Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions

The adsorption dynamics of double-stranded DNA(dsDNA)molecules on a graphene oxide(GO)surface are important for applications of DNA/GO functional structures in biosensors,biomedicine and materials science.In this work,molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules(from 4 bp to24 bp)on the GO surface.The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface.For short dsDNA(4 bp)molecules,the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface.For long dsDNA molecules(from 8 bp to 24 bp)adsorption is stable.By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface,we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp.We attributed this behavior to the flexibility of dsDNA molecules.With increasing length,the flexibility of dsDNA molecules also increases,and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal.This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.

DNA Double-Strand Breaks,Potential Targets for HBV Integration

Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis.More and more researches were designed to find the relationship of the two.In this study,we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks(DSBs),one of the most detrimental DNA damage.An 18-bp I-SceI homing endonuclease recognition site was introduced into the DNA of HepG2 cell line by stable DNA transfection,then cells were incubated in patients’ serum with high HBV DNA copies and at the same time,DSBs were induced by transient expression of I-SceI after transfection of an I-SceI expression vector.By using nest PCR,the viral DNA was detected at the sites of the break.It appeared that integra-tion occurred between part of HBV x gene and the I-SceI induced breaks.The results suggested that DSBs,as the DNA damages,may serve as potential targets for hepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily.It provided a new site to investi-gate the integration.

Codon evolution in double-stranded organelle DNA: strong regulation of homonucleotides and their analog alternations

In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.

Mechanical properties of double-stranded DNA biofilm with Gaussian distribution

In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal and electrical properties of DNA biofilm. In this paper, the elastic properties of dsDNA biofilm are studied. First, the Parsegian＇s empirical potential based on a mesoscopic liq- uid crystal theory is employed to describe the interaction energy among coarse-grained DNA cylinders. Then, con- sidering a Gaussian distribution of DNA interaxial distance, the thought experiment method is used to derive an analyti- cal expression for Young＇s modulus of DNA biofilm with a stochastic packing pattern for the first time. Results show that Young＇s modulus of DNA biofilm is on the order of 10 MPa. These findings could provide a simple and effective method to evaluate the mechanical properties of soft biofilm on snbstrate.

Maternal gene Ooep may participate in homologous recombination-mediated DNA double-strand break repair in mouse oocytes

DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks （DSBs） are highly deleterious and can substantially impair genome integrity. Homologous recombination （HR）-mediated DNA DSB repair plays dominant roles in safeguarding oocyte quantity and quality. However, little is known regarding the key players of the HR repair pathway in oocytes. Here, we identified oocyte-specific gene Ooep as a novel key component of the HR repair pathway in mouse oocytes. OOEP was required for efficient ataxia telangiectasia mutated （ATM） kinase activation and Rad51 recombinase （RAD51） focal accumulation at DNA DSBs. Ooep null oocytes were defective in DNA DSB repair and prone to apoptosis upon exogenous DNA damage insults. Moreover, Ooep null oocytes exhibited delayed meiotic maturation. Therefore, OOEP played roles in preserving oocyte quantity and quality by maintaining genome stability. Ooep expression decreased with the advance of maternal age, suggesting its involvement in maternal aging.

Exposure to Long Magnetic Resonance Imaging Thermometry Does Not Cause Significant DNA Double-Strand Breaks on CF-1 Mice

The purpose of the study was to investigate if the high gradient strength and slew rate used for long MRI-thermometry monitoring could cause DNA double-stranded breaks (DSBs). To this end, an enzyme-linked immunosorbent assay (ELISA) was used to quantify γH2AX, a molecular marker for DSBs, in the blood of mice after a 6-hour exposure to magnetic resonance imaging (MRI). Fourteen CF-1 female mice were separated into 4 experimental groups: Untreated negative control, MRI-treated, MRI-Control, and exposed to ionizing radiation positive control. Untreated negative control was used as a baseline for ELISA to quantify γH2AX. MRI-treated consisted of a 6-hour continuous magnetic resonance imaging (MRI) echo planar imaging (EPI) sequence with a slew rate of 192 mT/m/s constituting a significantly longer imaging time than routine clinical imaging. MRI-control mice were maintained under the same conditions outside the MRI scanner for 6-hours. Mice in the irradiation group served as a positive control of DSBs and were exposed to either 2 Gy, 5 Gy or 10 Gy of ionizing radiation. DSBs in the blood lymphocytes from the treatment groups were analyzed using the γH2AX ELISA and compared. Total protein concentration in lysates was determined for each blood sample and averaged 1 ± 0.35 mg/mL. Irradiated positive controls were used to test radiation dose-dependency of the γH2AX ELISA assay where a linear dependency on radiation exposure was observed (r2 = 0.93) between untreated and irradiated samples. Mean and standard error mean of γH2AX formation were calculated and compared between each treatment group. Repeated measures 1-way ANOVA showed statistically significant differences between the means of irradiated controls and both the MRI-control and MRI-treated groups. There was no statistically significant difference between the MRI-treated samples and the MRI-control groups. Our results show that long MRI exposure at a high slew rate did not cause increased levels of γH2AX when compared to control mice, suggesting that no increase in DSBs was caused by the long MR thermometry imaging session. The novelty of this work contradicts other studies that have suggested MRI may cause DSBs;this work suggests an alternative cause of DNA damage.

还少丹对老年小鼠脂褐素含量和DNA分子结构稳定性的影响

目的 研究还少丹对老龄小鼠脂褐素含量和DNA分子结构稳定性的影响。方法将36只昆明种老年小鼠(20月龄),按体质量随机分为3组,另设12只2月龄同种小鼠作为青年对照组,共4组:①老年对照组;②老年还少丹组;③老年维生素E(VE)组;④青年对照组。连续喂养10周后,采用荧光分光光度法测定脑组织的脂褐素水平和肝组织DNA双链解旋剩余率;用紫外分光光度法测定肝组织DNA碱变性增色效应。结果青年对照组、老年还少丹组、老年VE组的脂褐素含量明显低于老年对照组,差异有统计学意义(P<0.05);与老年对照组比较,青年对照组和老年还少丹组的DNA碱变性增色效应明显降低,而DNA双链解旋剩余率显著增高,差异均具有统计学意义(P<0.05),而老年VE组的差异无统计学意义(P>0.05)。结论还少丹能有效降低脂褐素的含量,保护DNA结构的稳定性,达到延缓衰老的目的 。

利用荧光标记引物和DNA自动测序仪确定DNA的断裂位点

Determining the base sequence of DNA broken site is quite crucial for the study on the cleavage site specificity and mechanism of various natural or synthetic DNA cleavage regents,and on developing novel therapeutic drugs targeting at DNA.The most frequently used method depending on chemical reactions of the Maxam-Gilbert procedure,and the late arising methods used by Rui Ren et al.which were based on Sanger’s DNA sequencing strategy,all had some deficiencies,either the pollution of radioactive materials,or really complicated and difficult to operate.In the present paper,a new method for DNA cleavage site sequence determination was developed.The fluorescence FAM-labeled primer was annealed to the DNA fragments,which has been cleaved by restriction enzymes or other regents,and extended along the template sequence.The products then loaded onto the polyacrylamide electrophoresis gel of ABI 377 DNA Sequencer.Data was collected and analyzed by using ABI PRISM Data Collection Software and ABI PRISM Sequencing Analysis Software.It is proved to be a credible and simple new approach to determine the base sequence of DNA broken sites.

不同破壁方法对节旋藻DNA提取效果的影响

采用液氮研磨法、反复冻融法、反复冻融-溶菌酶法、溶菌酶法、超声波法、超声波-溶菌酶法对节旋藻TJCU-7的藻细胞进行破碎,用改进的CTAB法提取基因组DNA,通过凝胶电泳检测,核酸浓度、纯度测定及PCR扩增效果来评价各破壁方法的优劣。结果发现,6种方法对节旋藻均有较好的破壁效果：经反复冻融法、溶菌酶法及反复冻融-溶菌酶法破壁后所获得的DNA浓度（〉2000 ng/μL）显著高于其他方法,其中液氮研磨法所得的DNA浓度最低（〈40 ng/μL）。除超声波法所得DNA的OD260/OD280值大于2.00,说明有部分RNA污染外,其余方法所得DNA的OD260/OD280的值均在1.90-2.05,纯度较高。经PCR扩增后均得到了2 kb的目的片段,可以满足基本的生物学实验要求。综合考虑,反复冻融法,溶菌酶法简单、快速,破壁效果好,是节旋藻DNA提取时的优先考虑方法。

陈旧碎骨组织DNA检验

碎尸案中,因骨骼碎小且数量多又损毁严重,会使之难以与其他动物骨骼区分开,从而成为法医DNA鉴定的一大难题。本文利用扫描电镜进行骨骼种属鉴定,通过哈氏系统的形态学特征区分人骨与其他动物骨骼,大大减少了DNA检验的工作量,而后续脱钙与裂解处理同时进行又缩短了反应时间。一起10年前碎尸案的碎小骨块据此而成功地快速鉴定,一种适用于陈旧碎骨DNA的快速检验方法也因此建立。

超声处理导致交联DNA序列特异性断裂

目的:研究在交联状态下超声方法处理DNA是否导致DNA随机断裂。方法:通过建立一种新的Clone-Sequencing筛选技术,利用NCBI等相关网站,结合Vector-NTI等软件分析得到不同断裂位点的核苷酸序列,利用SPSS 18.0软件,对不同断裂位点核苷酸序列的分布进行统计学分析。结果:利用Clone-Sequencing技术得到216个来源于不同染色体位置的克隆片段,通过对其正义链和反义链的5'-DNA断裂末端的分析,得到432个超声断裂位点的核苷酸序列信息。对断裂位点核苷酸序列进行统计分析发现,超声处理后,交联DNA的断裂位点并不像过去认为的完全随机分布,而是存在明显的偏性,即对于所有16种不同的二核苷酸组合,超声处理导致交联DNA更易在5'-ApN-3'寡核苷酸中间的磷酸二酯键处断裂,且其相对断裂频率呈现d(ApN)>>d(GpN)>d(CpN)>d(TpN)的趋势。结论:传统的超声方法处理,交联DNA断裂位点并不是完全随机分布,而是存在着明显的序列偏好性,这一新发现提示,对于目前广泛使用的、涉及交联DNA超声处理的ChIP-Chip或ChIP-Seq等高通量及其衍生技术结果的统计分析,需要引入更加合理有效的分析策略。

Naked DNA in cells:An inducer of major histocompatibility complex molecules to evoke autoimmune responses?

The major histocompatibility complex(MHC) is the exclusive chaperone that presents intracellular antigens,either self or foreign to T cells.Interestingly,aberrant expression of MHC molecules has been reported in various autoimmune target tissues such as thyroid follicular cells in Grave's disease.Herein,we review the discovery of an unexpected effect of cytosolic doublestranded DNA(ds DNA),despite its origins,to induce antigen processing and presenting genes,including MHC molecules,in non-immune cells.Moreover,we highlight several recent studies that suggest cell injury endows thyroid epithelial cells with a phenotype of mature antigen presenting cells by inducing multiple antigen processing and presenting genes via releasing genomic DNA fragments into the cytosol.We discuss the possibility that such cytosolic ds DNA,in naked form without binding to histone proteins,might be involved in the development of cell damage-triggered autoimmune responses.We also discuss the possible molecular mechanism by which cytosolic ds DNA can induce MHC molecules.It is reasonable to speculate that cytosolic ds DNA-induced MHC class Ⅰ is partially due to an autocrine/paracrine effect of type Ⅰ interferon(IFN).While the mechanism of cytosolic ds DNA-induced MHC class Ⅱ expression appears,at least partially,distinct from that mediated by IFN-γ.Further in-depth are required to clarify this picture.

DETECTION OF STRAND BREAKS OF DNA IN HUMAN EARLY CHORIONIC VILLUS CELLS INDUCED BY DIAGNOSTIC ULTRASOUND USING ^(32)P-LABELED ALU HYBRIDIZATION

Objective To explore if strand breaks of DNA in human early chorionic villus cells in uterus were induced by diagnostic ultrasound and to evaluate the method used for detection of single-stranded breaks and double-stranded breaks in human DNA. Methods 60 normal pregnant women aged 20-30, who underwent artificial abortion during 6-8 weeks of gestation, were randomly divided into 2 experimental groups: All 30 cases were exposed to diagnostic ultrasound in uterus for 10 minutes, and 24 hours later chorionic villi were extracted; the other 30 cases were taken as the control group. Single-stranded DNA and double-stranded DNA in villus cells in all cases were isolated by the alkaline unwinding combined with hydroxylapatite chromatography, and were quantitatively detected using 32 P-labeled Alu probe for dot-blotting hybridization. Results There was no significant difference in quantity and percentage in single-stranded DNA and double-stranded DNA between 2 groups (P>0.05). 32 P-Alu probe could only hybridize with human DNA, and could detect DNA isolated from as few as 2.5×10 3 chorionic villus cells and 0.45ng DNA in human leukocytes. Conclusion The results suggested that there were no DNA strand damages in human chorionic villus cells when the uterus was exposed to diagnostic ultrasound for 10 minutes. The method,^(32)P-Alu probe for dot-blotting hybridization, was even more specific, sensitive and accurate than conventional approaches.

Ataxia-telangiectasia mutated plays an important role in cerebellar integrity and functionality

Accumulating evidence indicates that ataxia-telangiectasia mutated kinase is critical for maintaining cellular homeostasis and that it has both nuclear and cytoplasmic functions.However,the functions of ataxia-telangiectasia mutated that when lost lead to cerebellar degeneration are still unknown.In this review,we first describe the role of ataxia-telangiectasia mutated in cerebellar pathology.In addition to its canonical nuclear functions in DNA damage response circuits,ataxia-telangiectasia mutated functions in various cytoplasmic and mitochondrial processes that are critically important for cellular homeostasis.We discuss these functions with a focus on the role of ataxia-telangiectasia mutated in maintaining the homeostatic redox state.Finally,we describe the unique functions of ataxia-telangiectasia mutated in various types of neuronal and glial cells including cerebellar granule neurons,astrocytes,and microglial cells.

The DNA damage and regulatory strategy in hematopoietic stem cells after irradiation exposure:Progress and challenges

The hematopoietic system is susceptible to ionizing radiation(IR),which can cause acute hematopoietic failure or long-term myelosuppression.As the most primitive cells of the hematopoietic hierarchy,hematopoietic stem cells(HSCs)maintain lifelong hematopoietic homeostasis and promote hematopoietic regeneration during stress.Numerous studies have shown that nuclear and mitochondrial genomes are the main targets of radiation injury in HSCs.More importantly,the damage of DNA may trigger a series of biological responses that largely determine HSC fate following IR exposure.Although some essential pathways and factors involved in DNA injury and damage in HSCs have been revealed,a comprehensive understanding of the biological effects of radiation on HSCs still needs to be improved.This review focuses on recent insights into the molecular mechanisms underlying DNA damage and repair in HSCs after IR.Then summarize corresponding regulatory measures,which may provide a reference for further research in this field.

Analysis of the genetic interactions between Cyclin A1, Atm and p53 during spermatogenesis

Aim： To analyze the functional interactions of Cyclin with p53 and Atm in spermatogenesis and DNA double- strand break repair. Methods： Two lines of double knockout mice were generated. Spermatogenesis and double strand break repair mechanisms were analyzed in Cyclin A1 （Ccnal）; p53- and Ccnal; Atm-double knockout mice. Results： The block in spermatogenesis observed in Cyclin A1-/- （Ccnal-/-） testes at the mid-diplotene stage is associated with polynucleated giant cells. We found that Ccnal-deficient testes and especially the giant cells accumulate unrepaired DNA double-strand breaks, as detected by immunohistochemistry for phosphorylated H2AX. In addition, the giant cells escape from apoptosis. The development of giant cells occurred in meiotic prophase I, because testes lacking ATM, which are known to develop spermatogenic arrest earlier than prophase I, do not develop giant cells in the absence of cyclin A1. Cyclin A1 interacted with p53 and phosphorylated p53 in complex with CDK2. Interestingly, p53-deficiency significantly increased the number of giant cells in Ccnal-deficient testes. Gene expression analyses of a panel of DNA repair genes in the mutant testes revealed that none of the genes examined were consistently misregulated in the absence of cyclin A1. Conclusion： Ccnal-deficiency in spermatogenesis is associated with defects in DNA double-strand break repair, which is enhanced by loss of p53.

Role of deubiquitinating enzymes in DNA double-strand break repair

DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damage, including that caused by endogenous and exogenous agents, may cause DNA aberrations. Of all forms of DNA damage, DNA double-strand breaks(DSBs) are the most serious. If the repair function is defective, DNA damage may cause gene mutation, genome instability, and cell chromosome loss, which in turn can even lead to tumorigenesis. DNA damage can be repaired through multiple mechanisms. Homologous recombination(HR) and non-homologous end joining(NHEJ) are the two main repair mechanisms for DNA DSBs. Increasing amounts of evidence reveal that protein modifications play an essential role in DNA damage repair.Protein deubiquitination is a vital post-translational modification which removes ubiquitin molecules or polyubiquitinated chains from substrates in order to reverse the ubiquitination reaction. This review discusses the role of deubiquitinating enzymes(DUBs) in repairing DNA DSBs. Exploring the molecular mechanisms of DUB regulation in DSB repair will provide new insights to combat human diseases and develop novel therapeutic approaches.

Electrochemical investigation on the interaction of benzene sulfonyl 5-fluorouracil derivatives with double-stranded DNA and G-quadruplex DNA

The interaction of double-stranded(ds) and G-quadruplex(G4) DNA with sulfonyl 5-fluorouracil derivatives(5-fluoro-1-(arylsulfonyl) pyrimidine-2,4(1H,3H)-diones) was investigated in this research,in which Au electrodes modified with ds-DNA or G4-DNAs were used as a working electrode.The investigation showed that the binding affinity with G4-DNA was significantly increased when 5-fluorouracil(5-FU) was modified with arylsulfonyl groups.The presence of strong electron-withdrawing groups on benzene sulfonyl 5-FU greatly enhanced the binding selectivity(k G4-DNA /k ds-DNA).Such results provided new insights into the potential connections between the chemical structure of drug candidates and their anticancer activities.

Regulation of DNA double-strand break repair pathway choice:a new focus on 53BP1

Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break(DSB)signaling.P53-binding protein 1(53BP1)plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining(NHEJ)-mediated DSB repair pathway that rejoins DSB ends.New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination(HR)signaling.This review focuses on the up-and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair,which in turn promotes the sensitivity of poly(ADP-ribose)polymerase inhibitor(PARPi)in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.

MULTIPLE MUTATIONS ON DOUBLE-STRANDED DNA

The site-specific mutagenesis of the gene has become an important technique in gene modification and protein engineering. Among all methods, the primer extension one using single-stranded DNA (such as the infective form of the M13 phage ) as template and the gapped stranded one are commonly used. But some genes, especially those