The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
Annals of Microbiology volume 58, Article number: 313 (2008)
The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray were studied. Twelve virus-specific oligonucleotide probes for severe acute respiratory syndrome coronavirus (SARS-CoV) were divided into a high GC content group (≥ 50%) and a low GC content group (< 50%), and spotted onto four different chemically-modified glass surfaces: a poly-amine coating activated by 1,4-phenylene diisothiocyanate (Poly-Amine surface), an acrylic acid-co-acrylamide copolymer coating activated by 1-(3-dimethylamino propyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (AACA-Copolymer surface), a commercial Corning CMT-GAPS amino surface, and a Telechem SuperAmine amino surface. RNA samples from cultured SARS-CoV strain were labelled using direct cDNA labelling with restriction display in a single colour format. The background-subtracted signal intensities were analysed using two-way analysis of variance. The effects of glass surfaces on background-subtracted signal intensities were significant (p=0.003). Multiple comparisons showed that differences existed mainly between the AACA-Copolymer surface and the other glass surfaces, and that the AACA-Copolymer surface had the highest background-subtracted signal intensity. The probe GC content had no significant effect on signal intensities in the narrow range of GC content represented (p=0.07). The results suggested that the AACA-Copolymer surface may be a novel choice of microorganism survey based on long oligonucleotide microarray.
Bodrossy L., Sessitsch A. (2004). Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol., 7: 245–254.
Halliwell C.M., Cass A.E. (2001). A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces. Anal. Chem., 73: 2476–2483.
Hessner M.J., Meyer L., Tackes J., Muheisen S., Wang X. (2004). Immobilized probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics, 5: 53–61.
Lemarchand K., Masson L., Brousseau R. (2004). Molecular biology and DNA microarray technology for microbial quality monitoring of water. Crit. Rev. Microbiol., 30: 145–172.
Li L., Ma W.L., Zhu J., Shi R., Liu C.H., Chen J.K., Zheng W.L. (2003). A modified restriction display PCR method in sample-labeling of DNA microarray. J. Virol. Methods, 114: 71–75.
Mo X.Y., Ma W.L., Li L., Xu Q.L., Zhang Y.L., Zheng W.L. (2006). The effects of different sample labeling methods on signal intensities of a 60-mer diagnostic microarray. J. Virol. Methods, 134: 36–40.
Reed C., Fofanov V., Putonti C., Chumakov S., Slezak T., Fofanov Y. (2007). Effect of the mutation rate and background size on the quality of pathogen identification. Bioinformatics, 23: 2665–2671.
Sergeev N., Distler M., Courtney S., Al-Khaldi S.F., Volokhov D., Chizhikov V., Rasooly A. (2004). Multipathogen oligonucleotide microarray for environmental and biodefense applications. Biosens. Bioelectron., 20: 684–698.
Tembe W., Zavaljevski N., Bode E., Chase C., Geyer J., Wasieloski L., Benson G., Reifman J. (2007). Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics, 23: 5–13.
Vora G.J., Meador C.E., Stenger D.A., Andreadis J.D. (2004). Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Envir. Microbiol., 70: 3047–3054.
Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Ganem D., DeRisi J.L. (2002). Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci., 99: 15687–15692.
Wu Q.H., Ma W.L., Wang H.M., Mao X.M., Zhang B., Li L., Zheng W.L. (2005). Comparison of two amine-modified chemical platforms for DNA microarray preparation. Di Yi Jun Yi Da Xue Xue Bao, 25: 794–798.
Zhou J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol., 6: 288–294.
Zhou J., Thompson D.K. (2002). Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol., 13: 204–207.
These authors contributed equally to this paper.
About this article
Cite this article
Mo, X., Wu, Q., Hu, J. et al. The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray. Ann. Microbiol. 58, 313 (2008). https://doi.org/10.1007/BF03175336
- glass surfaces
- oligonucleotide probe
- diagnostic microarray