DNA水凝胶是具有三维聚合物网络的高保水性材料。研究人员设计了多种DNA水凝胶交联制备方法,并通过向其中引入其他功能分子或与其他类型的功能材料相互结合,构建了具有优异性能的DNA水凝胶,受到了广泛关注。适配体是基于指数富集的配体...DNA水凝胶是具有三维聚合物网络的高保水性材料。研究人员设计了多种DNA水凝胶交联制备方法,并通过向其中引入其他功能分子或与其他类型的功能材料相互结合,构建了具有优异性能的DNA水凝胶,受到了广泛关注。适配体是基于指数富集的配体系统进化(systematic evolution of ligands by exponential enrichment,SELEX)技术从随机寡核苷酸文库中筛选获得的对目标物质具有良好特异性与亲和力的寡核苷酸序列。适配体功能化的DNA水凝胶具有靶向范围广、稳定性好、易于修饰、操作简单和成本低等优点,得到了广泛应用。本文概述了构建适配体功能化的DNA水凝胶的基本设计原则与分类,重点介绍了适配体功能化的DNA水凝胶在食品安全检测中的最新策略,最后,讨论了适配体功能化的DNA水凝胶面临的挑战以及对未来的展望,旨在为其在食品安全领域的应用提供参考。展开更多
A comparative study on the phenotypic and genetic characteristics among Acidithiobacillus ferrooxidans （AF2）, a typic strain ATCC23270 and a previously isolated strain AF3 was performed. AF2 can use ferrous ion （F...A comparative study on the phenotypic and genetic characteristics among Acidithiobacillus ferrooxidans （AF2）, a typic strain ATCC23270 and a previously isolated strain AF3 was performed. AF2 can use ferrous ion （Fe^2＋） or elemental sulfur （S^0） as sole energy source, but oxidizes So more effectively than Fe^2＋, which is different from ATCC23270 and AF3. The G＋C content of AF2 is 51.8% （molar fraction）, however, ATCC23270 and AF3 strains have G＋C content of 63.7% and 64.8% （molar fraction）, respectively. The DNA-DNA hybridization results show that AF2 has 41.53% and 52.38% genome similarity to ATCC 23270 and AF3, respectively, but AF3 has a high genome similarity of 89.86% to ATCC 23270 strain. Rusticyanin （rus） and subunit III of aa3-type cytochrome oxidase （coxC） genes are not detected in AF2, but Fe^2＋ oxidase （iro） gene can be detected. To understand the genomic organization of iro gene, a cosmid library of AF2 genome was constructed and iro gene-containing clone was screened. The sequencing result shows that although the nucleotide sequence of iro gene in AF2 is completely identical to that of ATCC 23270 strain, its genomic organization is different from that of ATCC 23270. In AF2, iro is located at downstream ofpurA gene, while it is located at downstream ofpetC-2 gene in ATCC 23270 strain. These results indicate that AF2 is a novel strain ofA. ferrooxidans, and that phenotypic differences among the strains ofA. ferrooxidans are closely correlated with their genetic polymorphisms.展开更多
An electrochemical assay for single nucleotide polymorphisms (SNPs) genotyping is reported. Although electrochemical method is sensitive for DNA detection on surfaces, the ability of surface assay to precisely recogni...An electrochemical assay for single nucleotide polymorphisms (SNPs) genotyping is reported. Although electrochemical method is sensitive for DNA detection on surfaces, the ability of surface assay to precisely recognize DNA hybridization event is sacrificed to some extent due to the crowded confined surfaces environments that disfavor DNA hybridization. In the present study, we employed branched tetrahedron structure probes (TSPs) to replace regular linear single stranded DNA capture probes that were immobilized on solid surfaces. This three-dimensional DNA nanostructure lowers the density of immobilized DNA probes on confined surfaces, providing a hybridization environment that is similar to homogenous solution. This TSP-based electrochemical assay reveals excellent performance for SNPs genotyping with concentration as low as 1 nM.展开更多
Conventional rice breeding has long focused on exploiting the DNA sequence diversity.However,epigenetic diversity,reflected particularly in DNA methylation,can also contribute to phenotypic variation and should not be...Conventional rice breeding has long focused on exploiting the DNA sequence diversity.However,epigenetic diversity,reflected particularly in DNA methylation,can also contribute to phenotypic variation and should not be overlooked in rice breeding.In this study,20 parental lines of indica rice,which are widely used in hybrid rice breeding in China,were analyzed to investigate variations of DNA methylation and its inheritance.The results revealed a wide diversity in DNA methylation among these breeding lines.A positive correlation was seen between DNA methylation and genetic diversity.Furthermore,some of the methylated DNA was inherited in the subsequent generation,regardless of whether they were produced by selfing or hybrid-crossing.This study provides insight into the methylation patterns in rice,and suggests the importance of epigenetic diversity in rice breeding.展开更多
In the present study, we developed a highly sensitive and convenient biosensor consisting of gold nanoparticle （AuNP） probes and a gene chip to detect microRNAs （miRNAs）. Specific oligonucleotides were attached to...In the present study, we developed a highly sensitive and convenient biosensor consisting of gold nanoparticle （AuNP） probes and a gene chip to detect microRNAs （miRNAs）. Specific oligonucleotides were attached to the glass surface as capture probes for the target miRNAs, which were then detected via hybridization to the AuNP probes. The signal was amplified via the re- duction of HAuCI4 by H202. The use of a single AuNP probe detected 10 pmol L-1 of target miRNA. The recovery rate for miR-126 from fetal bovine serum was 81.5%-109.1%. The biosensor detection of miR-126 in total RNA extracted from lung cancer tissues was consistent with the quantitative PCR （qPCR） results. The use of two AuNP probes further improved the de- tection sensitivity such that even 1 fmol L-t of target miR-125a-5p was detectable. This assay takes less than 1 h to complete and the results can be observed by the naked eye, The platform simultaneously detected lung cancer related miR-126 and miR-125a-5p. Therefore, this low cost, rapid, and convenient technology could be used for ultrasensitive and robust visual miRNA detection.展开更多
Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-...Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-hairpin motif of ALKBH2 could play crucial roles in base-pair stability interrogation and damaged base flipping.Using chemical cross-linking strategy,we obtained two crystal structures of human ALKBH2 mutant bound to duplex DNA.The structural analysis suggests that theβ-hairpin motif is flexible in conformation and is likely to slide along the DNA duplex in local regions to search for damaged base.This study provides a new mechanistic insight into DNA damage detection by ALKBH2.展开更多
文摘DNA水凝胶是具有三维聚合物网络的高保水性材料。研究人员设计了多种DNA水凝胶交联制备方法,并通过向其中引入其他功能分子或与其他类型的功能材料相互结合,构建了具有优异性能的DNA水凝胶,受到了广泛关注。适配体是基于指数富集的配体系统进化(systematic evolution of ligands by exponential enrichment,SELEX)技术从随机寡核苷酸文库中筛选获得的对目标物质具有良好特异性与亲和力的寡核苷酸序列。适配体功能化的DNA水凝胶具有靶向范围广、稳定性好、易于修饰、操作简单和成本低等优点,得到了广泛应用。本文概述了构建适配体功能化的DNA水凝胶的基本设计原则与分类,重点介绍了适配体功能化的DNA水凝胶在食品安全检测中的最新策略,最后,讨论了适配体功能化的DNA水凝胶面临的挑战以及对未来的展望,旨在为其在食品安全领域的应用提供参考。
基金Project(200805032) supported by the Scientific Research Program of Marine Public Welfare Industry of China
文摘A comparative study on the phenotypic and genetic characteristics among Acidithiobacillus ferrooxidans （AF2）, a typic strain ATCC23270 and a previously isolated strain AF3 was performed. AF2 can use ferrous ion （Fe^2＋） or elemental sulfur （S^0） as sole energy source, but oxidizes So more effectively than Fe^2＋, which is different from ATCC23270 and AF3. The G＋C content of AF2 is 51.8% （molar fraction）, however, ATCC23270 and AF3 strains have G＋C content of 63.7% and 64.8% （molar fraction）, respectively. The DNA-DNA hybridization results show that AF2 has 41.53% and 52.38% genome similarity to ATCC 23270 and AF3, respectively, but AF3 has a high genome similarity of 89.86% to ATCC 23270 strain. Rusticyanin （rus） and subunit III of aa3-type cytochrome oxidase （coxC） genes are not detected in AF2, but Fe^2＋ oxidase （iro） gene can be detected. To understand the genomic organization of iro gene, a cosmid library of AF2 genome was constructed and iro gene-containing clone was screened. The sequencing result shows that although the nucleotide sequence of iro gene in AF2 is completely identical to that of ATCC 23270 strain, its genomic organization is different from that of ATCC 23270. In AF2, iro is located at downstream ofpurA gene, while it is located at downstream ofpetC-2 gene in ATCC 23270 strain. These results indicate that AF2 is a novel strain ofA. ferrooxidans, and that phenotypic differences among the strains ofA. ferrooxidans are closely correlated with their genetic polymorphisms.
基金support from the National Natural Science Foundation of China, Ministry of Health (2009ZX10004-301)Science and Technology Commission of Shanghai Munipality (0952nm04600)
文摘An electrochemical assay for single nucleotide polymorphisms (SNPs) genotyping is reported. Although electrochemical method is sensitive for DNA detection on surfaces, the ability of surface assay to precisely recognize DNA hybridization event is sacrificed to some extent due to the crowded confined surfaces environments that disfavor DNA hybridization. In the present study, we employed branched tetrahedron structure probes (TSPs) to replace regular linear single stranded DNA capture probes that were immobilized on solid surfaces. This three-dimensional DNA nanostructure lowers the density of immobilized DNA probes on confined surfaces, providing a hybridization environment that is similar to homogenous solution. This TSP-based electrochemical assay reveals excellent performance for SNPs genotyping with concentration as low as 1 nM.
基金supported by the National Natural Science Foundation of China(31071379)the Post-Doctoral Foundation of China(20090450616)a grant from"Yellow Crane"Special Talent Program of Wuhan
文摘Conventional rice breeding has long focused on exploiting the DNA sequence diversity.However,epigenetic diversity,reflected particularly in DNA methylation,can also contribute to phenotypic variation and should not be overlooked in rice breeding.In this study,20 parental lines of indica rice,which are widely used in hybrid rice breeding in China,were analyzed to investigate variations of DNA methylation and its inheritance.The results revealed a wide diversity in DNA methylation among these breeding lines.A positive correlation was seen between DNA methylation and genetic diversity.Furthermore,some of the methylated DNA was inherited in the subsequent generation,regardless of whether they were produced by selfing or hybrid-crossing.This study provides insight into the methylation patterns in rice,and suggests the importance of epigenetic diversity in rice breeding.
基金supported by the National Basic Research Program of China (2012CB933303)the National Natural Science Foundation of China (61571429, 61571077, 61401442)+2 种基金the Innovation Team of Henan University of Science and Technology (2015XTD003)the Science and Technology Commission of Shanghai Municipality (12441902600, 1402H233900)the Shanghai Clinical Center/Shanghai Xuhui Central Hospital, Chinese Academic of Sciences (BRC2012002)
文摘In the present study, we developed a highly sensitive and convenient biosensor consisting of gold nanoparticle （AuNP） probes and a gene chip to detect microRNAs （miRNAs）. Specific oligonucleotides were attached to the glass surface as capture probes for the target miRNAs, which were then detected via hybridization to the AuNP probes. The signal was amplified via the re- duction of HAuCI4 by H202. The use of a single AuNP probe detected 10 pmol L-1 of target miRNA. The recovery rate for miR-126 from fetal bovine serum was 81.5%-109.1%. The biosensor detection of miR-126 in total RNA extracted from lung cancer tissues was consistent with the quantitative PCR （qPCR） results. The use of two AuNP probes further improved the de- tection sensitivity such that even 1 fmol L-t of target miR-125a-5p was detectable. This assay takes less than 1 h to complete and the results can be observed by the naked eye, The platform simultaneously detected lung cancer related miR-126 and miR-125a-5p. Therefore, this low cost, rapid, and convenient technology could be used for ultrasensitive and robust visual miRNA detection.
基金financially supported by the Hundred Talents Program of the Chinese Academy of Sciences,Key Project of Chinese National Programs for Fundamental Research and Development(2009CB918502)
文摘Mammalian AlkB homologue 2(ALKBH2)is the primary housekeeping DNA demethylase,effectively repairing endogenously formed methylated lesions in double-stranded DNA.Our previous studies demonstrated that a hydrophobicβ-hairpin motif of ALKBH2 could play crucial roles in base-pair stability interrogation and damaged base flipping.Using chemical cross-linking strategy,we obtained two crystal structures of human ALKBH2 mutant bound to duplex DNA.The structural analysis suggests that theβ-hairpin motif is flexible in conformation and is likely to slide along the DNA duplex in local regions to search for damaged base.This study provides a new mechanistic insight into DNA damage detection by ALKBH2.
