Effect of co-axially hybridized gene targets on hybridization efficiency of microarrayed DNA probes

• Published in: Journal of the Taiwan Institute of Chemical Engineers Vol. 42; no. 1; pp. 5 - 12
• Main Authors: Jiang, Kai Ren, Huang, Jie-Len, Chen, Chia-Chun, Su, Hung-Ju, Wu, Jui-Chuang
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2011; Taiwan Institute of Chemical Engineers. Published by Elsevier Inc
• Subjects: DNA biochips; DNA microarray; DNA pre-hybridization; Hybridization efficiency; Molecular steric hindrance; DNA microarray; Hybridization efficiency; DNA biochips; DNA pre-hybridization; Molecular steric hindrance
• ISSN: 1876-1070; 1876-1089
• DOI: 10.1016/j.jtice.2010.04.012

The effect of relative size of two co-axially hybridized gene targets on the hybridization efficiency was studied for two DNA probe configurations and various probe concentrations. Each of two sets of microarrayed probes contained a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on the hybridization efficiency is investigated by comparing the dye signals between configurations of one-target and two-target hybridization scenarios. The results show that a low probe concentration gives better hybridization efficiency and the first-hybridization conducted by a shorter-size DNA target improves the hybridization efficiency of the second target coupling onto the same probe.