DNA microarrays on a dendron-modified surface improve significantly the detection of single nucleotide variations in the p53 gene

Abstract

Selectivity and sensitivity in the detection of single nucleotide polymorphisms (SNPs) are among most important attributes to determine the performance of DNA microarrays. We previously reported the generation of a novel mesospaced surface prepared by applying dendron molecules on the solid surface. DNA microarrays that were fabricated on the dendron-modified surface exhibited outstanding performance for the detection of single nucleotide variation in the synthetic oligonucleotide DNA. DNA microarrays on the dendron-modified surface were subjected to the detection of single nucleotide variations in the exons 5–8 of the p53 gene in genomic DNAs from cancer cell lines. DNA microarrays on the dendron-modified surface clearly discriminated single nucleotide variations in hotspot codons with high selectivity and sensitivity. The ratio between the fluorescence intensity of perfectly matched duplexes and that of single nucleotide mismatched duplexes was >5–100 without sacrificing signal intensity. Our results showed that the outstanding performance of DNA microarrays fabricated on the dendron-modified surface is strongly related to novel properties of the dendron molecule, which has the conical structure allowing mesospacing between the capture probes. Our microarrays on the dendron-modified surface can reduce the steric hindrance not only between the solid surface and target DNA, but also among immobilized capture probes enabling the hybridization process on the surface to be very effective. Our DNA microarrays on the dendron-modified surface could be applied to various analyses that require accurate detection of SNPs.

Apoptosis-related mRNA expression profiles of ovarian cancer cell lines following cisplatin treatment

“…27 The 70-mer genespecific probes for 374 apoptosis-associated genes (Operon, Huntsville, AL, USA) were spotted on the DSC-activated slide. …”

Surface chemistries for antibody microarrays

“…Since the size of the dendron is controllable, an antibody can potentially be cross-linked at only one or two residues (47). While these slides have been shown to work well for DNA microarray assays (48)(49)(50)(51), we know of no reports on the utility of dendrons for antibody microarrays.…”

Uses of Dendrimers for DNA Microarrays

“…These particular arrays have been used to detect a successful discrimination ratio of 100:<1 between a complementary pair and three internal single-base mismatched pairs [22]. Single nucleotide variations in the exons 5-8 of the p53 gene in genomic DNAs from cancer cell lines were also detected with a high selectivity and sensitivity [23]. A wide range of temperature (37-50°C) is usable, and in general the hybridization behavior on these arrays is similar to the solution one [24].…”