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

Kai Ren Jiang; Jie-Len Huang; Chia-Chun Chen; Hung-Ju Su; Jui-Chuang Wu

doi:10.1016/j.jtice.2010.04.012

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

J Taiwan Inst Chem Eng. 2011 Jan;42(1):5-12. doi: 10.1016/j.jtice.2010.04.012. Epub 2010 Oct 30.

Authors

Kai Ren Jiang¹, Jie-Len Huang², Chia-Chun Chen², Hung-Ju Su², Jui-Chuang Wu¹

Affiliations

¹ Chemical Engineering Department, Chung Yuan Christian University, Chung Li, Tao Yuan 32023, Taiwan.
² Biomedical Engineering Center, Industrial Technology Research Institute, Chu Tung, Hsin Chu 31040, Taiwan.

Abstract

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.

Keywords: DNA biochips; DNA microarray; DNA pre-hybridization; Hybridization efficiency; Molecular steric hindrance.