基于错配修复系统的基因突变检测生物芯片研究

许多人类疾病和微生物抗药性的产生都是由基因组中单个碱基的替换、插入或缺失等基因突变引起的。因此，迫切需要发展快速、高通量基因突变检测方法来实现对基因疾病和细菌抗药性的早期诊断。本研究针对匕述需求发展了纂于DN八错配修复系统的墓因突变检测生物芯片方法。根据DNA错配修复MtltS蛋白结构与功能上的高度保守性，通过PCR从E.coli K-12基因组中扩一增出DNA错配修复基因，甩石（2.56kb）。通过基因水平的分子操纵，构建了Trx-His6-MutS（THM）、Trx-His6-Linker peptide-Muts（THLM）、Trx-His6-GFP-Linker peptide-MutS（THGLM）和Trx-His6-Linker peptide-Strep-tagll-Linker peptide-MutS（THLSLM）的融合基因并在大肠杆菌中进行了IPTG诱导表达。SDS-PAGE分析表明均有一与预期分子量相应的诱导表达条带出现，其表达量占菌体蛋白的30％左右，且以可溶形式存在。融合蛋白中Trx和His6亲和肤能增加表达蛋白的可溶性及便于蛋白的纯化。连接肤的加入增大了融合蛋白各个成分之间的距离，减少空间位阻，使各个蛋白能够较大程度地保持其原有的生物活性。MLltS融合蛋白的生物活性鉴定结果表明：它们既能识别、结合含有错配碱基的DNA双链，又保留了其它融合成分的生物活性。利用融合蛋白THLSLM中的Strep-tagII与Streptavidin相互作用的天然特性，使融合蛋白THLSLM在StrePtavidin修饰过的芯片基质上自动布阵沉积，制作成蛋白质芯片来识别、结合样品中含有错配或未配刘碱基的DNA双链。THGLM、THLM-Cy3和THLSLM能够使MutS蛋白显示不同的标记信号，通过它们识别并结合固定在DNA芯片基质上的基因片段来发展基因突变检测DNA芯片方法。利用基于MutS的蛋白质芯片和DNA芯片方法对含有不同错配类型、不同长度的DNA片段和错配序列背景对错配结合的影响做了深入研究，证明了MutS介导的基因突变检测生物芯片方法的可行性。基于MutS蛋白的鳌因突变检测生物芯片方法借用了生物系统本身的DNA错配修复（Mismatch Repair，MMR）机制。DNA错配修复过程是许多修复蛋白之间的相互作用共同完成的，其中蛋白MutS、MutL和MutH在肠道细菌例如大肠杆菌的甲基定向错配修复中起决定作用。这些修复蛋白的相关研究也引起了越来越多学者的关注，但对于MutL蛋白的体外生物功能一直存在争议，从而限制了该蛋白的应用研究。本研究利用基因的体外拼接技术构建了融合蛋白Trx-Hi56-Linker peptide-MutL（THLL）、Trx-His6-GFP-Linker peptide-MutL（THGLL）和Trx-His6-Linker peptide-Strep-tagII-Linker peptide-MutL（THLSLL）。非变性凝胶电泳鉴定MutL融合蛋白体外生物功能结果表明：THLL、THGLL和THLsLL都能增加融合蛋白Trx-His6-Linker peptide-MutS（THLM）与含有错配碱基DNA双链的结合，但受ATP浓度变化的影响很大。通过融合蛋白THGLL中绿色荧光蛋白（Green Fluorescent Protein，GFP）的荧光信号或THLSLL中Strep-tagII的特性并利用酶学反应来指示该蛋白的存在，发展了体外研究DNA错配修复蛋白MtuS和MutL之间相互作用的简便方法。本研究以构建的MutS融合蛋白为分子识别元件发展了基因突变检测生物芯片并利用构建的MutL融合蛋白发展了体外研究DNA错配修复蛋白MLuS和MutL之间相互作用的简便方法。建立的融合分子系统方法也为研究其它的蛋白质或生物大分子之间的相互作用提供了一个技术平台。此外，本研究构建的融合蛋白THGLL及其 DNA错配修复蛋白与GFP的融合构想还可用来进行DNA错配修复基因产物的表达与基因突变频率和人类肿瘤恶性程度的相关性研究。

Effect of DNA flanking sequence on charge transport in short DNA duplexes

Several factors can influence charge transport (CT)-mediated DNA, such as sequence, distance, base stacking, base pair mismatch, conformation, tether length, etc. However, the DNA context effect or how flanking sequences influence redox active drugs in the DNA CT reaction and later in DNA enzymatic repair and synthesis is still not well understood. The set of seven DNA molecules in this study have been characterized well for the study of flanking sequence effects. These DNA duplexes are formed from self-complementary strands and contain the common central four-base sequence 5'-A-G-C-T-3', flanked on both sides by either (AT)(n) or (AA)(n) (n = 2, 3, or 4) or AA(AT)(2). UV-vis, fluorescence, UV melting, circular dichroism, and cyclic voltammetry experiments were used to study the flanking sequence effect on CT-mediated DNA by using daunomycin or adriamycin cross-linked with these seven DNA molecules. Our results showed that charge transport was related to the flanking sequence, DNA melting free energy, and ionic strength. For (AA)(n) or (AT)(n) species of the same length, (AA)(n) series were more stable and more efficient CT was observed through the (AA)(n) series. The same trend was observed for (AA)(n) and (AT)(n) series at different ionic strengths, further supporting the idea that flanking sequence can result in different base stacking and modulate charge transport through these seven DNA molecules.

Potential role of DNA-dependent protein kinase in cellular resistance to ionizing radiation

In this paper, we study the ability of DNA-PK-deficient (M059J) and -proficient (M059K) cells to undergo the rate of cellular proliferation, cell cycle distribution and apoptosis after 10 Gy X-ray irradiation, and the role of DNA-PK in radiosensitivity. The results showed that M059J cells exhibited hyper-radiosensitivity compared with M059K cells. A strong G2 phase arrest was observed in M059J cells post irradiation. Significant accumulation in the G2 phase in M059J cells was accompanied by apoptosis at 12 h. Altogether, the data suggested that DNA-PK may have two roles in mammalian cells after DNA damage, a role in DNA DSB repair and a second role in DNA-damaged cells to traverse a G2 checkpoint, by which DNA-PK may affect cellular sensitivity to ionizing radiation. 地址: [Li Ning; Zhang Hong; Wang Yanling; Hao Jifang] Chinese Acad Sci, Inst Modern Phys, Lanzhou 730000, Peoples R China; [Li Ning; Zhang Hong; Wang Yanling; Hao Jifang] Key Lab Heavy Ion Radiat Med Gansu Prov, Lanzhou 730000, Peoples R China; [Li Ning; Wang Yanling] Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China; [Wang Xiaohu] Gansu Tumor Hosp, Dept Radiotherapy, Lanzhou 730050, Peoples R China

Cd、Cu污染胁迫对拟南芥幼苗错配修复相关基因表达的影响

土壤重金属污染问题已成为影响我国持续农业和生态环境质量的重要因素，引起了人们的广泛关注。由于传统污染诊断方法的缺点，急需建立土壤污染生态毒理学诊断方法，生物标记物技术则是其中的研究热点之一。本文采用营养液培养的方法，以模式植物拟南芥为试材，采用半定量反转录聚合酶链式反应（RT-PCR）技术，结合传统分析方法研究了Cd、Cu在不同胁迫水平下对拟南芥幼苗的形态、生理及分子水平的毒性效应，并在此基础上，比较和分析不同测试指标对Cd、Cu胁迫响应的敏感性，进而筛选对Cd、Cu胁迫响应敏感的生物标记物。主要结果如下： 1 不同浓度Cd和Cu污染胁迫下，拟南芥幼苗生长均受到不同程度的影响 幼苗初生根伸长均受到明显抑制，而地上部叶片数、地上部鲜重却没有显著的变化。重金属首先作用于植物的根系，根系的生长对胁迫响应的敏感性高于地上部。 2 幼苗地上部的可溶性蛋白含量受到不同程度干扰，而在不同浓度的Cd、 Cu处理下，叶绿素含量变化不明显，表明幼苗地上部可溶性蛋白质含量对胁迫的敏感性高于叶绿素含量的变化。 3 幼苗地上部错配修复（MMR）和增殖细胞核抗原（PCNA）基因都明显 地出现了表达诱导或表达抑制，表明MMR和PCNA基因表达的变化对Cd、Cu胁迫表现出较高的敏感性。 4 幼苗地上部的可溶性蛋白质含量及幼苗地上部MMR和PCNA基因表达 均对Cd和Cu污染胁迫具有较高的敏感性，两者均可用于指示Cd和Cu污染的敏感生物标记物。基因表达变化图谱虽然对污染胁迫响应比较敏感，是一种污染胁迫响应敏感的生物标记物，但其在生态毒理诊断中的应用还需进一步的实验对其予以证明。

镉胁迫对拟南芥幼苗错配修复相关基因表达及突变的影响

土壤重金属污染是影响农业可持续发展和生态环境的重要问题，而通过生物标记物方式对污染土壤进行早期诊断已成为环境科学领域的研究热点。本文以M&S营养液为培养介质，以拟南芥为供试材料，以错配修复基因MutS 2 homolog (atMSH2)，atMSH3，atMSH7，细胞增殖核抗原1 和2 (atPCNA1和atPCNA2)为检测目的基因，分别采用半定量反转录-聚合酶链式反应（RT-PCR）技术、克隆及测序技术研究了Cd在不同胁迫水平（0，0.125，0.25，1.0，3.0 mg•L-1 ）上对上述错配修复相关基因表达和atMSH2基因突变的影响，并与拟南芥幼苗形态、生理指标的毒性效应进行比较分析，筛选出对Cd污染胁迫敏感的生物标记物。主要结果如下： 1. 不同浓度（0，0.125，0.25，1.0，3.0 mg•L-1 ）Cd处理7天后，拟南芥幼苗叶片数、地上部鲜重变化与对照相比差异均不显著；而根长随Cd胁迫强度的增加明显降低； 2. 不同浓度（0，0.125，0.25，1.0，3.0 mg•L-1 ）Cd处理7天后，叶绿素含量变化与对照相比差异均不显著； 地上部可溶性蛋白含量随Cd浓度的增加变化明显，0.125 mg•L-1 Cd处理下，地上部可溶性蛋白含量显著增加，而在0.25，1.0和3.0 mg•L-1 Cd时降低，但仍高于对照； 3. 地上部atMSH2，atPCNA1，atPCNA2基因表达量的变化与Cd胁迫浓度呈明显的倒U字型关系，分别在0.125mg•L-1，0.25mg•L-1和0.125mg•L-1 Cd时达到最大值。地上部可溶性蛋白含量变化趋势与atMSH2，atPCNA1，atPCNA2基因表达量的变化相似，均可作为对Cd污染胁迫敏感的潜在生物标记物。 4. 对不同浓度（0，0.125，0.25，1.0，3.0 mg•L-1 ）Cd处理7天后，拟南芥atMSH2基因PCR后的扩增产物进行回收、纯化、克隆和测序。测序结果表明，0.25 mg•L-1 Cd处理拟南芥atMSH2基因在第8个和第9个外显子之间的内含子有一个碱基转换；在1.0 mg•L-1 Cd处理下，拟南芥在第10个外显子有一个碱基转换。

HMLH1 gene mutation in gastric cancer patients and their kindred

AIM: To study the status of hMLH1 gene point mutations of gastric cancer kindreds and gastric cancer patients from northern China, and to find out gene mutation status in the population susceptible to gastric cancer.

DIFFERENT RATES OF MITOCHONDRIAL-DNA SEQUENCE EVOLUTION IN KIRK DIK-DIK (MADOQUA-KIRKII) POPULATIONS

We have investigated evolutionary rates of the mitochondrial genome among individuals of Madoqua kirkii using the relative rate test. Our results demonstrate that individuals of two chromosome races, East African cytotype A and Southwest African cytotype D, evolve about 2.3 times faster than East African cytotype B. Cytogenetic changes, DNA repair efficiency, mutagens, and more likely, hitherto unrecognized factors will account for the rate difference we have observed. Our results suggest additional caution when using molecular clocks in the estimation of divergence time, even within lineages of closely related taxa. Rate heterogeneity in microevolutionary timescales represents a potentially important aspect of basic evolutionary processes and may provide additional insights into factors which affect genome evolution. (C) 1995 Academic Press, Inc.

Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism

An oligonucleotide ligation assay-based DNA chip has been developed to detect single nucleotide polymorphism. Synthesized nonamers, complementary to the flanking sequences of the mutation sites in target DNA, were immobilized onto glass slides through disulfide bonds on their 5' terminus. Allele-specific pentamers annealed adjacent to the nonamers on the complementary target DNA, containing 5'-phosphate groups and biotin labeled 3'-ends, were mixed with the target DNA in tube. Ligation reactions between nonamers and pentamers were carried out on chips in the presence of T4 DNA ligase. Ligation products were directly visualized on chips through enzyme-linked assay. The effect of G:T mismatch at different positions of pentamers on the ligation were evaluated. The results showed that any mismatch between pentamer and the target DNA could lead to the decrease of ligation, which can be detected easily. The established approach was further used for multiplex detection of mutations in rpoB gene of rifampin-resistant Mycobacterium tuberculosis clinical isolates. (C) 2003 Elsevier B.V. All rights reserved.

MutS蛋白识别DNA错配机制的研究

DNA生物合成过程中DNA聚合酶会错误的掺入一些碱基而导致错配，这些错配的碱基如果不能被及时地更正将会引起机体广泛的突变。DNA错配修复系统正是基于这样一种需要而产生的，它能够切除含有错配的DNA片段并重新合成出一段正确的DNA，因此对于维持基因组的稳定性具有重要的意义。 大肠杆菌DNA错配修复系统包含11种蛋白活性，并可分为起始、切割和修复三个阶段。起始阶段的第一个步骤是错配识别，这一功能是由一种叫作MutS的蛋白来完成的，它能够特异性的识别并且结合到错配上，然后引发下游一系列的修复反应。为了更深入的理解MutS蛋白识别镶嵌在随机DNA序列中的错配的机制，我们纯化了MutS及其突变体蛋白，构建了一个2279 bp的在1/4位置带有G/T错配的DNA片段和一个具有同样长度与序列的完全配对的DNA片段，然后在原子力显微镜下观察MutS及突变体蛋白与这两种DNA底物的作用方式。结果表明MutS蛋白不但能与错配的DNA结合也能与完全配对的DNA结合，而且MutS蛋白能够诱导这两种DNA底物形成一种形似a字母的环状结构，在这种结构中MutS蛋白位于两条DNA臂的交叉处。我们发现这些环状结构是在MutS蛋白寻找错配的过程中形成的，因为随着时间推移越来越多的错配位点会被MutS蛋白占据。这些结果表明MutS蛋白非特异性的结合到DNA上，然后诱导DNA形成a环状结构，并且凭借a环结构的形成对DNA的两条臂同时进行扫描以便寻找出错配的碱基对。根据以上结果我们推测a环模式是MutS蛋白寻找错配的一种机制。这些研究也为用单分子的手段研究蛋白与DNA的相互作用提供了一种可行的方法。

Loss of p15/Ink4b accompanies tumorigenesis triggered by complex DNA double-strand breaks

DNA double-strand breaks (DSBs) are the most deleterious lesion inflicted by ionizing radiation. Although DSBs are potentially carcinogenic, it is not clear whether complex DSBs that are refractory to repair are more potently tumorigenic compared with simple breaks that can be rapidly repaired, correctly or incorrectly, by mammalian cells. We previously demonstrated that complex DSBs induced by high-linear energy transfer (LET) Fe ions are repaired slowly and incompletely, whereas those induced by low-LET gamma rays are repaired efficiently by mammalian cells. To determine whether Fe-induced DSBs are more potently tumorigenic than gamma ray-induced breaks, we irradiated 'sensitized' murine astrocytes that were deficient in Ink4a and Arf tumor suppressors and injected the surviving cells subcutaneously into nude mice. Using this model system, we find that Fe ions are potently tumorigenic, generating tumors with significantly higher frequency and shorter latency compared with tumors generated by gamma rays. Tumor formation by Fe-irradiated cells is accompanied by rampant genomic instability and multiple genomic changes, the most interesting of which is loss of the p15/Ink4b tumor suppressor due to deletion of a chromosomal region harboring the CDKN2A and CDKN2B loci. The additional loss of p15/Ink4b in tumors derived from cells that are already deficient in p16/Ink4a bolsters the hypothesis that p15 plays an important role in tumor suppression, especially in the absence of p16. Indeed, we find that reexpression of p15 in tumor-derived cells significantly attenuates the tumorigenic potential of these cells, indicating that p15 loss may be a critical event in tumorigenesis triggered by complex DSBs.

重离子照射后肿瘤细胞辐射敏感性和DNA双链断裂及修复的研究

本论文的实验内容立足于我所重离子治癌研究的基础之上，本着进行基础研究的目的，研究了肿瘤细胞对于重离子的辐射敏感性和重离子引起肿瘤细胞DNA双链断裂(DSB)及修复的情况，这可为我所开展重离子治癌提供有效的基础数据和理论参考，对于治疗计划的制定也具有重要的意义。实验从四个方面开展，首先考察了不同肿瘤细胞对低LETγ射线的辐射敏感性差异及其与修复可能存在的联系，其次考察了重离子在放射治疗中的优势及重离子用于肿瘤放射治疗的优越性，第三为了进一步寻求重离子对肿瘤细胞强杀伤能力的原因所在，对重离子引起的肿瘤细胞DSB及修复水平进行了研究，最后通过分次照射实验，考察细胞存活与细胞DSB修复水平之间可能存在的相关性。实验取得了一系列有意义的结果和结论： 1． 低LET电离辐射作用后，不同组织来源的肿瘤细胞的辐射敏感性有较大差 异，其各自的修复功能也有相应的差异，且肿瘤细胞的辐射敏感性与其修复能力呈负相关。 2．重离子具有的独特物理特性及其高LET下对肿瘤细胞的强杀伤作用，使得重离子成为肿瘤治疗的热点。与此同时，重离子还显示出其它值得关注的优势，它可以同样有效的杀伤不同肿瘤细胞，减弱了细胞间的敏感性差异，这对于治疗计划的制定和治疗对常规辐射抗性较高的肿瘤来说，具有重大的意义。对于临床的分次照射，重离子治疗时，细胞的亚致死修复明显降低，可以采取较少的照射次数就达到杀伤肿瘤的目的，这样大大提高了肿瘤治疗效率，同时减轻了病人的痛苦。 3．在两种高LET重离子引起细胞DSB及其修复实验中，初始DSB量均与剂量呈线性关系。 DSB的片段分布检测结果显示两种重离子辐照后DSB的分布呈明显的非随机分布，剂量增大时，大片段的DSB和小片段的DSB变化趋势不同：剂量超过一定数值后，小片段的DSB随剂量增大而呈现出高的增加速度，而大片段的DSB则呈现微弱增加甚至减少。同时LET变化对于这一现象存在影响。除了离子种类和LET之外，剂量也影响了DSB分布形式。修复实验结果显示4h后，残余的DSB相差不大。由于氩离子引起的初始DSB高于碳离子，在相同时间内，高LET的氩离子完成了对DSB更多的修复，这似乎提示，LET升高引起了更强的修复，但是这里值得考虑的有两点，一是慢修复的DSB所占的比例，二是错修复的问题，即使高LET的氩离子照射后DSB得到了更多的修复，但是其修复的忠实性并未得到证明，更多的工作还需要进行。 4．分次照射实验发现高LET的碳离子辐照后的剂量存活曲线不再存在明显肩区，分次照射细胞的存活也没有明显上升，这与光子辐照情况不同，应证了随着LET升高，分次效应降低的结论。同时检测DSB的引入情况，发现分次照射和单次照射时，DSB的引入并未发生明显变化，这显示在分次照射的间隙中，重离子引入的DSB并未得到明显的修复。提示细胞对高LET照射更为敏感与其对高LET辐照引起的DSB修复能力降低之间的相关性

Label free electrochemiluminescence protocol for sensitive DNA detection with a tris(2,2'-bipyridyl)ruthenium(II) modified electrode based on nucleic acid oxidation

Label free electrochemiluminescence (ECL) DNA detection based on catalytic guanine and adenine bases oxidation using tris(2,2'-bipyridyl)ruthenium(II) [Ru(bpy)(3)(2+)] modified glassy carbon (GC) electrode was demonstrated in this work. The modified GC electrode was prepared by casting carbon nanotubes (CNT)/Nafion/Ru(bpy)(3)(2+) composite film on the electrode surface. ECL signals of doublestranded DNA and their thermally denatured counterparts can be distinctly discriminated using cyclic voltammetry (CV) with a low concentration (3.04 x 10(-8) mol/L for Salmon Testes-DNA). Most importantly, sensitive single-base mismatch detection of p53 gene sequence segment was realized with 3.93 x 10(-10) mol/L employing CV stimulation (ECL signal of C/A mismatched DNA oligonucleotides was 1.5-fold higher than that of fully base-paired DNA oligonucleotides). Label free, high sensitivity and simplicity for single-base mismatch discrimination were the main advantages of the present ECL technique for DNA detection over the traditional DNA sensors.