[Optimization of cDNA microarray fabrication].

Abstract

To optimize and screen the most suitable target gene length,concentration and printing solution in cDNA microarray, housekeeping genes, such as beta actin and GAPDH, were selected as targets and hepatitis B virus gene as negative control. The RT-PCR primers that spanned at least one intron and whose products were at between 189 bp and 1078 bp were designed with primer premier 5.0, so did the hepatitis B virus gene PCR primer. After polymerase chain reaction, the products were purified with ethanol and dissolved in 3xSSC, 50% DMSO and 0.5 mol/L carbonate buffer(pH=9.0)respectively. The concentrations of target genes were adjusted at 0.5 microg/microL, 1.0 microg/microL and 1.5 microg/microL. The hybridization signals had a good specificity. No signal showed in either negative control (HBV) or blank control (printing solution only). There was no significant difference in target gene lengths. The P value of beta actin (189 bp,491 bp,974 bp) and GAPDH (227 bp,552 bp,1078 bp) was 0.378 and 0.866 respectively. There was no significant difference among concentrations(P=0.648),too. However, the higher the concentration was, the stronger the signals would be. Among the three kinds of printing solution, 50% DMSO was the best (P=0.0001), while the other two had no difference by multi-comparison (P=0.142). The target gene at length between 200 bp and 1000 bp has got the same hybridization signals.50% DMSO printing solution and the target gene concentration of 0.5 microg/microl are suitable for good hybridization.