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. 2008;58(2):313. doi: 10.1007/BF03175336

The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray

Xiaoyang Mo 1,✉, Qinghua Wu 2, Junjian Hu 1, Wenli Ma 2, Min Wei 2, Wuzhou Yuan 1, Yuequn Wang 1, Yongqin Li 1, Yun Deng 1, Xiushan Wu 1
PMCID: PMC7097383  PMID: 32226355

Abstract

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.

Key words: glass surfaces, oligonucleotide probe, ANOVA, diagnostic microarray

Footnotes

These authors contributed equally to this paper.

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