Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid
Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid
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DOI：
10.2144/05391rr01
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发表时间：
2005-07-01
期刊：
影响因子：
2.7
通讯作者：
Bergeron, MG
中科院分区：
文献类型：
--
作者：
Peytavi, R;Tang, LY;Bergeron, MG
排列在载玻片上的小寡核苷酸的杂交行为目前是不可预测的。为了检查捕获探针沿着靶核酸的杂交效率，设计20-mer寡核苷酸探针，使其在距从靶DNA扩增的两个重叠的402-和432-bp ermB产物的5'末端不同距离处杂交。将这些探针通过其5'端固定在载玻片上，并与两种标记产物杂交。对每个探针的杂交信号的评估揭示了与捕获链的5'突出端的长度和杂交信号强度的负相关性。进一步的实验表明，这种现象取决于捕获的DNA链的游离悬垂尾部与其互补链的再结合动力学。这项研究描绘了关键的可预测的参数，管理短捕获探针排列在载玻片上的杂交效率。这对于设计用于检测PCR产物和核苷酸多态性的阵列是最有用的。
The hybridization behavior of small oligonucleotides arrayed on glass slides is currently unpredictable. In order to examine the hybridization efficiency of capture probes along target nucleic acid, 20-mer oligonucleotide probes were designed to hybridize at different distances from the 5' end of two overlapping 402- and 432-bp ermB products amplified from the target DNA. These probes were immobilized via their 5' end onto glass slides and hybridized with the two labeled products. Evaluation of the hybridization signal for each probe revealed an inverse correlation with the length of the 5' overhanging end of the captured strand and the hybridization signal intensity. Further experiments demonstrated that this phenomenon is dependent on the reassociation kinetics of the free overhanging tail of the captured DNA strand with its complementary strand. This study delineates key predictable parameters that govern the hybridization efficiency of short capture probes arrayed on glass slides. This should be most useful for designing arrays for detection of PCR products and nucleotide polymorphisms.