel detection method of longer alleles in the presence of shorter alleles.     

Rapid genotyping of factor V Leiden mutation using single-tube bidirectional allele-specific amplification and automated ultrathin-layer agarose gel electrophoresis

We report a novel, high-throughput genotyping method by single nucleotide polymorphism (SNP) analysis using bidirectional allele-specific amplification with polymerase chain reaction (PCR) in a single-step/single-tube format. Blood coagulation factor V G1691A (also referred to as Leiden) mutation was chosen as a model system for SNP detection, as this is one of the most common inherited risk factors of thrombosis, effecting 2-5% of the human population. The rationale of our method is the production of allele-specific PCR fragments, different in size, which was achieved by bidirectional amplification, starting from the position of the mutation. Thus, both homozygosity and heterozygosity were readily identified from a single reaction by simply determining the sizes of the resulting PCR products. The advantage of our assay, compared to other single-tube systems, is that this method did not require the use of pre-PCR labeled (fluorophore) primers or probes. Preferential production of the allele-specific products was achieved by a hot-start, time release PCR system. Specificity was increased by introducing a mismatch in the 3'-antepenultimate position of the allele-specific primers. This method made possible the large-scale screening for the factor V Leiden mutation using single-tube PCR followed by automated ultrathin-layer agarose gel electrophoresis, with real-time detection of the "in migratio" ethidium-bromide-labeled fragments.     

全血直接扩增结合焦磷酸测序法测定亚甲基四氢叶酸还原酶基因多态性

亚甲基四氢叶酸还原酶基因677C>T和1298A>C两个位点的多态性与临床常用抗肿瘤药物甲氨喋呤及氟尿嘧啶的作用密切相关,对这两个位点多态性的检测能指导临床合理用药。为进一步缩短检测时间,降低检测成本,本研究建立了基于全血直接PCR的焦测序检测方法,采用"HpH Buffer"直接扩增全血模板,仅需1μL全血样本即可对两个位点进行高效扩增。扩增产物经碱变性法制备单链模板后进行焦磷酸测序,经过条件优化,仅需5μL扩增产物和1μL微球即可完成高灵敏的焦测序反应。为验证方法的准确性,检测了12例临床样本,均能正确检测两个位点的基因多态性。本研究为临床基因多态性检测提供了一种操作简便,耗时短,成本低,准确度高的方法,本方法可用于指导甲氨喋呤和5-氟尿嘧啶的个体化用药。     

商品化血糖仪用于乙型肝炎病毒的便携式体外分子诊断

为解决当前乙型肝炎病毒(HBV)基因检测技术在一定程度上存在成本高、操作繁琐、误诊率高等问题,在此提出了一种便携式生物传感平台用于HBV基因的超灵敏检测,可检出低至2 copies/μL的HBV基因.首次通过设计针对HBV检测序列的环介导等温扩增(LAMP)反应,实现了在40 min之内对HBV基因型单拷贝基因的检测....     

一种基于磁性纳米粒子PCR的高通量SNP分型方法

利用磁性纳米粒子PCR扩增(MNPs-PCR)和等位基因特异性双色荧光探针(Cy3, Cy5)杂交, 建立了一种单核苷酸多态性(SNP)分型的新方法. 应用该方法对9个样本MTHFR基因的C677T多态进行检测, 野生和突变型样本正错配信号比大于9.0, 杂合型正错配信号比接近1.0, 分型结果经测序验证. 此方法无须产物纯化、浓缩, 扫描分型结果快速、直观, 是一种操作简单、快速、高通量、高灵敏度的分型方法.     

Electrochemical genosensor array for the simultaneous detection of multiple high-risk human papillomavirus sequences in clinical samples

An electrochemical genosensor array for the simultaneous detection of three high-risk human papillomavirus (HPV) DNA sequences, HPV16, 18 and 45, exhibiting high sensitivity and selectivity is presented. The electrodes of a 4 × 4 array were modified via co-immobilization of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated bipodal thiol. Detection of synthetic and PCR products was carried out in a sandwich type format, with the target hybridized between a surface immobilized probe and a horseradish peroxidase-labelled secondary reporter probe. The detection limits obtained in the detection of each individual target were in the pM range, allowing the application of this sensor for the detection of samples obtained from PCR amplification of cervical scrape samples. The results obtained exhibited an excellent correlation with the HPV genotyping carried out within a hospital laboratory. Multiplexing and cross-reactivity studies demonstrated high selectivity over potential interfering sequences, facilitating application of the developed platform for the high-throughput screening of multiple high-risk DNA sequences.     

Selective genotyping of individual cells by capillary polymerase chain reaction

On-line capillary polymerase chain reaction (PCR) coupled with laser-induced fluorescence detection was successfully demonstrated for individual human cells. A single 50 num inner diameter (ID) fused-silica capillary served both as the reaction vessel and for isolating single cells. SYBR Green I dye was added into the reaction mixture for dynamic fluorescence labeling. Because of the small ID of the capillary, PCR-amplified DNA fragments from single cells were localized in the capillary, providing discrete product zones with concentrations at readily detectable levels. With selective primer design, only cells containing the DNA of interest were amplified. By counting the number of peaks in the capillary via electromigration past a detection window, the number of targeted cell templates could be determined. Identification of the 295 bp fragment beta-actin gene from individual human lymphoblast cell was demonstrated. Independent on-column cell counting provided positive correlation between the starting cell templates and the final PCR products. This opens up the possibility of highly selective and sensitive disease diagnosis at an early stage, when only a few cells in the population are defective.     

基于双纳米金探针杂交法检测HBV DNA

利用双纳米金探针结合基因芯片平台建立了一种检测乙肝病毒基因(HBV DNA)的新方法. 根据HBV DNA的保守序列设计捕获探针和信号报告探针, 通过一对互补的纳米金检测探针的双杂交法对HBV DNA进行信号放大, 最后进行银染, 达到对HBV DNA的可视化检测. 该方法的灵敏度高, 可检测10 fmol/L的HBV DNA, 且能在1.5 h内完成检测. 其具有的快速、 高灵敏度及低成本等优势使其有望发展成为一种检测HBV DNA的新方法.     

Integrated continuous flow polymerase chain reaction and micro-capillary electrophoresis system with bioaffinity preconcentration

An integrated and modular DNA analysis system is reported that consists of two modules: (i) A continuous flow polymerase chain reaction (CFPCR) module fabricated in a high T(g) (150°C) polycarbonate substrate in which selected gene fragments were amplified using biotin and fluorescently labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones as opposed to heating and cooling large thermal masses typically performed in batch-type thermal reactors. (ii) μCE (micro-capillary electrophoresis) module fabricated in poly(methylmethacrylate) (PMMA), which utilized a bioaffinity selection and purification bed (2.9 μL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to electrophoretic sorting. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed, where they were extracted onto the surface of micropillars. The affinity bed was also fabricated in PMMA and was populated with an array of microposts (50 μm width; 100 μm height) yielding a total surface area of ～117 mm(2). This solid-phase extraction (SPE) process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (K(d) = 10(-15) M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single-stranded DNA released for injection into a 7-cm-long μCE channel for size-based separations and fluorescence detection. The utility of the system was demonstrated using Alu DNA typing for gender and ethnicity determinations as a model. Compared with the traditional cross-T injection procedure typically used for μCE, the affinity pre-concentration and injection procedure generated signal enhancements of 17- to 40-fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation.     

富含胞嘧啶单链DNA-银纳米簇荧光探针用于S1核酸酶的灵敏检测

以富含胞嘧啶（C）的单链DNA为模板合成银纳米簇,将其作为功能化探针,建立了一种无标记荧光检测S1核酸酶的方法.S1核酸酶可以特异性识别单链DNA,在最适的酶催化反应条件下,可将其降解为单核苷酸或寡核苷酸片段.当S1核酸酶不存在时,富含C的单链DNA可以有效地合成荧光银纳米簇;当S1核酸酶存在时,单链DNA模板被特异性识别并降解,导致无法形成银纳米簇,使体系荧光信号降低.实验结果表明,银纳米簇的荧光强度随着S1核酸酶浓度的增加而降低.在优化的条件下,体系荧光信号（F/F₀）与S1核酸酶的浓度在5.0×10^-5~4.0×10^-3 U/μL范围内呈线性关系,检出限为2.0×10^-6 U/μL.该荧光探针选择性好,可用于RPMI 1640细胞培养基中S1核酸酶的检测,回收率达到91.8%~109.5%.     

Lateral flow dipstick test for genotyping of 15 beta-globin gene (HBB) mutations with naked-eye detection

For definitive diagnosis of thalassemia carriers and patients, as well as for prenatal diagnosis, genotype analysis is of fundamental importance. We report a dry-reagent, lateral flow dipstick test that enables visual genotyping (detection by naked eye) of 15 mutations common in Mediterranean populations in the beta-globin gene (HBB). The method comprises 3 simple steps: (i) PCR amplification of a single 1896 bp segment of the beta globin gene flanking all 15 mutations; (ii) a multiplex (10-plex and/or 30-plex) primer extension reaction of the unpurified amplification product using allele-specific primers. Biotin is incorporated in the extended product; (iii) a dry-reagent multi-allele (10-plex) dipstick assay for visual detection of the primer extension reaction products within minutes. The total time required for PCR, primer extension reaction and the dipstick assay is ∼2 h. The method was evaluated by genotyping 45 DNA samples of known genotypes and 54 blind samples. The results were fully concordant with reference methods. The method is simple, rapid, and cost-effective. Detection by the dipstick assay does not require specialized instrumentation or highly qualified personnel. The proposed method could be a particularly useful tool in laboratories with limited resources and a basis for point-of-care diagnostics especially in combination with PCR amplification from whole blood.     

Sequence-specific electrochemical detection of double-strand PCR amplicons of PML/RARα fusion gene in acute promyelocytic leukemia

A novel electrochemical method for the sequence-specific detection of double-stranded polymerase chain reaction (PCR) products of PML/RARα fusion gene in acute promyelocytic leukemia (APL) was described in detail. Based on a “sandwich” sensing mode involving a pair of locked nucleic acids probes (capture probe and reporter probe), this DNA sensor exhibited excellent selectivity and specificity. The direct and quantitative analysis of double-stranded complementary was firstly performed by our sensor without the use of alkali, helicase enzymes, or denaturants. Finally, combining PCR technique with electrochemical detection scheme, PCR amplicons (191 bp) of the PML/RARα fusion gene were obtained and rapidly identified with a low detection limit of 79 fmol in the 100-μL hybridization system. The results clearly showed the power of sensor as a promising tool for the sensitive, specific, and portable detection of APL and other diseases.     

Several concerns about the primer design in the universal molecular beacon real-time PCR assay and its application in HBV DNA detection

A universal hepatitis B virus (HBV) DNA detection kit is appealing for the worldwide diagnosis and monitoring of the treatment of different mutant types of hepatitis B virus. A sensitive and reproducible real-time PCR assay based on the universal molecular beacon (U-MB) technique was developed for the detection of HBV DNA in serum. The U-MB probe used in the assay has no interaction with the HBV DNA sequence. The U-MB technique not only reduced the cost of HBV detection but also had the potential for the development of a universal detection kit for different mutant HBV types and other DNA systems. To demonstrate its clinical utility, 90 serum samples were analyzed using the U-MB real-time PCR method. In the experiments we found that several crucial factors needed to be considered in the primer design, such as the avoidance of formation of severe primer–dimer and primer self-hairpin structure. With the optimized primer sets, satisfactory results were obtained for all the tested samples. We concluded that this assay would be an excellent candidate for a universal HBV DNA detection method. Principle of the U-MB real-time PCR method for HBV DNAdetection     

Human dopamine D4 receptor allele genotyping by ultrathin agarose gel electrophoresis with To-Pro-3 complexation

Growing evidence shows the correlation between the allelic type of the dopamine D4 receptor and the human novelty-seeking personality trait. A sensitive, ultrathin agarose gel electrophoresis-based, high-throughput screening method was developed for genotyping the dopamine D4 receptor (D4DR) exon III 48 base pair repeat polymorphism. The efficiency of the method was increased by reamplification nested polymerase chain reaction (PCR) - of the 48 base pair repeat containing the PCR product with internal primers. The nested PCR fragments were analyzed by ultrathin layer agarose gel electrophoresis with an automated real-time laser-induced fluorescent detection system. Noncovalent affinity complexation was accomplished during the separation process by the addition of a very low concentration of intercalation dye, To-Pro-3 (2 nM) to the gel buffer system. This resulted in instant fluorescent labeling of the migrating PCR fragments. This method can readily facilitate genetic association studies between dopamine receptor genotypes and some human behavioral and neuropsychiatric disorders.     

Capillary electropherograms for restriction fragment length polymorphism of Helicobacter pylori

Rapid identification of Helicobacter pylori strains is of importance for diagnosis and then treatment of duodenal and gastric ulcers. We developed a CE approach for the analysis of RFLP of the PCR products of urease (UreAB) gene and flagellin A (FlaA) gene fragments. Prior to CE analysis, the 2.4-kbp UreAB and 1.5-kbp FlaA PCR products were digested with the restriction enzymes HaeIII and HhaI, respectively. The DNA fragments were then separated by CE in conjunction with laser-induced fluorescence detection using poly(ethylene oxide) in the presence of electroosmotic flow. The DNA fragments range in sizes 259-1831 bp and 12-827 bp for UreAB and FlaA restriction fragments, respectively. Of 27 samples, the CE approach provided five and ten different RFLP patterns of the HaeIII and HhaI digests. The RFLP of PCR products of the two genes allow great sensitivity of identification of H. pylori strains. When compared with slab gel electrophoresis, the present CE approach provides advantages of rapidity (within 6 min per run), simplicity, and automation. The preliminary results have shown great practicality of the CE approach for screening H. pylori strains.