Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
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DOI：
10.1093/nar/gku556
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发表时间：
2014-09
影响因子：
14.9
通讯作者：
Westerlund F
中科院分区：
文献类型：
--
作者：
Nilsson AN;Emilsson G;Nyberg LK;Noble C;Stadler LS;Fritzsche J;Moore ER;Tegenfeldt JO;Ambjörnsson T;Westerlund F
我们展示了一种单DNA分子光学作图分析方法，能够将特定的大肠杆菌菌株从其他菌株中分离出来。该检测是基于荧光染料YOYO-1和AT特异性抗生素netropsin的竞争结合。光学图谱是通过在纳米流体通道中拉伸DNA分子而可视化的。我们对实验条件进行了优化，以获得包含尽可能多信息的可重现条形码。我们实现了一种多配体转移矩阵方法来计算已知DNA序列的理论条形码。我们的方法将以前的两种类型的配体竞争结合的理论方法扩展到多种类型的配体，并引入了一种递归方法，允许用标准的计算机浮点格式计算长条形码。一种特定的大肠杆菌菌株(CCUG 10979)的鉴定是基于利用发展的理论将50-160千碱基的实验DNA片段映射到理论基因组上。我们的识别协议引入了两个理论结构：用于最佳实验-理论匹配的P值和信息得分阈值。所开发的方法为细菌种类和菌株的鉴定提供了一个新的光学作图工具箱。该方案不需要细菌培养或DNA扩增，从而实现了对细菌病原体的超快鉴定。
We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50–160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
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影响因子：
3.8
作者：
DiCera, E;Kong, Y
通讯作者：
Kong, Y
影响因子：
56.9
作者：
SCHWARTZ, DC;LI, XJ;WANG, YK
通讯作者：
WANG, YK
影响因子：
14.9
作者：
RYE, HS;YUE, S;GLAZER, AN
通讯作者：
GLAZER, AN
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
8.4
作者：
Neely, Robert K.;Dedecker, Peter;Hofkens, Johan
通讯作者：
Hofkens, Johan