Bypass of N²-ethylguanine by human DNA polymerase κ

The efficiency and fidelity of nucleotide incorporation and next-base extension by DNA polymerase (pol) κ past N(2)-ethyl-Gua were measured using steady-state and rapid kinetic analyses. DNA pol κ incorporated nucleotides and extended 3' termini opposite N(2)-ethyl-Gua with measured efficiencies and fidelities similar to that opposite Gua indicating a role for DNA pol κ at the insertion and extension steps of N(2)-ethyl-Gua bypass. The DNA pol κ was maximally activated to similar levels by a twenty-fold lower concentration of Mn(2+) compared to Mg(2+). In addition, the steady state analysis indicated that high fidelity DNA pol κ-catalyzed N(2)-ethyl-Gua bypass is Mg(2+)-dependent. Strikingly, Mn(2+) activation of DNA pol κ resulted in a dramatically lower efficiency of correct nucleotide incorporation opposite both N(2)-ethyl-Gua and Gua compared to that detected upon Mg(2+) activation. This effect is largely governed by diminished correct nucleotide binding as indicated by the high K(m) values for dCTP insertion opposite N(2)-ethyl-Gua and Gua with Mn(2+) activation. A rapid kinetic analysis showed diminished burst amplitudes in the presence of Mn(2+) compared to Mg(2+) indicating that DNA pol κ preferentially utilizes Mg(2+) activation. These kinetic data support a DNA pol κ wobble base pairing mechanism for dCTP incorporation opposite N(2)-ethyl-Gua. Furthermore, the dramatically different polymerization efficiencies of the Y-family DNA pols κ and ι in the presence of Mn(2+) suggest a metal ion-dependent regulation in coordinating the activities of these DNA pols during translesion synthesis.     

低能N+辐照拟南芥诱导基因组DNA碱基变异分析

用低能N~+离子束注入拟南芥后获得的稳定突变体T80Ⅱ作为实验材料,对突变体植株进行了RAPD标记,并将T80Ⅱ和对照部分RAPD特异条带进行克隆测序和DNA序列分析。结果显示,在可分辨的总计397个RAPD条带中,T80Ⅱ株系中有52个条带表现出差异,包括条带的缺失和增加,条带变异率为13.1％;克隆的T80Ⅱ序列中,平均每16.8个碱基出现1个碱基变异位点,表现出较高频率的碱基突变。碱基突变类型包括碱基的颠换、转换、缺失、插入等。在检测到的275个碱基突变中,主要是单碱基置换(97.09％),碱基缺失或者插入的比例较小(2.91％)。在碱基置换中,转换的频率(66.55％)高于颠换的频率(30.55％)。此外,构成DNA的4种碱基均可以被离子束辐照诱发变异,而且每一种碱基都可以被其他3种碱基所替换,但是胸腺嘧啶(T)的辐射敏感性要高于其他3种碱基。通过分析突变碱基周边序列,对低能N~+离子注入拟南芥突变体引发的碱基突变热点进行了讨论。     

低能N+辐照拟南芥诱导基因组DNA碱基变异分析

用低能N+离子束注入拟南芥后获得的稳定突变体T80Ⅱ作为实验材料, 对突变体植株进行了RAPD标记, 并将T80Ⅱ和对照部分RAPD特异条带进行克隆测序和DNA序列分析. 结果显示, 在可分辨的总计397个RAPD条带中, T80Ⅱ株系中有52个条带表现出差异, 包括条带的缺失和增加, 条带变异率为13.1%; 克隆的T80Ⅱ序列中, 平均每16.8个碱基出现1个碱基变异位点, 表现出较高频率的碱基突变. 碱基突变类型包括碱基的颠换、转换、缺失、插入等. 在检测到的275个碱基突变中, 主要是单碱基置换(97.09%), 碱基缺失或者插入的比例较小(2.91%). 在碱基置换中, 转换的频率(66.55%)高于颠换的频率(30.55%). 此外, 构成DNA的4种碱基均可以被离子束辐照诱发变异, 而且每一种碱基都可以被其他3种碱基所替换, 但是胸腺嘧啶(T)的辐射敏感性要高于其他3种碱基. 通过分析突变碱基周边序列, 对低能N+离子注入拟南芥突变体引发的碱基突变热点进行了讨论.     

甲型H1N1流感病毒DNA序列碱基的预测

甲型流感H1N1亚型曾给人类带来了重大灾难。本文提出了一种利用时间序列模型预测碱基的方法,对所选取的1970年～2010年同源性相对较高的41条H1N1流感病毒数据利用ARIMA(p,d,q)模型对前20个位置去拟合并且预测,除极个别外由预报区域图显示原始数据都在预报区域内,表明模型建立的比较合理,预报效果很好,这对H1N1病毒的研究有着重要的意义。     

STAT6识别N4位点DNA的结构基础被揭示

正天然免疫又称为固有免疫,存在于所有多细胞生物中,从1883年发现细胞的吞噬现象至今,天然免疫的研究经历了130多年,但是直到20世纪90年代,法国科学家Jules Hoffmann和美国科学家Bruce Beutler     

以减毒沙门氏菌为SARS-CoV N DNA口服疫苗载体的初步研究

目的:以减毒沙门氏菌为载体运送SARS-CoV N DNA疫苗至小鼠体内,研究其诱导的免疫应答情况,评价减毒鼠伤寒沙门氏菌作为口服疫苗的免疫效果。方法：将含SARS-CoV N基因的pcDNA-N质粒导入减毒鼠伤寒沙门氏菌CS022中,采用口服和滴鼻相结合的方法免疫BALB/c小鼠,以ELISA检测不同时间免疫小鼠血清中抗体及其亚型;以MTT法测定特异性淋巴细胞增殖反应;ELISPOT检测细胞因子;流式检测T细胞亚型。结果：pcDNA-N DNA疫苗口服免疫后2周就可以诱生特异性IgG抗体,且以IgG2a占优势;诱导了较高水平的淋巴细胞特异性增殖反应和IFN-γ,主要以Th1免疫为主。结论：减毒沙门氏菌可以有效运送pcDNA-N重组质粒并诱导产生特异体液和细胞免疫应答,为减毒细菌作为DNA疫苗运送载体的研究提供了参考依据,也为SARS疫苗研究开辟了新方法。     

植物DNA和mRNA中N6-甲基腺嘌呤的比较研究

DNA、RNA的甲基化作为重要的表观遗传标记,在真核生物多个细胞过程中发挥作用。DNA中的N6-甲基腺嘌呤(N6-methyladenine in DNA, 6mA)和RNA中的N6-甲基腺嘌呤(N6-methyladenine in RNA, m6A)均为来自腺嘌呤第6位的甲基化修饰,在合成和功能上有相似性也有区别。6mA或m6A的修饰缺陷影响植物胚胎发育、干细胞分化、组织器官发生及应激反应等。meRIPseq等技术的发展为全组甲基化位点鉴定提供了基础,未来将更加注重于功能研究。该文对近年来植物6mA或m6A甲基化位点的全组鉴定、合成、调控及成员功能研究进行回顾和比较,并展望未来的研究方向。     

Characterization of Family D DNA polymerase from Thermococcus sp. 9°N

Accurate DNA replication is essential for maintenance of every genome. All archaeal genomes except Crenarchaea, encode for a member of Family B (polB) and Family D (polD) DNA polymerases. Gene deletion studies in Thermococcus kodakaraensis and Methanococcus maripaludis show that polD is the only essential DNA polymerase in these organisms. Thus, polD may be the primary replicative DNA polymerase for both leading and lagging strand synthesis. To understand this unique archaeal enzyme, we report the biochemical characterization of a heterodimeric polD from Thermococcus. PolD contains both DNA polymerase and proofreading 3′–5′ exonuclease activities to ensure efficient and accurate genome duplication. The polD incorporation fidelity was determined for the first time. Despite containing 3′–5′ exonuclease proofreading activity, polD has a relatively high error rate (95 × 10^?5) compared to polB (19 × 10^?5) and at least 10-fold higher than the polB DNA polymerases from yeast (polε and polδ) or Escherichia coli DNA polIII holoenzyme. The implications of polD fidelity and biochemical properties in leading and lagging strand synthesis are discussed.     

Curcumin-Induced DNA Damage and Inhibited DNA Repair Genes Expressions in Mouse–Rat Hybrid Retina Ganglion Cells (N18)

Curcumin is reported to be a potent inhibitor of the initiation and promotion of many cancer cells. We investigated to examine whether or not curcumin induce DNA damage in mouse–rat hybrid retina ganglion cell line N18 cells. The Comet assay showed that incubation of N18 cells with 10, 25 and 30 μM of curcumin led to a longer DNA migration smear (Comet tail). The DNA gel electrophoresis showed that 20 μM of curcumin for 24 and 48 h treatment induced DNA damage and fragments in N18 cells. The real time PCR analysis showed that 20 μM of curcumin for 48 h treatment decreased ATM, ATR, BRCA1, 14-3-3σ, DNA-PK and MGMT mRNA, and ATM and MGMT mRNA expression were inhibited in a time-dependent manner. Our results indicate that curcumin caused DNA damage and inhibited DNA repair genes which may be the factors for curcumin-inhibited cell growth. H.-F. Lu and J.-S. Yang are contributed equally to this study.     

线粒体DNA与DNA甲基化

线粒体是除细胞核之外唯一携带遗传物质的细胞器,其线粒体DNA（mitochondrial DNA,mtDNA）控制着线粒体一些最基本的性质,对细胞功能有着重要影响.DNA甲基化是调节基因表达的重要方式之一.研究表明mtDNA存在CpG位点的低甲基化,并且mtDNA基因的表达受核DNA（nuclear DNA,nDNA）及线粒体自身DNA甲基化的调控,mtDNA和nDNA协同作用参与机体代谢调节和疾病发生发展过程.就近年来mtDNA与DNA甲基化的关系作一综述.     

人H5N1流感病毒血凝素蛋白DNA疫苗的构建及其免疫原性研究

将我国分离的首株人H5N1亚型禽流感病毒A/Anhui/1/2005作为研究对象,扩增其HA和HA1基因片段并克隆至真核表达载体pStar,构建成真核表达质粒。通过Western blot和间接免疫荧光检测方法确认,构建的重组质粒在真核细胞中成功地表达了目的蛋白HA和HA1。将重组质粒免疫BALB/c小鼠,检测免疫后外周血中HA/HA1特异性抗体的效价,并比较HA和HA1的免疫原性。结果表明,重组质粒免疫后成功地诱导了体液免疫反应,且二者的血清抗体效价无显著性差异。     

N—水杨醛氨基葡萄糖希夫碱配合物对O2和DNA的效应

采用比色法、荧光和吸收光谱法研究了Ｎ－水杨醛氨基葡萄糖希夫碱的铜Ⅱ）、锌（ｋⅡ）、钴９Ⅲ）配合物对超氧阴离子自由基和ＤＮＡ的作用。结果表明：ＣｕＳＧ和ＺｎＳＧ能显著地抑制超氧阴离子自由基的生成,抑制能力ＣｕＳＧ＞ＺｎＳＧ。     

Studies of physicochemical properties of N-H•••N hydrogen bonds in DNA, using selective 15N-labeling and direct 15N 1D NMR

15N-15N scalar coupling constants across base pair hydrogen bonds (2hJ(NN)) were studied using residue- and atom-specifically 15N labeled DNA oligomers. The N3 atom selectively 15N enriched 2'-deoxycytidine and thymidine, and the uniformly 15N enriched 2'-deoxyadenosine and 2'-deoxyguanosine, were chemically prepared and incorporated into two DNA oligomers, d(CGCGAATTCGCG)2 and d(CGCAAAAAGCG).d(CGCTTTTTGCG). This isotope labeling enabled us to determine the 2hJ(NN) value from the splitting of the 15N 1D spectrum. Additionally, it enabled the determination of 2hJ(NN) in D2O quite easily and highly quantitatively. The temperature and DNA sequence dependence were examined for these oligomers. The sequence dependence was not clear; however, a significant decrease of 2hJ(NN) was observed by elevating the temperature. This temperature dependence was not due to the hydrogen exchange, since the addition of 20 mM NH3 did not change the 2hJ(NN) values. The 2hJ(NN) values in D2O were somewhat smaller than those in H2O. As compared to our 15N 1D method, the quantitative HNN-COSY method gave systematically smaller 2hJ(NN) values in our system, due to the lower 15N fraction of our sample (79 and 88% for dA and the other nucleotides, respectively) and the insufficient power of the 15N RF pulse (B1 = 6.6 kHz). These systematic differences were recovered by theoretical correction of the 15N isotope fraction contribution, by using the composite 15N 180 degrees pulse in a quantitative HNN-COSY experiment.     

Dilute-‘N’-Go dideoxy sequencing of all DNA strands generated in multiplex LATE-PCR assays

We have recently described a Dilute-‘N’-Go protocol that greatly simplifies preparation and sequencing of both strands of an amplicon generated using linear-after-the-exponential (LATE)-PCR, an advanced form of asymmetric PCR . The same protocol can also be used to sequence all limiting primer strands in a multiplex LATE-PCR, by adding back each of the depleted limiting primers to a separate aliquot of the multiplex reaction. But, Dilute-‘N’-Go sequencing cannot be used directly to sequence each of the excess primer strands in the same multiplex reaction, because all of the excess primers are still present at high concentration. This report demonstrates for the first time that it is possible to sequence each of the excess primer strands using a modified Dilute-‘N’-Go protocol in which blockers are added to prevent all but one of the excess primers serving as the sequencing primer in separate aliquots. The optimal melting temperatures, positions and concentrations of blockers relative to their corresponding excess primers are defined in detail. We are using these technologies to measure DNA sequence changes in mitochondrial genomes that accompany aging and exposure to certain drugs.     

流感病毒NP表位序列增强H7N9 HA DNA疫苗免疫效果研究

为增强H7N9流感病毒HA DNA疫苗的免疫效果,本文构建了含有流感病毒NP的5个重复优势T表位或B表位(包括B_1线性表位和B_2构象表位)的表达质粒(简称NPT和NPB),以小鼠为动物模型,将NPT和NPB分别与H7N9流感病毒HA DNA混合免疫BALB/c小鼠1次,21 d后用致死剂量(20 LD_(50))的H7N9流感病毒攻击小鼠。通过检测免疫后小鼠血清特异性抗体滴度和攻毒后的免疫保护性指标-存活率、肺部残余病毒滴度及体重丢失率,评价表位质粒与HA DNA疫苗混合免疫对小鼠的保护效果。试验结果表明:用致死性H7N9流感病毒攻击小鼠后,HA DNA组小鼠全部死亡,HA+NPT免疫组小鼠存活率达到100%,HA+NPB1和HA+NPB2免疫组,小鼠存活率分别为30%和75%;混合免疫HA+NPT后小鼠抗体滴度升高明显,攻毒后小鼠体重丢失明显降低。综上表明,含有5个NP优势T表位或B表位的表达质粒能增强H7N9流感病毒HA DNA疫苗的免疫效果,混合免疫一次可以使小鼠得到较好的保护。HA DNA和表位疫苗的混合免疫,节约了疫苗用量,降低了免疫成本,为流感病毒核酸疫苗的临床开发提供了一定的试验基础。     

DNA杂交与DNA指纹技术

Southern印迹杂交和DNA指纹技术在分子生物学研究以及疾病的诊断、亲缘关系鉴定、犯罪分子确认等过程中发挥了重要作用。回顾了2种技术的发明、发展历程和在生命科学研究中的作用,并探讨了可能的发展方向,从中可以从一个侧面了解分子生物学的发展历程和体会科学家的智慧在科学技术发展中所起的重要作用。