Homologous recombination （HR） comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks （DSBs） and interstrand crosslinks （ICLs）. In addition, recombination provides c...Homologous recombination （HR） comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks （DSBs） and interstrand crosslinks （ICLs）. In addition, recombination provides critical support for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR： homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modalities of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.展开更多
DNA double-strand breaks （DSBs） are critical lesions that can result in cell death or a wide variety of genetic alterations including largeor small-scale deletions, loss of heterozygosity, translocations, and chromo...DNA double-strand breaks （DSBs） are critical lesions that can result in cell death or a wide variety of genetic alterations including largeor small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining （NHEJ） and homologous recombination （HR）, and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources including reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1（XRS2） complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit （DNA-PKcs）, and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.展开更多
In addition to well-defined DNA repair pathways, all living organisms have evolved mechanisms to avoid cell death caused by replication fork collapse at a site where replication is blocked due to disruptive covalent m...In addition to well-defined DNA repair pathways, all living organisms have evolved mechanisms to avoid cell death caused by replication fork collapse at a site where replication is blocked due to disruptive covalent modifications of DNA. The term DNA damage tolerance （DDT） has been employed loosely to include a collection of mechanisms by which cells survive replication-blocking lesions with or without associated genomic instability. Recent genetic analyses indicate that DDT in eukaryotes, from yeast to human, consists of two parallel pathways with one being error-free and another highly mutagenic. Interestingly, in budding yeast, these two pathways are mediated by sequential modifications of the proliferating cell nuclear antigen （PCNA） by two ubiquitination complexes Rad6-Rad18 and Mms2-Ubc13-Rad5. Damage-induced monoubiquitination of PCNA by Rad6-Rad18 promotes translesion synthesis （TLS） with increased mutagenesis, while subsequent polyubiquitination of PCNA at the same K164 residue by Mms2-Ubc13-Rad5 promotes error-free lesion bypass. Data obtained from recent studies suggest that the above mechanisms are conserved in higher eukaryotes. In particular, mammals contain multiple specialized TLS polymerases. Defects in one of the TLS polymerases have been linked to genomic instability and cancer.展开更多
Post-translational modifications play a crucial role in coordinating cellular response to DNA damage. Recent evidence suggests an interplay between multiple protein modifications, including phosphorylation, ubiquityla...Post-translational modifications play a crucial role in coordinating cellular response to DNA damage. Recent evidence suggests an interplay between multiple protein modifications, including phosphorylation, ubiquitylation, acetylation and sumoylation, that combine to propagate the DNA damage signal to elicit cell cycle arrest, DNA repair, apoptosis and senescence. Utility of specific post-translational modifiers allows temporal and spatial control over protein relo-calization and interactions, and may represent a means for trans-regulatory activation of protein activities. The ability to recognize these specific modifiers also underscores the capacity for signal amplification, a crucial step for the maintenance of genomic stability and tumor prevention. Here we have summarized recent findings that highlight the complexity of post-translational modifications in coordinating the DNA damage response, with emphasis on the DNA damage signaling cascade.展开更多
The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated...The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at –35, –8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to –8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.展开更多
Aptamers are molecular recognition elements with high specificity that are selected from deoxyribonucleic acid/ribonucleic acid (DNA/RNA) library. Compared with the traditional protein recognition elements,aptamers ha...Aptamers are molecular recognition elements with high specificity that are selected from deoxyribonucleic acid/ribonucleic acid (DNA/RNA) library. Compared with the traditional protein recognition elements,aptamers have excellent properties such as cost-effective,stable,easy for synthesis and modification. In recent years,electrochemistry plays an important role in biosensor field because of its high sensitivity,high stability, fast response and easy miniaturization. Through the combination of these two technologies and our rational design,we constructed a series of biosensors and biochips that are simple,fast,cheap and miniaturized. Firstly,we designed an adenosine triphosphate (ATP) electrochemical biosensor based on the strand displacement strategy. We can detect as low as 10 nmol/L of ATP both in pure solution and complicated cell lysates. Secondly,we creatively split the aptamers into two fragments and constructed the sandwich assay platform only based on single aptamer sequence. We successfully transferred this design on biochips with multiple micro electrodes (6×6) and accomplished multiplex detection. In the fields of biochips and biocomputers,we designed several DNA logic gates with electric (electrochemical) signal as output which paves a new way for the development of DNA computer.展开更多
Organophosphorous pesticide(OP) contamination has serious adverse effects on human health and the environment. Due to the toxicity of OPs and the threat presented by their accidental or intentional release in populate...Organophosphorous pesticide(OP) contamination has serious adverse effects on human health and the environment. Due to the toxicity of OPs and the threat presented by their accidental or intentional release in populated areas, the determination and monitoring of these OPs in food products and environment is of great importance. OPs are present in very small quantities and therefore, methods for their detection need to be highly sensitive and selective. Here, we aimed to develop a simple and selective aptamer-based colorimetric assay for the detection of omethoate, which is one of the commonly used OPs. The principle of the assay is that single-stranded DNA(ss DNA)-wrapped gold nanoparticles(Au NPs) are resistant to salt-induced aggregation. By employing an "artificial antibody" organophosphorous pesticide-binding aptamer(OBA) as the recognition element, aptamer-wrapped Au NPs(Au-apta) show high selectivity towards omethoate, resulting in the disconnection of aptamers from Au NPs and the aggregation of Au NPs. As there is a significant color change from the interparticle plasmon coupling during the aggregation of Au NPs, the established assay showed good linearity between 0.1 and 10 μmol/L, with a low detection limit of 0.1 μmol/L. Other OPs such as profenofos, phorate, and isocarbophos would not interfere with the detection of omethoate despite having similar structures. Thus, the colorimetric method shows potential for use in the detection of omethoate in real soil samples.展开更多
The maximal matching problem （MMP） is to find maximal edge subsets in a given undirected graph, that no pair of edges are adjacent in the subsets. It is a vitally important NP-complete problem in graph theory and ap...The maximal matching problem （MMP） is to find maximal edge subsets in a given undirected graph, that no pair of edges are adjacent in the subsets. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications in optimal combination and linear programming fields. It can be difficultly solved by the electronic computer in exponential level time. Meanwhile in previous studies deoxyribonucleic acid （DNA） molecular operations usually were used to solve NP-complete continuous path search problems, e.g. HPP, traveling salesman problem, rarely for NP-hard problems with discrete vertices or edges solutions, such as the minimum vertex cover problem, graph coloring problem and so on. In this paper, we present a DNA algorithm for solving the MMP with DNA molecular operations. For an undirected graph with n vertices and m edges, we reasonably design fixed length DNA strands representing vertices and edges of the graph, take appropriate steps and get the solutions of the MMP in proper length range using O（n^3） time. We extend the application of DNA molecular operations and simultaneously simplify the complexity of the computation.展开更多
文摘Homologous recombination （HR） comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks （DSBs） and interstrand crosslinks （ICLs）. In addition, recombination provides critical support for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR： homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modalities of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.
文摘DNA double-strand breaks （DSBs） are critical lesions that can result in cell death or a wide variety of genetic alterations including largeor small-scale deletions, loss of heterozygosity, translocations, and chromosome loss. DSBs are repaired by non-homologous end-joining （NHEJ） and homologous recombination （HR）, and defects in these pathways cause genome instability and promote tumorigenesis. DSBs arise from endogenous sources including reactive oxygen species generated during cellular metabolism, collapsed replication forks, and nucleases, and from exogenous sources including ionizing radiation and chemicals that directly or indirectly damage DNA and are commonly used in cancer therapy. The DSB repair pathways appear to compete for DSBs, but the balance between them differs widely among species, between different cell types of a single species, and during different cell cycle phases of a single cell type. Here we review the regulatory factors that regulate DSB repair by NHEJ and HR in yeast and higher eukaryotes. These factors include regulated expression and phosphorylation of repair proteins, chromatin modulation of repair factor accessibility, and the availability of homologous repair templates. While most DSB repair proteins appear to function exclusively in NHEJ or HR, a number of proteins influence both pathways, including the MRE11/RAD50/NBS1（XRS2） complex, BRCA1, histone H2AX, PARP-1, RAD18, DNA-dependent protein kinase catalytic subunit （DNA-PKcs）, and ATM. DNA-PKcs plays a role in mammalian NHEJ, but it also influences HR through a complex regulatory network that may involve crosstalk with ATM, and the regulation of at least 12 proteins involved in HR that are phosphorylated by DNA-PKcs and/or ATM.
基金Acknowledgments The authors wish to thank Landon Pastushok, Michelle Hanna and other members from the Xiao laboratory for helpful discussion. This work was supported by the Canadian Institutes of Health Research operating grants MOP-38104 and MOP-53240 to W Xiao, and the National Natural Science Foundation of China（Grant no. 30560132） to F Xu.
文摘In addition to well-defined DNA repair pathways, all living organisms have evolved mechanisms to avoid cell death caused by replication fork collapse at a site where replication is blocked due to disruptive covalent modifications of DNA. The term DNA damage tolerance （DDT） has been employed loosely to include a collection of mechanisms by which cells survive replication-blocking lesions with or without associated genomic instability. Recent genetic analyses indicate that DDT in eukaryotes, from yeast to human, consists of two parallel pathways with one being error-free and another highly mutagenic. Interestingly, in budding yeast, these two pathways are mediated by sequential modifications of the proliferating cell nuclear antigen （PCNA） by two ubiquitination complexes Rad6-Rad18 and Mms2-Ubc13-Rad5. Damage-induced monoubiquitination of PCNA by Rad6-Rad18 promotes translesion synthesis （TLS） with increased mutagenesis, while subsequent polyubiquitination of PCNA at the same K164 residue by Mms2-Ubc13-Rad5 promotes error-free lesion bypass. Data obtained from recent studies suggest that the above mechanisms are conserved in higher eukaryotes. In particular, mammals contain multiple specialized TLS polymerases. Defects in one of the TLS polymerases have been linked to genomic instability and cancer.
文摘Post-translational modifications play a crucial role in coordinating cellular response to DNA damage. Recent evidence suggests an interplay between multiple protein modifications, including phosphorylation, ubiquitylation, acetylation and sumoylation, that combine to propagate the DNA damage signal to elicit cell cycle arrest, DNA repair, apoptosis and senescence. Utility of specific post-translational modifiers allows temporal and spatial control over protein relo-calization and interactions, and may represent a means for trans-regulatory activation of protein activities. The ability to recognize these specific modifiers also underscores the capacity for signal amplification, a crucial step for the maintenance of genomic stability and tumor prevention. Here we have summarized recent findings that highlight the complexity of post-translational modifications in coordinating the DNA damage response, with emphasis on the DNA damage signaling cascade.
文摘The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at –35, –8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to –8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.
基金100 Talents Program of Chinese Academy of SciencesNational Key Basic Research Program of China ("973"Program) (No. 2012CB932600)
文摘Aptamers are molecular recognition elements with high specificity that are selected from deoxyribonucleic acid/ribonucleic acid (DNA/RNA) library. Compared with the traditional protein recognition elements,aptamers have excellent properties such as cost-effective,stable,easy for synthesis and modification. In recent years,electrochemistry plays an important role in biosensor field because of its high sensitivity,high stability, fast response and easy miniaturization. Through the combination of these two technologies and our rational design,we constructed a series of biosensors and biochips that are simple,fast,cheap and miniaturized. Firstly,we designed an adenosine triphosphate (ATP) electrochemical biosensor based on the strand displacement strategy. We can detect as low as 10 nmol/L of ATP both in pure solution and complicated cell lysates. Secondly,we creatively split the aptamers into two fragments and constructed the sandwich assay platform only based on single aptamer sequence. We successfully transferred this design on biochips with multiple micro electrodes (6×6) and accomplished multiplex detection. In the fields of biochips and biocomputers,we designed several DNA logic gates with electric (electrochemical) signal as output which paves a new way for the development of DNA computer.
基金supported by the National Natural Science Foundation of China(6137103921305067+5 种基金21105048)China Postdoctoral Science Foundation Funded Project(2012T50475)Science Foundation of Jiangsu Province(BK20130754)Ph D Fund of the Ministry of Education for Young Teachers(0133219120019)King Saud University(Distinguished Scientist Fellowship Program)Graduate Education Innovation Program of Nanjing University of Science and Technology and Chinese Academy of Sciences
文摘Organophosphorous pesticide(OP) contamination has serious adverse effects on human health and the environment. Due to the toxicity of OPs and the threat presented by their accidental or intentional release in populated areas, the determination and monitoring of these OPs in food products and environment is of great importance. OPs are present in very small quantities and therefore, methods for their detection need to be highly sensitive and selective. Here, we aimed to develop a simple and selective aptamer-based colorimetric assay for the detection of omethoate, which is one of the commonly used OPs. The principle of the assay is that single-stranded DNA(ss DNA)-wrapped gold nanoparticles(Au NPs) are resistant to salt-induced aggregation. By employing an "artificial antibody" organophosphorous pesticide-binding aptamer(OBA) as the recognition element, aptamer-wrapped Au NPs(Au-apta) show high selectivity towards omethoate, resulting in the disconnection of aptamers from Au NPs and the aggregation of Au NPs. As there is a significant color change from the interparticle plasmon coupling during the aggregation of Au NPs, the established assay showed good linearity between 0.1 and 10 μmol/L, with a low detection limit of 0.1 μmol/L. Other OPs such as profenofos, phorate, and isocarbophos would not interfere with the detection of omethoate despite having similar structures. Thus, the colorimetric method shows potential for use in the detection of omethoate in real soil samples.
文摘The maximal matching problem （MMP） is to find maximal edge subsets in a given undirected graph, that no pair of edges are adjacent in the subsets. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications in optimal combination and linear programming fields. It can be difficultly solved by the electronic computer in exponential level time. Meanwhile in previous studies deoxyribonucleic acid （DNA） molecular operations usually were used to solve NP-complete continuous path search problems, e.g. HPP, traveling salesman problem, rarely for NP-hard problems with discrete vertices or edges solutions, such as the minimum vertex cover problem, graph coloring problem and so on. In this paper, we present a DNA algorithm for solving the MMP with DNA molecular operations. For an undirected graph with n vertices and m edges, we reasonably design fixed length DNA strands representing vertices and edges of the graph, take appropriate steps and get the solutions of the MMP in proper length range using O（n^3） time. We extend the application of DNA molecular operations and simultaneously simplify the complexity of the computation.
