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Complexities for High-Temperature Two-Handed Tile Self-assembly 高温双手瓷砖自组装的复杂性
Pub Date : 2017-09-24 DOI: 10.1007/978-3-319-66799-7_7
R. Schweller, Andrew Winslow, Tim Wylie
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引用次数: 12
The Design Space of Strand Displacement Cascades with Toehold-Size Clamps 带脚尺寸夹具的链位移级联的设计空间
Pub Date : 2017-09-24 DOI: 10.1007/978-3-319-66799-7_5
Boya Wang, Chris Thachuk, A. Ellington, D. Soloveichik
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引用次数: 9
Simplifying Analyses of Chemical Reaction Networks for Approximate Majority 简化近似多数化学反应网络的分析
Pub Date : 2017-09-24 DOI: 10.1007/978-3-319-66799-7_13
A. Condon, Monir Hajiaghayi, D. Kirkpatrick, Ján Manuch
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引用次数: 7
Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates 具有局部环境依赖的阿伦尼乌斯速率的DNA结构动力学的基本阶跃模型的参数推断
Pub Date : 2017-09-24 DOI: 10.1007/978-3-319-66799-7_12
Sedigheh Zolaktaf, Frits Dannenberg, X. Rudelis, A. Condon, Joseph M. Schaeffer, Mark W. Schmidt, Chris Thachuk, E. Winfree
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引用次数: 10
Automated, Constraint-Based Analysis of Tethered DNA Nanostructures 捆绑DNA纳米结构的自动约束分析
Pub Date : 2017-09-24 DOI: 10.1007/978-3-319-66799-7_1
Matthew R. Lakin, Andrew Phillips
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引用次数: 2
Chemical Boltzmann Machines 化学玻尔兹曼机
Pub Date : 2017-07-19 DOI: 10.1007/978-3-319-66799-7_14
W. Poole, Andrés Ortiz-Muñoz, A. Behera, N. S. Jones, T. Ouldridge, E. Winfree, Manoj Gopalkrishnan
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引用次数: 28
Robust Detection in Leak-Prone Population Protocols 易泄漏群体协议中的鲁棒检测
Pub Date : 2017-06-29 DOI: 10.1007/978-3-319-66799-7_11
Dan Alistarh, Bartłomiej Dudek, A. Kosowski, D. Soloveichik, P. Uznański
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引用次数: 20
Mapping contacts between unpurified human progesterone receptor and the hormone response element of mouse mammary tumor virus. 未纯化的人孕酮受体与小鼠乳腺肿瘤病毒激素应答元件的定位联系。
Pub Date : 1989-12-01 DOI: 10.1089/dna.1989.8.703
B Kühnel, D el-Ashry, D P Edwards, S K Nordeen
Binding of steroid hormone receptors to specific recognition sites of hormone-inducible genes is one of the events required for hormonal regulation of gene transcription. We have employed an immunoprecipitation assay to map the interaction between unpurified human progesterone receptors from crude nuclear extracts of T47D cells and the hormone response element of the mouse mammary tumor virus (MMTV). DNase I footprints and methylation interference patterns are similar to those reported with highly purified rabbit progesterone receptors, suggesting that both human and rabbit receptors recognize similar features in the hormone response element. More importantly, these patterns suggest that if other factors are associated with unpurified nuclear receptor, they do not alter the contacts made by receptor nor do they make contacts themselves with MMTV DNA in a manner detected by DNase I or methylation interference assays. The sites of interaction of receptors bound with the clinically important progestin antagonist, RU 486, are comparable to those observed with an agonist-receptor complex. These results suggest that the antagonist prevents receptor action at a step after its recognition and binding to specific sites on a hormone-responsive enhancer element.
类固醇激素受体与激素诱导基因的特异性识别位点结合是激素调控基因转录所需的事件之一。我们采用免疫沉淀法绘制了从T47D细胞粗核提取物中提取的未纯化的人孕酮受体与小鼠乳腺肿瘤病毒(MMTV)激素反应元件之间的相互作用。dna酶I足迹和甲基化干扰模式与高度纯化的兔孕酮受体相似,表明人和兔受体在激素反应元件中识别出相似的特征。更重要的是,这些模式表明,如果其他因素与未纯化的核受体有关,它们不会改变受体的接触,也不会以DNA酶I或甲基化干扰试验检测到的方式与MMTV DNA发生接触。受体与临床重要的黄体酮拮抗剂RU 486结合的相互作用位点与激动剂-受体复合物的相互作用位点相当。这些结果表明,拮抗剂在识别并结合到激素反应增强元件上的特定位点后,会阻止受体的作用。
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引用次数: 5
Analysis of possible repressor elements in the 5'-flanking region of the human beta-globin gene. 人-珠蛋白基因5'侧区可能的抑制元件分析。
Pub Date : 1989-12-01 DOI: 10.1089/dna.1989.8.715
J M Krakowsky, E S Panke, R F Lee, J McNeish, S S Potter, J B Lingrel

Human beta-globin gene expression is confined predominantly to the adult with little or no expression of this gene occurring during embryonic or fetal life. The lack of expression of this gene in embryonic and fetal erythroid tissue could be due to the absence of required positive regulatory factors in these cells or the presence of negative regulatory factors which prevent expression of the adult globin gene. To test the repressor model, we have used a gel electrophoretic mobility shift assay to identify regions in the human beta-globin gene which bind proteins found in K562 cells, a cell line that expresses embryonic and fetal globins but not adult beta-globin. DNA fragments comprising the entire human beta-globin gene were assayed using nuclear proteins from K562 cells, and four regions were found that bind proteins. These are located within the 5'-flanking region, within the first and second introns, and at the 3'-flanking region of the gene. Previous studies have suggested the presence of potential repressor sites 5' of exon 2. For this reason, we examined whether the lack of the binding regions in the 5'-flanking sequence allow expression of the human beta-globin gene in transgenic mice during embryonic life. beta-globin gene expression was confined to adult life, indicating that if a transcriptional repressor is responsible for inactivating this gene in embryonic tissue, it is not regulated solely by sequences upstream from -122 bp in the 5'-flanking region of the human beta-globin gene.

人类β -珠蛋白基因的表达主要局限于成人,在胚胎或胎儿期很少或不表达该基因。该基因在胚胎和胎儿红系组织中缺乏表达可能是由于这些细胞中缺乏所需的正调节因子或存在阻止成人珠蛋白基因表达的负调节因子。为了测试抑制因子模型,我们使用了凝胶电泳迁移转移法来鉴定人类β -珠蛋白基因中与K562细胞中发现的蛋白质结合的区域,K562细胞表达胚胎和胎儿珠蛋白,但不表达成人β -珠蛋白。利用K562细胞的核蛋白分析了包含整个人类β -珠蛋白基因的DNA片段,发现了四个结合蛋白的区域。它们位于基因的5'侧区,第一和第二内含子内,以及3'侧区。先前的研究表明外显子2的潜在抑制位点5'的存在。出于这个原因,我们研究了5'侧序列中缺乏结合区域是否允许在胚胎期转基因小鼠中表达人-珠蛋白基因。β -珠蛋白基因的表达仅限于成人,这表明如果一个转录抑制因子在胚胎组织中负责使该基因失活,那么它并不仅仅受人类β -珠蛋白基因5'侧区- 122bp上游序列的调控。
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引用次数: 5
Superpolylinkers in cloning and expression vectors. 克隆和表达载体中的超多连接子。
Pub Date : 1989-12-01 DOI: 10.1089/dna.1989.8.759
J Brosius

Versatile DNA polylinkers of more than 300 bp were constructed. They contain the recognition sequences of all restriction enzymes--whether known or still to be discovered--that recognize palindromic hexamers. In addition to these 64 uninterrupted hexameric recognition sites, a number of sites containing interrupted palindromes and nonpalindromic sequences and two recognition sequences with 8 bp are present. Polylinkers (in several variants) were inserted into frequently utilized Escherichia coli cloning vectors such as pBluescript (yielding pSLJ10, pSL250, pSL260, pSL270, and pSL300), pUC18/pUC19 (yielding pSL180 and pSL190, respectively), or pUC118/pUC119 (yielding pSL1180 and pSL1190, respectively). A subtle color discrimination between presence and absence of insert in pSL300 (mid-blue to light-blue or white) was seen in a number of test ligations. The mid-blue color that is generated by pSL300 is presumably due to translational restarts. A different intergenic region for translational restarts was used in plasmids pSL251, pSL261, pSL271, and pSL301. The polylinker was also inserted into expression vector pUC120, yielding pSE1200, and into expression vector pKK233-2, yielding pSE220 and a shortened version thereof, pSE280. Finally, the polylinker was inserted into pTrc99A, resulting in pSE380, which carries a lac repressor gene. This expands the use of the expression system beyond lacIq strains to other bacterial hosts. These versatile vectors have broad applications in genetic engineering.

构建了长度超过300 bp的多功能DNA多连锁体。它们包含所有识别回文六聚体的限制性内切酶的识别序列——无论是已知的还是尚待发现的。除了这64个不间断的六聚体识别位点外,还存在一些包含中断的回文序列和非回文序列的位点以及两个8bp的识别序列。将多个变体中的多连接子插入到常用的大肠杆菌克隆载体中,如pBluescript(产pSLJ10、pSL250、pSL260、pSL270和pSL300)、pUC18/pUC19(分别产pSL180和pSL190)或pUC118/pUC119(分别产pSL1180和pSL1190)。在许多测试结扎中可以看到pSL300中插入物存在和不存在之间的微妙颜色区分(中蓝色到浅蓝色或白色)。pSL300产生的中蓝色大概是由于平移重启造成的。在质粒pSL251、pSL261、pSL271和pSL301中使用了不同的基因间区域进行翻译重启。将多联子插入表达载体pUC120中,得到pSE1200;将多联子插入表达载体pKK233-2中,得到pSE220及其缩短版pSE280。最后,将该多联体插入pTrc99A中,得到携带lac抑制基因的pSE380。这将表达系统的使用范围从lacIq菌株扩展到其他细菌宿主。这些多功能载体在基因工程中有着广泛的应用。
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引用次数: 155
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DNA (Mary Ann Liebert, Inc.)
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