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Nucleic Acids Research 2005 33(10):e90; doi:10.1093/nar/gni087
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Published online 6 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

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

Soon Jin Oh, Jimin Ju, Byung Chul Kim, Eunsil Ko, Bong Jin Hong, Jae-Gahb Park1, Joon Won Park and Kwan Yong Choi*

Division of Molecular and Life Sciences, Pohang University of Science and Technology Pohang 790-784, Korea 1Research Institute and Hospital, National Cancer Center Goyang, 411-764, Korea

*To whom correspondence should be addressed. Tel: +82 54 279 2295; Fax: +82 54 279 8290; Email: kchoi{at}postech.ac.kr

Received April 9, 2005. Revised May 16, 2005. Accepted May 16, 2005.

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.


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