Effect of Target Length on Specificity and Sensitivity of Oligonucleotide Microarrays: A Comparison between Dendrimer and Modified PCR based Labelling Methods



Abdullah Gibriel*, 1, 2
1 Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Ahram Canadian University (ACU)
2 Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom


Article Metrics

CrossRef Citations:
0
Total Statistics:

Full-Text HTML Views: 615
Abstract HTML Views: 442
PDF Downloads: 223
Total Views/Downloads: 1280
Unique Statistics:

Full-Text HTML Views: 393
Abstract HTML Views: 198
PDF Downloads: 119
Total Views/Downloads: 710



© Abdullah Gibriel; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; ; Tel: + 202 23809703; Fax: + 202 23594097; E-mail: strsceap@googlemail.com


Abstract

DNA microarrays are widely used as end point detectors for gene expression analysis. Several methods have been developed for target labelling to enable quantification but without taking target length into consideration. Here we highlight the importance of choosing the optimum target length that would ensure specificity without compromising sensitivity of the assay. For this, eight plasmids that are identical to each other except for a closely related 23 bp unique reporter (UR) sequence were used to examine the hybridization efficiency for these URs. Targets of various lengths were generated and labelled as follows: full length and 330 bases transcripts using a dendrimer labelling method, 120 bp amplicons by the modified PCR end labelling method and synthetic labelled targets of 33 bases. This report also shows the advantages of using the modified PCR method over other labelling methods in generating labelled amplicons of the desired lengths to maximize hybridization efficiency.

Keywords: : Oligonucleotide microarrays, Secondary structure, Hybridization specificity, Sensitivity, PCR, Dendrimer.