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A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses
  • ISSN号:1674-0769
  • 期刊名称:《中国病毒学:英文版》
  • 时间:0
  • 分类:R373[医药卫生—病原生物学;医药卫生—基础医学]
  • 作者机构:[1]Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China, [2]The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, Tianjin 300071, China, [3]School of Computing, National University of Singapore, 3 Science Drive 2, 117543, Singapore, [4]Tianfin Key Laboratory of Microbial Functional Genomics, College of Life Sciences, Nankai University, Tianjin 300071, China
  • 相关基金:Research funding for undergraduate students of Nankai University; NSFC grant (30270308); NSFC grant (30370053); Tianjin grant (05YFJZJC01301). We are grateful to Professor Huxin Diao for valuable suggestions. We thank Jun Tang and Jia Xie for the critical reading of our manuscript.
中文摘要:

脱氧核糖核酸微数组被承认了为病毒的病原体的察觉代表一条有希望的途径。然而,为当前的数组设计的探针能盖住仅仅给定的病毒的变体的部分,那能导致假否定或模糊的数据。如果所有变体将被盖住,为更多的探针的要求将显示许多更高的点密度;数组的因此更高的费用。这里,我们为 oligonucleotide 设计开发了新策略。用类型我人的免疫不全病毒(HIV-1 ) 作为一个例子梭织基因,我们设计了数组探针;在 silico 验证了优化参数。结果证明 oligo 数字显著地被减少与存在方法作比较,当时特性;杂交效率遗体未经触动。在减少 oligo 数字的这个方法的采纳能为脱氧核糖核酸微数组增加察觉能力,;将为做的显著地更低的生产费用穿薄片。

英文摘要:

DNA microarrays have been acknowledged to represent a promising approach for the detection of viral pathogens. However, the probes designed for current arrays could cover only part of the given viral variants, that could result in false-negative or ambiguous data. If all the variants are to be covered, the requirement for more probes would render much higher spot density and thus higher cost of the arrays. Here we have developed a new strategy for oligonucleotide probe design. Using type Ⅰ human immunodeficiency virus (HIV-1) tat gene as an example, we designed the array probes and validated the optimized parameters in silico. Results show that the oligo number is significantly reduced comparing with the existing methods, while specificity and hybridization efficiency remain intact. The adoption of this method in reducing the oligo numbers could increase the detection capacity for DNA microarrays, and would significantly lower the manufacturing cost for making array chips.

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期刊信息
  • 《中国病毒学:英文版》
  • 中国科技核心期刊
  • 主管单位:中国科学院
  • 主办单位:中国科学院武汉病毒研究所 中国微生物学会
  • 主编:陈新文
  • 地址:湖北省武汉市武昌区小洪山中区44号
  • 邮编:430071
  • 邮箱:info@virosin.org
  • 电话:027-87199157
  • 国际标准刊号:ISSN:1674-0769
  • 国内统一刊号:ISSN:42-1760/Q
  • 邮发代号:38-351
  • 获奖情况:
  • 湖北省第1、2、3、4、5、6届优秀期刊,中国科学技术学会 优秀国际科技期刊,2012年中国国际影响力优秀学术期刊
  • 国内外数据库收录:
  • 美国化学文摘(网络版),波兰哥白尼索引,荷兰医学文摘,美国生物医学检索系统,美国剑桥科学文摘,美国生物科学数据库,中国中国科技核心期刊
  • 被引量:208