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Virologica Sinica, 22 (4) : 326-335, 2007
Research Article
A Strategy to Optimize the Oligo-Probes for Microarray-based Detection of Viruses*
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.Tianjin Key Laboratory of Microbial Functional Genomics, College of Life Sciences, Nankai University, Tianjin 300071, China
 Correspondence:
(248.77KB)  
Abstract
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.
  Published online: 20 Aug 2007
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