Comprehensive viral oligonucleotide probe design using conserved protein regions

Jabado, Omar J.; Liu, Yang; Conlan, Sean; Quan, P. Lan; Hegyi, Hédi; Lussier, Yves; Briese, Thomas; Palacios, Gustavo; Lipkin, W. I.

Hybridizing a WNV isolate of known sequence allowed prediction of probe-viral hybrid strength and correlation to fluorescence data. To predict hybrids with high accuracy, Smith-Waterman alignments of the virus sequence against microarray probes were generated using the EMBOSS bioinformatics suite (26) . The number of mismatches was calculated for each expected probe-target pair. The change in Gibbs free energy at 658C (hybridization temperature) was calculated using PairFold version 1.7 (27) as a separate measure of probe-template binding strength. PairFold employs a dynamic programming algorithm to compute the minimum free energy structure (excluding pseudo-knots); the standard free energy model is used (28) with empirical nearest neighbor energies (29) . The arrays were visualized with an Agilent slide scanner, then processed with the quantile normalization technique (30) . SPSS version 14 was used for statistics and data plots (http://www.spss.com/), fluorescence data is available as supplementary material.