Analysis of DNA adducts bases by capillary electrophoresis with amperometric detection.

We have developed a method for the detection of DNA adducts by combining capillary electrophoresis (CE) with the specificity of amperometric detection. Guanine is the most easily damaged base of the four normal DNA bases and many adducts of guanine have been found in DNA. These guanine adducts are often electrochemically active, while the normal bases with the exception of guanine are not. Therefore, CE with amperometric detection will be a promising method to study DNA damage. The four normal deoxynucleosides and two damaged deoxnucleosides N2-ethyldeoxyguanosine (N2-ethyl-dG) and 8-hydroxydeoxyguanosine (8-OH-dG), were completely separated by micellar electrokinetic chromatography (MEKC). Deoxyguanosine and the two damaged deoxynucleosides were identified using amperometric detection. The sensitivity of our system was comparable to that of UV detection. Analysis of DNA hydrolysis products was also performed briefly using this method.     

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.     

Detection of single-base mutation by affinity capillary electrophoresis using a DNA-polyacrylamide conjugate

We have developed an affinity capillary electrophoresis (ACE) method for detection of gene point mutations using a DNA-polyacrylamide conjugate as a pseudostationary affinity phase. In this study, the target DNA was prepared by mixing two PCR products: the wild type of K-ras gene and its codon 12 point mutant. The ligand DNA was designed to be complementary to codons 11 and 12 of the wild type. The target DNA was denatured by the addition of formamide and by heating at 95 degrees C for 5 min, and then electrophoretically separated by difference in affinity to the pseudoimmobilized ligand DNA. The method successfully separated a mixture of the wild-type DNA and each of six codon 12 point mutants by the same ligand DNA. The limit of mutation detection was determined by mixing the wild-type DNA with decreasing concentrations of the mutant DNA. The lowest level of detection was 10% mutant DNA in a background of the wild type. The practicability of this method has been confirmed using a colorectal carcinoma cell line. This study is the first demonstration of detection of gene point mutation in polymerase chain reaction (PCR) products using ACE, and opens up a new possibility of CE-based gene diagnosis.     

A novel approach for the detection of DNA using immobilized peptide nucleic acid (PNA) probes and signal enhancement by real-time immuno-polymerase chain reaction (RT-iPCR)

A new approach for the detection of DNA target molecules is described, using capture probes and subsequent signal enhancement by a uniform polymerase chain reaction (PCR). Peptide nucleic acid probes were immobilized in real-time PCR-compatible microtiter plates. After hybridization of biotinylated DNA targets, detection was performed by real-time immuno-PCR, a method formerly used for protein detection. We demonstrate the feasibility of this strategy for the qualitative detection of DNA oligonucleotides with a detection limit (LOD) of 6 attomol. Furthermore, the method was applied to PCR-amplified samples from genetically modified maize DNA (Mon810). A 483-bp DNA fragment was detected in mixture with 99.9% of noncomplementary DNA with a sensitivity down to the level of attomole. Figure       

Development of a polymerase chain reaction and capillary gel electrophoresis method for the detection of chicken or turkey meat in heat-treated pork meat mixtures

A polymerase chain reaction and capillary gel electrophoresis (PCR-CGE) method with ultraviolet (UV) or laser induced fluorescence detection (LIF) was established for the detection of chicken or turkey in heat-treated pork meat mixtures. Mitochondrial DNA samples extracted from heat treated meat were amplified with their corresponding specific primers yielding PCR products between 200 and 300 bp. LIF detection was superior than UV detection in terms of precision and sensitivity for the study of DNA fragments. The CGE-LIF method was highly reproducible and accurate for determining DNA fragment size. The PCR-CGE-LIF was sensitive since a significant fluorescent signal was obtained at the minimum admixture level employed of 1% in meat mixtures. Thus, the PCR-CGE-LIF method established was useful for the detection of chicken or turkey in heat treated meat mixtures and may prove to be useful for the detection of poultry meat in pork processed products.     

Electrochemical DNA Hybridization Detection Using DNA Cleavage

We report the new method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture probe DNA, thiolated single strand DNA labeled with electroactive ferrocene group, was immobilized on a gold electrode. After hybridization of target DNA of complementary and noncomplementary sequences, nonhybridized single strand DNA was cleaved using S1 nuclease. The difference of enzymatic cleavage on the modified gold electrode was characterized by cyclic voltammetry and differential pulse voltammetry. We successfully applied this method to the sequence‐selective discrimination between perfectly matched and mismatched target DNA including a single‐base mismatched target DNA. Our method does not require either hybridization indicators or other exogenous signaling molecules which most of the electrochemical hybridization detection systems require.     

A cost-effective detection of low-abundance mutation with DNA three-way junction structure and lambda exonuclease

We presented a low-abundance mutation detection method with lambda exonuclease and DNA threeway junction structure.The assistant strand in the DNA three-way junction structure could regulate the reaction system from the kinetics and thermodyna mics aspects.The optimization of the assista nt strand helps to improve the selectivity of the mutant-type DNA to the wild-type DNA about 35 times.Moreover,the cost of the optimization process could be saved by about 90%.The method was applied to the detection of a human ovarian cancer-related gene mutation BRCA1(rs1799949,c.2082 CT).The limit of detection to the mutation abundance in the DNA three-way junction structure system(0.2%) was one order lower compared with that in the double-stranded DNA structure system(2%).The mutation abundance in different standard samples was quantitively measured,and the results were consistent with the initial abundance in the standard samples.     

Nicking endonuclease and target recycles signal amplification assisted quantum dots for fluorescence detection of DNA

An ultrasensitive fluorescence detection method for DNA based on nicking endonuclease (NEase) and target recycles assisted with CdTe quantum dots (QDs) is reported. In the detection system, when the target DNA is present, it hybridizes with a linker strand to from a duplex, in which the NEase recognizes specific nucleotide sequences and cleaves the linker strand. After nicking, the fragments of the linker strand spontaneously dissociate from the target DNA and another linker strand hybridizes to the target to trigger another strand-scission cycle. On the other hand, when the target was absent, no duplex is formed and no fragment of linker strand is produced. Then CdTe QDs and magnetic beads (MBs), which were all modified with DNA sequences complementary to that of the linker strands are added to the solution to detect the presence of a target DNA. The signal was generated through the difference in F?rster resonance energy transfer (FRET) between the MB and CdTe QDs. This method indicates that one target DNA leads to cleavage of hundreds of linker DNA, increasing detection sensitivity by nearly three orders of magnitude. This method should be applicable whenever there is a requirement to detect a specific DNA sequence and can also be used for multicomponent detection.     

酸性条件下的DNA构象变化加速DNA变性解链

调控DNA的变性解链过程是DNA扩增与检测的关键步骤。对于传统的热循环DNA扩增策略,由于变温过程中热量分布不均一以及变温速度慢等不利因素,会直接影响DNA变性解链过程,从而降低DNA检测放大的效果、延长检测的时长。因此,探索快速、高效的调控DNA变性解链的方法具有重要的研究意义。本文发展了以胞嘧啶在酸性条件下的质子化反应为基础,通过改变溶液的pH值,来诱导DNA构象在Watson-Crick（WC）碱基对与Hoogsteen（HG）碱基对之间的分子构象转换,从而实现精准、快速、高效的DNA变性解链调控目标。结果表明,相较于传统的温控方法,pH调控方法能显著提高DNA变性的速率约6倍以上。本文发现pH调控方法通过降低双链DNA的反应焓约160 kJ/mol,从而提高双链DNA变性速率和效率。该方法具有用于DNA信号放大与检测等相关应用的潜力。     

Sequence-selective DNA detection using multiple laminar streams: a novel microfluidic analysis method

On-site detection methods for DNA have been demanded in the pathophysiology field. Such analysis requires a simple and accurate method, rather than high-throughput. This report describes a novel microfluidic analysis method and its application for simple sequence-selective DNA detection. The method uses a microchannel device with a serpentine structure. Sequence-specific binding of probe DNA can be detected at one side of the microchannel. This method is capable of sequence-specific detection of DNA with high accuracy. Single base mutations can also be analyzed. Combination of laminar stream and laminar secondary flow in the microchannel enable specific detection of probe-bound DNA.     

A sensitive fluorimetric biosensor for detection of DNA hybridization based on Fe/Au core/shell nanoparticles

In this study, we reported a sensitive fluorescent biosensor for detection of DNA hybridization based on Fe/Au core/shell (Fe@Au) nanoparticles (NPs). First, Fe@Au NPs were synthesized using a reverse micelle method, with gold as the shell and iron as the core. The nanoparticle size was confirmed by transmission electron microscopy (TEM). Scanning electron microscopy (SEM) was performed in order to elucidate the morphology of the Fe@Au NPs. Then probe DNA with -SH at the 5'-phosphate end was covalently immobilized onto the surface of the Fe@Au NPs. The DNA hybridization event can be detected by a fluorescent method and methylene blue (MB) as the fluorescent probe. The decline of the fluorescence intensity of MB (ΔF) was linear with the concentration of the complementary DNA from 3.0 × 10(-13) to 1.0 × 10(-9) M with a detection limit of 1.0 × 10(-13) M (S/N = 3). In addition, this approach of DNA detection exhibited excellent selectivity, even for single-mismatched DNA detection.     

DNA detection based on Mn-doped ZnS quantum dots/methylene blue nanohybrids

Nanohybrids were formed from 3-mercaptopropionic acid(MPA)-coated Mn-doped ZnS quantum dots(QDs) and methylene blue(MB) via electrostatic interaction, and then used in the detection of trace DNA.The principle of detection is as follows: MB binds with Mn-doped ZnS QDs via electrostatic interaction,and then quenches the room temperature phosphorescence(RTP) of the QDs through photoinduced electron-transfer(PIET). After the addition of DNA, MB binds with DNA through intercalation and electrostatic interaction, and desorbs from the surfaces of Mn-doped ZnS QDs, which recovers the RTP of the QDs. On this basis, a DNA detection method based on the properties of RTP was set up. This method shows a detection range of 0.2–20 mg/L, and a detection limit of 0.113 mg/L. Since this method is based on the RTP of QDs, it is not interfered by the background fluorescence or scattering light in vivo, and thus,avoids complex sample pretreatment. Thus, this method is very feasible for detection of trace DNA in biofluids.     

Silver staining method for DNA in polyacrylamide gels using eriochrome black T as a silver-ion sensitizer

A sensitive silver staining method using eriochrome black T as a silver-ion sensitizer for DNA detection in polyacrylamide gels was developed. The sensitivity of this staining method was significantly improved by the new silver-ion sensitizer containing a diazo group, which has reducing power. The staining method lasted a total of approximately 15 min following a fixing step for 2 x 20 min. The detection limit of this staining method was 1-4 pg for PhiX174 DNA/HaeIII in both nondenaturing and denaturing polyacrylamide gels. This staining method was especially effective in low-base pair DNA, with a sensitivity that was approximately ten-fold higher than previously published silver staining methods.     

SYBR green real-time PCR used to detect celery in food

Celery was found to provoke human allergenic response in some countries. Labeling of celery ingredients was required by the European Union, and the threshold set at 10 mg/kg (0.001%). In our study, a celery mannitol transporter (Mat3) gene-based detection method was established by means of SYBR Green real-time PCR technique. No cross-reactivity was found between celery and the other food materials. Absolute detection limit (LODa), relative detection limit (LODr), and practical detection limit (LODp) of the method were determined through experiments on pure celery DNA, DNA mix, and spiked food samples. The method was able to detect 0.001% raw food sample and 0.01% heated food sample. The utility of the method was confirmed by the investigation of 13 commercial foods.     

新型超支状液晶核酸传感器用于p53突变基因的检测

基于核酸杂交链式反应影响液晶取向的原理, 构建了一种新型的超支状液晶核酸传感器用于检测p53突变基因. 本文突破传统构建超支状分子的方式, 采用杂交链式反应方法, 以目标序列p53突变基因作为引发剂, 3种不同的发卡探针Hairpin A, Hairpin B和Hairpin C为单体, 在温和的条件下, 通过改变单体的浓度和反应时间自发杂交组装形成尺寸和分子量可控的超支状DNA(branched-like DNA, bDNA). 借助捕获探针将该超支状DNA连接到液晶传感基底表面, 观察液晶分子取向改变前后的光学信号, 实现了p53基因含249密码子突变序列的快速检测. 本方法有望为核酸诊断的发展提供一种新的方法和思路.     

基于金纳米颗粒信号放大效应电化学检测DNA聚合酶

基于金纳米颗粒(AuNPs)比表面积大、 尺寸小和能够承载大量DNA片段的特点, 建立了一种免标记、 简便、 快速检测DNA聚合酶Klenow fragment exo-(KF^-)的电化学方法. 首先将巯基化的DNA引物片段修饰在金电极上, 然后加入模板DNA链以及修饰有报告DNA链的金纳米颗粒(AuNPs-DNA), 模板DNA链能同时与DNA引物片段和修饰在AuNPs上的报告DNA链进行互补杂交形成"三明治"结构, 从而将AuNPs-DNA修饰在电极表面; 当加入电活性物质钌铵(RuHex)后, RuHex可通过静电吸附作用结合在DNA上. AuNPs上修饰的报告DNA链能够吸附大量RuHex, 导致电化学信号放大. 当加入脱氧核糖核苷三磷酸(dNTPs)以及KF^-聚合酶后, 引物片段发生延伸反应, 将与模板DNA链杂交的AuNPs-DNA竞争下来, 带走大量的RuHex, 使电信号降低, 从而实现对聚合酶的检测. 实验结果表明, 利用该方法可以检测到5 U/mL的KF^-.     

DNA在纳米金标上的组装、杂交、检测与银增强

利用电化学方法进行DNA的杂交检测.将目标ss-DNA固定在玻碳电极表面, 使其与纳米金标记的互补DNA发生杂化反应, 通过银增强试剂（该种试剂可以使银在纳米金表面沉积, 达到信号增强的效果）在纳米金上沉积银, 形成银包金的核壳结构.在酸性介质中沉积的银被氧化释放, 以离子状态存在于溶液中.用阳极溶出伏安法(ASV)检测银离子从而达到间接检测目标DNA的目的.测定结果表明，ss-DNA的浓度在100～1 000 pmol•L－1 范围内有非常好的线性关系, 检测限为10 pmol•L－1.     

基于纳米金胶标记DNA探针的电化学DNA传感器研究

以纳米金胶为标记物,将其标记于人工合成的5-端巯基修饰的寡聚核苷酸片段上,制成了具有电化学活性的金胶标记DNA电化学探针;在一定条件下,使其与固定在玻碳电极表面的靶序列进行杂交反应,利用ssDNA与其互补链杂交的高度序列选择性和极强的分子识别能力,以及纳米金胶的电化学活性,实现对特定序列DNA片段的电化学检测以及对DNA碱基突变的识别.     

Colorimetric detection of hepatitis B virus (HBV) DNA based on DNA-templated copper nanoclusters

DNA detection plays an important role in early diagnosis of genetic disease. The conventional detection methods of DNA are based on expensive equipment, which do not meet the demands of developing countries. Thus, we developed a colorimetric method, which could be observed with naked eye and used copper nanoclusters for cost-effective. Moreover, the target of this method is the DNA in Hepatitis B virus that is one of the most popular chronic viral infections in developing countries over the past years. Our method was sensitive and the limit of detection was 12 × 10⁹ molecules. Three-base-pair mismatches target DNA was detected easily. These results revealed the favorable sensitivity and selectivity of this approach. Most importantly, our method may have potential applications in correct diagnosis of genetic disease and monitoring of gene therapy in the poverty-stricken areas.     

Visual detection of lead(II) using a label-free DNA-based sensor and its immobilization within a monolithic hydrogel

Lead is highly toxic and its detection has attracted a lot of research interests. In recent years, DNA has been used for Pb(2+) recognition and many fluorescent sensors with low to sub-nM detection limits have been reported. These figures of merit were typically measured using a spectrophotometer that can detect nM DNA with a high signal-to-noise ratio. For visual detection, however, μM DNA or dye was required, making it difficult to detect low nM targets. We recently achieved a visual sensitivity of 10 nM Hg(2+) by immobilizing a DNA probe in a hydrogel. This was made possible because the gel was able to actively adsorb Hg(2+). In this work, we aim to test whether this method can be extended to the detection of Pb(2+). First, a new Pb(2+) sensor was designed based on a guanine-rich DNA and DNA binding dyes such as thiazole orange and SYBR Green I. The free DNA showed a detection limit of 8 nM Pb(2+) using 40 nM DNA. For visual detection in solution with 1 μM of the DNA probe, however, ～300 nM Pb(2+) was required. After immobilization in a monolithic polyacrylamide hydrogel, even 20 nM Pb(2+) could be visually detected with a sample volume of 50 mL. Therefore, sensitive detection without signal amplification was achieved. Finally, we demonstrated simultaneous detection of both Hg(2+) and Pb(2+) in the same water sample with shape encoded hydrogel sensors.