基于分子信标实时监测大肠杆菌DNA连接酶催化的DNA连接过程

报道了一种对DNA连接过程进行实时监测的方法,利用分子信标核酸探针作为DNA连接反应的模板和检测探针,实时监测了 E.coli DNA连接酶催化的DNA连接反应,克服了传统的凝胶电泳技术操作复杂、周期长及无法实时监测DNA连接过程的缺点,为核酸连接过程的实时监测和连接酶催化机理的研究提供了更为丰富的信息.在此基础上,发展了一种快速、准确测定 E.coli DNA连接酶的方法,线性响应范围为4.0×10^-6～2.0×10^-4U/μL,检测下限为4.0×10^-6U/μL.     

分子信标用于核酸连续复制过程的体外实时监测

利用分子信标核酸探针实时监测了核酸连续复制过程. 分子信标不仅作为模板参与复制反应, 而且同步将复制过程的信息转换为荧光信号, 实现复制过程的体外实时监测. 该方法不仅为DNA复制检测提供了一种实时研究手段, 而且为核酸复制动力学及与复制相关疾病的深入研究提供了一种新的思路.     

发夹型荧光分子探针用于DNA甲基化酶的活性分析及其在药物筛选中的应用

报道了一种基于发夹型荧光探针的甲基化酶活性的分析方法, 甲基化酶和相应的限制性内切酶的识别位点被设计在发夹型探针的茎部, 四甲基罗丹明(TAMRA)被连接在探针的5'端, 其荧光被连在3'端的熄灭基团4-(4'-二甲基对胺基偶氮苯)苯甲酸(DABCYL)所熄灭. 限制性内切酶可切割未发生甲基化修饰的探针, 导致探针的发夹结构遭到破坏, 引起TAMRA荧光信号的恢复. 根据荧光信号的恢复程度可实现对甲基化酶活性的分析. 在此基础上, 建立了一种简便、快速分析抗肿瘤药物对DNA甲基化酶活性的影响的方法, 为筛选针对基因甲基化异常引起的恶性肿瘤的治疗药物提供了一种新的思路和方法.     

基于聚合酶反应和发夹型核酸适体的蛋白质荧光检测新方法

设计合成了一种发夹型核酸适体(Aptamer), 结合聚合酶反应建立了蛋白质荧光分析新方法. 该核酸适体同时作为蛋白质配体和聚合反应模板, 与靶蛋白特异结合后, 其构象发生了变化, 启动聚合反应, 从而在未直接标记核酸适体的情况下, 通过监测聚合反应进程来检测蛋白质的浓度. 采用该方法检测凝血酶的线性范围为0.5~8 nmol/L, 检测下限为0.5 nmol/L, 为蛋白质检测提供了一种简便快速的非直接标记的荧光分析方法, 有望在蛋白质组学的研究中得到广泛的应用.     

信号核酸识体用于药物托普霉素的高灵敏度检测

提出了一种利用RNA核酸识体和光开关化合物[Ru(phen)2dppz\]2+ (RU)高灵敏检测药物分子的荧光分析新方法. 以托普霉素(TOB)为靶分子, 检测限可达到10 nmol/L, 同时该方法有较好的选择性, 能在溶液中实现无需分离的实时检测. 这种无标记检测方法有利于不稳定RNA核酸识体在分析检测中的应用, 简化实验操作, 为其它药物分子的检测提供了新思路.     

基于链置换循环无标记检测端粒酶RNA的荧光法

以氧化石墨烯(GO)作为DNA载体和荧光猝灭剂, SYBR Green Ⅰ(SGⅠ)为荧光信号探针, 发夹核酸探针为分子识别探针, 基于目标物启动的发夹核酸探针链置换循环反应, 建立了一种利用荧光共振能量转移和链置换循环放大技术检测端粒酶RNA(hTR)的荧光新方法. 发夹核酸探针hpDNA1和hpDNA2吸附在GO表面, 嵌插在发夹DNA探针茎部的SGⅠ的荧光信号被GO猝灭. 当人工合成的目标物(T1)存在时, T1与hpDNA1杂交打开hpDNA1的茎-环结构而引发hpDNA2与T1之间的链置换循环反应, 由此累积产生大量的hpDNA1/hpDNA2杂交双链. 刚性的双链DNA脱离GO表面, 导致所嵌插的SGⅠ产生较强的荧光信号. 基于荧光信号的变化, 可定量检测0.2~50 nmol/L的T1, 检出限为90 pmol/L. 该方法为端粒酶RNA检测提供了一种高灵敏、 高特异性且无需标记的荧光新途径.     

基于核酸适配体信号置换结合循环扩增的液相色谱法检测4种生物胺

生物胺的含量是衡量食品卫生状况和药物纯度的重要标志之一,建立食品药品中生物胺的精准、灵敏检测具有重要的实际意义。该文基于核酸适配体置换生物胺信号源并结合荧光信号循环扩增的策略,建立了一种新型的同时检测鱼肉、猪肉和抗生素中4种生物胺的高效液相色谱法(HPLC)。首先通过两步信号置换,将无荧光信号的目标物转换为有荧光信号的核酸探针;再结合双链特异性核酸酶辅助信号扩增策略,获取大量不同长度和碱基序列的核酸探针;最后借助HPLC平台实现实际样品中多种生物胺信号的精确识别。文章研究了核酸探针的碱基序列和长度对出峰时间和前后顺序的影响,以提高荧光信号的区分度。通过正交实验探讨了柱温、流速和梯度洗脱过程、反应温度、孵化时间等对信号分离的影响,确定最优条件,提高信号的分离效率。该方法对目标物酪胺、组胺、精胺和色胺的检出限分别为0.25、0.21、0.27和0.19 pmol/L,线性范围为1 pmol/L~1 μmol/L。通过对硫酸大庆霉素、鱼肉和猪肉样品中生物胺含量进行检测,研究了该方法检测实际样品的可行性。该方法可精准识别、捕获和分离复杂基质样品中的生物胺组分,能有效提高对目标分析物的选择性,并降低实际样品中的基质干扰,有望为食品药品分析领域提供一种新的思路。     

基于链置换循环无标记检测端立酶RNA的荧光法

以氧化石墨烯(GO)作为DNA载体和荧光猝灭剂,SYBRGreen Ⅰ(SGⅠ)为荧光信号探针,发夹核酸探针为分子识别探针,基于目标物启动的发夹核酸探针链置换循环反应,建立了一种利用荧光共振能量转移和链置换循环放大技术检测端粒酶RNA (hTR)的荧光新方法.发夹核酸探针hpDNA1和hpDNA2吸附在GO表面,嵌插在发夹DNA探针茎部的SG Ⅰ的荧光信号被GO猝灭.当人工合成的目标物(T1)存在时,T1与hpDNA1杂交打开hpDNA1的茎-环结构而引发hpDNA2与T1之间的链置换循环反应,由此累积产生大量的hpDNA1/hpDNA2杂交双链.刚性的双链DNA脱离GO表面,导致所嵌插的SG Ⅰ产生较强的荧光信号.基于荧光信号的变化,可定量检测0.2～50 nmoL/L的T1,检出限为90 pmol/L.该方法为端粒酶RNA检测提供了一种高灵敏、高特异性且无需标记的荧光新途径.     

基于脱氧核酶的无标记端粒酶检测新方法

设计了一种发卡型核酸探针,结合脱氧核酶(DNAzyme)与支点介导链置换技术建立了一种检测端粒酶的新方法.该发卡型探针通过阻碍G-四链体的形成来抑制DNAzyme的过氧化物酶活性.当体系中的端粒酶引物TS被催化延伸后,可以通过链置换反应破坏该发卡结构,从而释放出自由的DNAzyme以催化过氧化氢氧化ABTS2-,产生可被检测的吸收信号变化.实验结果表明,应用该方法可以检测低至500个Hela细胞等当量的端粒酶,且该方法操作简单、不需要荧光标记和复杂的表面修饰,有望在肿瘤细胞端粒酶活性分析中获得广泛应用.     

一种快速鉴别食用油的气相色谱指纹法

本发明公开了提供一种实时荧光定量PCR检测HC．MVgBn的分型方法,在PCR反应体系中加入荧光探针,利用荧光信号积累实时监测PCR进程,进行定量定性分析确定HCMVgBn型。本发明封闭反应,无需PCR后处理,避免污染;特异性强,灵敏度高采用对数期分析,摒弃终点数据,定量准确;实时荧光定量PCR技术既可对HCMVgB进行分型,又可对其进行定量;仪器在线式实时检测,结果直观,避免人为判断;可实现一管双检或多检;操作安全,缩短时间,     

RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon

A novel RNA-templated single-base mutation detection method based on T4 DNA ligase and reverse molecular beacon (rMB) has been developed and successfully applied to identification of single-base mutation in codon 273 of the p53 gene. The discrimination was carried out using allele-specific primers, which flanked the variable position in the target RNA and was ligated using T4 DNA ligase only when the primers perfectly matched the RNA template. The allele-specific primers also carried complementary stem structures with end-labels (fluorophore TAMRA, quencher DABCYL), which formed a molecular beacon after RNase H digestion. One-base mismatch can be discriminated by analyzing the change of fluorescence intensity before and after RNase H digestion. This method has several advantages for practical applications, such as direct discrimination of single-base mismatch of the RNA extracted from cell; no requirement of PCR amplification; performance of homogeneous detection; and easily design of detection probes.     

A self-assembled deoxyribonucleic acid concatemer for sensitive detection of single nucleotide polymorphism

Polymerase-free and label-free strategies for DNA detection have shown excellent sensitivity and specificity in various biological samples. Herein, we propose a method for single nucleotide polymorphism (SNP) detection by using self-assembled DNA concatemers. Capture probes, bound to magnetic beads, can joint mediator probes by T4 DNA ligase in the presence of target DNA that is complementary to the capture probe and mediator probe. The mediator probes trigger self-assembly of two auxiliary probes on magnetic beads to form DNA concatemers. Separated by a magnetic rack, the double-stranded concatemers on beads can recruit a great amount of SYBR Green I and eventually result in amplified fluorescent signals. In comparison with reported methods for SNP detection, the concatemer-based approach has significant advantages of low background, simplicity, and ultrasensitivity, making it as a convenient platform for clinical applications. As a proof of concept, BRAF^T1799A oncogene mutation, a SNP involved in diverse human cancers, was used as a model target. The developed approach using a fluorescent intercalator can detect as low as 0.1 fM target BRAF^T1799A DNA, which is better than those previously published methods for SNP detection. This method is robust and can be used directly to measure the BRAF^T1799A DNA in complex human serum with excellent recovery (94–103%). It is expected that this assay principle can be directed toward other SNP genes by simply changing the mediator probe and auxiliary probes.     

Nanoliter droplet array for microRNA detection based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR

In this paper, a nanoliter droplet array based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR for quantification of microRNA was developed. By employing T4 RNA ligase 2 instead of T4 DNA ligase, we designed simplified stem-loop probes to perform microRNA-templated DNA ligation and reduced the non-specific ligation of T4 DNA ligase. SYBR green I dye was employed instead of TaqMan probes in present miniaturized real-time PCR systems. Specifically, we optimized the dosage of SYBR Green I dye in nanoliter droplet and verified the performance of this system by detecting synthetic mir-122 with a 6 logs dynamic range (from 1.5 × 10⁵ to 1.5 × 10¹⁰ copies). Linear relationship of the standard curve (R² = 0.9997) and high PCR amplification efficiency (96.83%) were obtained under the optimized conditions. We detected the expression of mir-122 across five mouse tissues and the result was consistent with that TaqMan microRNA assay. We think this miniaturized real-time PCR platform reduced the detection cost considerably, thus showing the great potential to quantitative biology.     

Enzyme-regulated activation of DNAzyme: a novel strategy for a label-free colorimetric DNA ligase assay and ligase-based biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label-free and DNAzyme-based strategy to detect DNA ligase activity. This novel strategy relies on the ligation-trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin-DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40?U?mL(-1) and a detection limit of 0.2?U?mL(-1). Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a "split DNA machine" to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01?U?mL(-1).     

Quantum dot-based isothermal chain elongation for fluorescence detection of specific DNA sequences via template-dependent surface-hybridization

A new quantum dot-based method to detect specific sequences of DNA is proposed. The capture and reporter probes do not hybridize to each other, but in the presence of a template they can anneal to each other via the formation of a stable ternary complex. Because of the specific design of the capture and reporter probes, the 5' end of the template target DNA remains free to hybridize with another reporter. In this way, each capture DNA is an initiator strand that triggers a cascade of hybridization events between the target DNA and the reporter probe. This forms a superstructure, enhances base stacking, and produces a strong fluorescent signal. The introduction of T4 DNA ligase further stabilizes the superstructure and greatly increases the fluorescence intensity, and the detection limit is as low as 10 fM. This fluorescence method is advantageous over conventional techniques because of its excellent ability to discriminate single base-pair mismatches and single nucleotide gap or flap. This simple technique is promising for improving medical diagnosis and treatment.     

Hydrolytic cleavage of DNA by quercetin manganese(II) complexes

Quercetin manganese(II) complexes were investigated focusing on its DNA hydrolytic activity. The complexes successfully promote the cleavage of plasmid DNA, producing single and double DNA strand breaks. The amount of conversion of supercoiled form (SC) of plasmid DNA to the nicked circular form (NC) depends on the concentration of the complex as well as the duration of incubation of the complexes with DNA. The maximum rate of conversion of the supercoiled form to the nicked circular form at pH 7.2 in the presence of 100 μM of the complexes is found to be 1.32 × 10⁻⁴ s⁻¹. The hydrolytic cleavage of DNA by the complexes was supported by the evidence from free radical quenching, thiobarbituric acid-reactive substances (TBARS) assay and T4 ligase ligation.     

来源于Alcaligenes A-6的D-氨基酰化酶基因的合成与融合表达

将来源于Alcaligenes A-6的D-氨基酰化酶基因用大肠杆菌中的丰沛密码子替换, 利用化学和基于聚合酶链反应(PCR)技术的酶促方法进行基因全合成, 利用pET-32a构建重组表达载体pET-dan, 转化进E.coil BL21(DE3)中进行融合表达. 经SDS-PAGE电泳、 Western-blot检测和活性测定发现, D-ANase可在大肠杆菌中高效表达, 目的蛋白可达到菌体总蛋白的69.2%, 密码子优化后基因构建的工程菌发酵活性为96 U/mL, 重组蛋白经超声细胞破碎及Ni²⁺柱亲和层析纯化, 比活可达1692.3 U/mg, 纯度可达95%以上.     

Ligating DNA with DNA

Cloning DNA typically involves the joining of target DNAs with vector constructs by enzymatic ligation. A commonly used enzyme for this reaction is bacteriophage T4 DNA ligase, which requires ATP as the energy source to catalyze the otherwise unfavorable formation of a phosphodiester bond. Using in vitro selection, we have isolated a DNA sequence that catalyzes the ligation of DNA in the absence of protein enzymes. We have used the action of two catalytic DNAs, an ATP-dependent self-adenylating deoxyribozyme (AppDNA) and a self-ligating deoxyribozyme, to create a ligation system that covalently joins oligonucleotides via the formation of a 3',5'-phosphodiester linkage. The two-step process is conducted in separate reaction vessels wherein the products of deoxyribozyme adenylation are purified before their use as substrates for deoxyribozyme ligation. The final ligation step of the deoxyribozyme-catalyzed sequence of reactions mimics the final step of the T4 DNA ligase reaction. The initial rate constant (k(obs)) of the optimized deoxyribozyme ligase was found to be 1 x 10(-)(4) min(-)(1). Under these conditions, the ligase deoxyribozyme promotes DNA ligation at least 10(5)-fold faster than that generated by a simple DNA template. The self-ligating deoxyribozyme has also been reconfigured to generate a trans-acting construct that joins separate DNA oligonucleotides of defined sequence. However, the sequence requirements of the AppDNA and that of the 3' terminus of the deoxyribozyme ligase limit the range of sequences that can be ligated.     

Detection of DNA methylation by hyperbranched rolling circle amplification and DNA microarray

Aberrant DNA methylation of CpG sites has been confirmed to be closely associated with carcinogenesis.Based on the hyperbranched rolling circle amplification(HRCA) and microarray techniques,a new method for qualitative detection of methylation was developed.In the present study,padlock probes hybridize the sample DNA at the methylation site to form a probe-DNA complex which is ligated and digested simultaneously by methylation specific enzymes.Only at the methylated CpG site is the padlock probe ligated successfully to form a circle template for the HRCA reaction.Utilizing the method of 3-dimensional polyacrylamide gel-based microarray,the HRCA product will be immobilized on the slide to form a DNA microarray,which can universally hybridize the Cy3-labeled oligonucleotide probe to detect the methylation status of CpG sites.To control the false positive signals,DNA ligase and temperature of ligation/digestion are optimized.Methylation status of four CpG sites located in P15,Ecadherin,hMLH1 and MGMT genes were analyzed successfully with this method and all the results were compatible with that of methylation-specific PCR.Our research proves that this method is simple and inexpensive,and could be applied as a high-throughput tool to qualitatively determine the methylation status of CpG sites.