A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses

• 作 者: Zhuo ZHOU Zhi-xun DOU Chen ZHA
• 机 构: Department of Biochemistry and Molecular Biology,The Key Laboratory of Bioactive Materials,School of
• 出 处: 中国病毒学
• 发表日期: 2004年期
• 关键词: Microarray Oligonucleotide Viral Detection
• 基金项目: 国家自然科学基金;国家自然科学基金;Research funding for undergraduate students of Nankai University;Tianjin grant

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.