人类PIF1蛋白质N-末端多肽的表达纯化和生物学活性研究

解螺旋酶参与几乎体内所有的DNA代谢,具有重要的生理功能。为了从分子水平阐述人类PIF1解螺旋酶的生理功能,我们以HeLa细胞的cDNA文库为模版,PCR扩增得到PIF1基因5’端含有1～534核苷酸的cDNA序列一PIFAC。在PIF△C的5’端引入六组氨酸标签后插入pET15b表达载体,得到重组质粒pET15-PIF△C。以此重组质粒转化Rosetta TM2（DE3）感受态细胞,使PIFAC蛋白质在大肠杆菌中得到表达。在4℃通过快速液相色谱纯化系统,通过一系列色谱层析柱纯化了PIFAC蛋白质。以纯化的PIFAC蛋白质免疫家兔制备了抗血清,并检测了纯化的PIFAC的生物化学活性。结果显示不含解旋酶模序的人类PIF1蛋白质的N-末端,具有使单链DNA复性的特性。PIF1解螺旋酶具有解开DNA双链和使双链DNA复性这一矛盾的特性,暗示了人类PIF1解螺旋酶可能参与损伤DNA的修复,包括断裂的双链DNA的修复。     

人类PIF1蛋白质N-末端多肽的表达纯化和

解螺旋酶参与几乎体内所有的DNA代谢,具有重要的生理功能.为了从分子水平阐述人类PIF1解螺旋酶的生理功能,我们以HeLa细胞的cDNA文库为模版,PCR扩增得到PIF1基因5′端含有1～534核苷酸的cDNA序列-PIFΔC.在PIFΔC的 5′端引入六组氨酸标签后插入pET15b表达载体,得到重组质粒pET15-PIFΔC.以此重组质粒转化RosettaTM 2(DE3)感受态细胞,使PIFΔC蛋白质在大肠杆菌中得到表达.在4℃通过快速液相色谱纯化系统,通过一系列色谱层析柱纯化了PIFΔC蛋白质.以纯化的PIFΔC蛋白质免疫家兔制备了抗血清,并检测了纯化的PIFΔC的生物化学活性.结果显示不含解旋酶模序的人类PIF1蛋白质的N-末端,具有使单链DNA复性的特性.PIF1解螺旋酶具有解开DNA双链和使双链DNA复性这一矛盾的特性,暗示了人类PIF1解螺旋酶可能参与损伤DNA的修复,包括断裂的双链DNA的修复.     

结构特异性核酸内切酶FEN1及其与肿瘤的关系

FEN1是一种结构特异性的多功能核酸酶,具有5'-3'flap核酸内切酶(FEN)、缺口核酸内切酶(GEN)和核酸外切酶(EXO)三大酶切活力.在细胞内,FEN1在多条DNA代谢途径中起着重要作用,包括冈崎片段成熟、长片段碱基切除修复和端粒维持等.鉴于FEN1的复杂功能,细胞内必定存在着一套精确调控机制,以确保FEN1在合适的时间与地点发挥作用.FEN1功能失调将导致基因组的稳定性和完整性下降,最终诱发包括肿瘤在内的多种染色体相关的疾病.本文主要针对FEN1的功能调控、功能失调与肿瘤的关系做一个综述.     

高效热不对称交互式PCR技术克隆地黄基因

利用高效热不对称交互式PCR(hiTAIL-PCR)技术从地黄基因组中扩增出3个DNA片段,经过电泳检测、回收、纯化和测序获得2个片段的碱基序列.其中一个由578个bp组成,包含一个453bp的开放阅读框(ORF),编码151个氨基酸,与一些已知纤维素合酶基因在DNA水平和氨基酸水平的同源性分别高达81%~91%和83%~99%,而且推测蛋白质具有纤维素合酶的结构域;另一个由385个bp组成,没有ORF,不编码蛋白质,但是,预测其包含启动子元件.这些结果表明使用hiTAIL-PCR技术可以克隆地黄基因,克隆的基因将为地黄基因分子作用机制和分子育种研究奠定基础.     

用细小病毒H-1探测人细胞中的直接诱变与间接诱变途径

用细小病毒H-1为探针,可在人细胞中检测由紫外线照射诱导的三种不同致突变途径.直接突变产生于细胞的结构性复制(或修复)功能对受损DNA模板的复制;间接无靶突变和间接有靶突变分别产生于紫外线诱导的易错修复功能对完整模板和模板上的靶损伤的作用.在低剂量范围内,间接无靶突变在某些DNA毒剂诱导的细胞突变中起主要作用.某些DNA损伤,如烷化剂诱导的次级损伤(无碱基位损伤)可作为诱导性易错修复功能的靶损伤.     

Pfu DNA聚合酶在大肠杆菌Rosetta(DE3)中的表达及快速纯化

来源于Pyrococcus furiosus COM1菌的Pfu DNA聚合酶具有保真性高、延伸速度快、热稳定性强等特点,能够提高PCR反应过程中的扩增效率,减少错误碱基掺入率.以大肠杆菌Rosetta(DE3)为重组细胞,利用一种快速表达纯化方法,让Pfu DNA聚合酶的表达纯化过程变得更加简便,并维持其高活性.结果表明,Pfu DNA聚合酶在大肠杆菌Rosetta(DE3)中能够进行大量表达,同时60℃高温水浴能有效去除杂蛋白,简化纯化步骤及提高Pfu DNA聚合酶纯度.经过一系列纯化步骤处理后,Pfu DNA聚合酶仍然能够保持较好的酶活,且在100μL PCR反应体系中,加入4μL的1 mg/mL Pfu DNA聚合酶液效果最佳.     

压力脉动固态发酵微生物蛋白质及机理的初步研究

研究了固态发酵微生物蛋白质的提取、纯化条件以及压力脉动对固态发酵微生物蛋白质的影响，并初步探讨了压力脉动固态发酵的作用机理。结果表明在发酵后的酶曲中，加入Tris-HCl提取液，可得胞内蛋白质，FPA酶活与CMCase酶活回收率分别为83.6%与67%,纯化效果较好。从压力脉动外界周期刺激固态发酵干酶曲中提取的胞内蛋白质与从未加周期刺激的微生物中提取的相比，胞外蛋白质的质量、FPA酶活和CMCase酶活分别提高了17.75%、60.08%和21.17%。压力脉动固态发酵5d的微生物胞外蛋白质的酶活,与静态固态发酵6d的相当，发酵周期缩短。压力脉动外界周期刺激使蛋白质组分有所变化，减少了相对分子质量约为80400的组分，但增加了相对分子质量约为28520的组分。     

Klebsiella aerogenes染色体DNA的分离和纯化

<正> 基因工程是在分子水平上进行人工拼接,获得具有生物活性的杂种DNA分子,然后通过转化或转染,使其在有机体或细胞中得到表达。在基因工程操作技术中,由于经常需要将染色体上的某一目的基因重组到载体DNA上,因此制备纯净的染色体DNA是十分必要的。迄今为止,从动、植物或微生物材料中分离、纯化染色体DNA的方法已有不少报导。Marmur的方法至今仍被广泛地应用于微生物染色体DNA的制备。这个方法的基本要点是:(1)用溶菌酶和十二烷基硫酸钠破坏细菌的细胞壁,使细胞内容物释出。(2)在高氯酸盐存在时用氯仿-异戊醇进行抽提,除去蛋白质。(3)用核糖核酸酶除去与染色体DNA混杂在一起的RNA。(4)用乙醇或异丙醇改变溶的极性,使染色体DNA呈纤维状析出,得以与细胞中其它成分分开。我们以细菌K.aerogenes为材料,按照Koh改进的Marmur法,获得了电泳纯的染色体DNA,     

GST-Jab1融合蛋白表达载体的构建及表达纯化

目的获取GST-Jab1蛋白,进一步研究Jab1的功能。方法以pMSCVneo-Jab1为模板,PCR扩增Jab1 DNA片断,EcoRI和XhoI双酶切后克隆至pGEX-5X-1表达载体,测序验证。将正确重组的pGEX-5X-1-Jab1表达质粒转化E.coli BL21,IPTG诱导后,超声破碎细胞,用GST琼脂糖珠对上述表达产物进行纯化,SDS-PAGE、Western Blot分析和鉴定诱导表达和纯化的GST-Jab1蛋白质。结果成功构建了pGEX-5X-1-Jab1重组表达载体,SDS-PAGE分析结果显示表达和纯化的蛋白质与融合蛋白GST-Jab1预期分子量一致,Western Blot鉴定结果证实纯化的蛋白质为GST-Jab1。结论成功地表达、纯化了GST-Jab1融合蛋白。     

限制性内切核酸酶 HindⅢ及 HindⅡ的提纯及 HindⅢ某些性质的探讨

从流感嗜血杆菌(Haemophilus influenzae)Rd 株中纯化了限制性内切核酸酶HindⅢ及部份纯化了Hind Ⅱ;探讨了纯化过程中的某些问题;检查了酶对底物双链DNA 的特异性内切作用,从琼脂糖平板凝胶电泳中观察到的经消化后产生的DNA 断片表明:酶对各种底物具有专一性作用;通过DNA 断片的重新连接证明:经Hind Ⅲ消化后生成的断片具有粘性末端,也说明纯化的Hind Ⅲ中不合明显的外切酶活力;用聚丙烯酰胺-十二烷基硫酸钠平板凝胶电泳,葡聚糖凝胶G150分子筛层析及蔗糖密度梯度离心法测定了Hind Ⅲ的分子量并对其亚单位进行了讨论.     

An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3' mispaired DNA

Human apurinic/apyrimidinic endonuclease (APE1) is an essential enzyme in DNA base excision repair that cuts the DNA backbone immediately adjacent to the 5' side of abasic sites to facilitate repair synthesis by DNA polymerase beta (ref. 1). Mice lacking the murine homologue of APE1 die at an early embryonic stage. Here we report that APE1 has a DNA exonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules. The efficiency of this activity is inversely proportional to the gap size in DNA. In a base excision repair system reconstituted in vitro, the rejoining of nicked mismatched DNA depended on the presence of APE1, indicating that APE1 may increase the fidelity of base excision repair and may represent a new 3' mispaired DNA repair mechanism. The exonuclease activity of APE1 can remove the anti-HIV nucleoside analogues 3'-azido-3'-deoxythymidine and 2',3'-didehydro-2', 3'-dideoxythymidine from DNA, suggesting that APE1 might have an impact on the therapeutic index of antiviral compounds in this category.     

DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected

Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone at a position 5' of AP sites to prime DNA repair synthesis. Here we report three co-crystal structures of human APE1 bound to abasic DNA which show that APE1 uses a rigid, pre-formed, positively charged surface to kink the DNA helix and engulf the AP-DNA strand. APE1 inserts loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized beta-anomer AP sites. Both the APE1 active-site geometry and a complex with cleaved AP-DNA and Mn2+ support a testable structure-based catalytic mechanism. Alanine substitutions of the residues that penetrate the DNA helix unexpectedly show that human APE1 is structurally optimized to retain the cleaved DNA product. These structural and mutational results show how APE1 probably displaces bound glycosylases and retains the nicked DNA product, suggesting that APE1 acts in vivo to coordinate the orderly transfer of unstable DNA damage intermediates between the excision and synthesis steps of DNA repair.     

A eukaryotic DNA glycosylase/lyase recognizing ultraviolet light-induced pyrimidine dimers.

Cyclobutane pyrimidine dimers (CPDs) are the predominant product of photodamage in DNA after exposure of cells to ultraviolet light and are cytotoxic, mutagenic and carcinogenic in a variety of cellular and animal systems. In prokaryotes, enzymes and protein complexes have been characterized that remove or reverse CPDs in DNA. Micrococcus luteus and T4 phage-infected Escherichia coli contain a specific N-glycosylase/apurinic-apyrimidinic lyase that catalyses a two-step DNA incision process at sites of CPDs, thus initiating base excision repair of these lesions. It is well established that CPDs are recognized and removed from eukaryotic DNA by excision repair processes but very little information exists concerning the nature of the proteins involved in CPD recognition and DNA incision events. We report here that an enzyme functionally similar to the prokaryotic N-glycosylase/apurinic-apyrimidinic lyases exists in Saccharomyces cerevisiae. To our knowledge, this is the first time such an activity has been found in a eukaryote and is also the first example of an organism having both direct reversal and base excision repair pathways for the removal of CPDs from DNA.     

Crystal structure of thymine DNA glycosylase conjugated to SUMO-1

Members of the small ubiquitin-like modifier (SUMO) family can be covalently attached to the lysine residue of a target protein through an enzymatic pathway similar to that used in ubiquitin conjugation, and are involved in various cellular events that do not rely on degradative signalling via the proteasome or lysosome. However, little is known about the molecular mechanisms of SUMO-modification-induced protein functional transfer. During DNA mismatch repair, SUMO conjugation of the uracil/thymine DNA glycosylase TDG promotes the release of TDG from the abasic (AP) site created after base excision, and coordinates its transfer to AP endonuclease 1, which catalyses the next step in the repair pathway. Here we report the crystal structure of the central region of human TDG conjugated to SUMO-1 at 2.1 A resolution. The structure reveals a helix protruding from the protein surface, which presumably interferes with the product DNA and thus promotes the dissociation of TDG from the DNA molecule. This helix is formed by covalent and non-covalent contacts between TDG and SUMO-1. The non-covalent contacts are also essential for release from the product DNA, as verified by mutagenesis.     

Two levels of protection for the B cell genome during somatic hypermutation

Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by cytosine deamination by the activation-induced deaminase (AID) and completed by error-prone processing of the resulting uracils by mismatch and base excision repair factors. Somatic hypermutation represents a threat to genome integrity and it is not known how the B cell genome is protected from the mutagenic effects of somatic hypermutation nor how often these protective mechanisms fail. Here we show, by extensive sequencing of murine B cell genes, that the genome is protected by two distinct mechanisms: selective targeting of AID and gene-specific, high-fidelity repair of AID-generated uracils. Numerous genes linked to B cell tumorigenesis, including Myc, Pim1, Pax5, Ocab (also called Pou2af1), H2afx, Rhoh and Ebf1, are deaminated by AID but escape acquisition of most mutations through the combined action of mismatch and base excision repair. However, approximately 25% of expressed genes analysed were not fully protected by either mechanism and accumulated mutations in germinal centre B cells. Our results demonstrate that AID acts broadly on the genome, with the ultimate distribution of mutations determined by a balance between high-fidelity and error-prone DNA repair.     

Renaturation of DNA catalysed by yeast DNA repair and recombination protein RAD10.

The RAD10 gene of Saccharomyces cerevisiae is required for the incision step of excision repair of ultraviolet-damaged DNA, and it functions in mitotic recombination. RAD10 has homology to the human excision repair gene ERCC-1. Here we describe the purification of the protein encoded by RAD10 and show that it is a DNA-binding protein with a strong preference for single-stranded DNA. We also show that RAD10 promotes the renaturation of complementary DNA strands.     

Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA

Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.     

Requirement for the replication protein SSB in human DNA excision repair

Replication and repair are essential processes that maintain the continuity of the genetic material. Dissection of simian virus 40 (SV40) DNA replication has resulted in the identification of many eukaryotic replication proteins, but the biochemistry of the multienzyme process of DNA excision repair is less well defined. One protein that is absolutely required for semiconservative replication of SV40 DNA in vitro is human single-stranded DNA-binding protein (SSB, also called RF-A and RP-A). SSB consists of three polypeptides of relative molecular mass 70,000, 34,000 and 13,000, and acts with T antigen and topoisomerases to unwind DNA, allowing the access of other replication proteins. Human SSB can also stimulate the activity of polymerases alpha and delta, suggesting a further role in elongation during DNA replication. We have now found a role for human SSB in DNA excision repair using a cell-free system that can carry out nucleotide excision repair in vitro. Monoclonal antibodies against human SSB caused extensive inhibition of DNA repair in plasmid molecules damaged by ultraviolet light or acetylaminofluorene. Addition of purified SSB reversed this inhibition and further stimulated repair synthesis by increasing the number of repair events. These results show that a mammalian DNA replication protein is also essential for repair.