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Open Access Methodology article

Compatible solutes from hyperthermophiles improve the quality of DNA microarrays

Nicoletta Mascellani1, Xiuping Liu2, Simona Rossi1, Jlenia Marchesini1, Davide Valentini15, Diego Arcelli3, Cristian Taccioli1, Mauro Helmer Citterich3, Chang-Gong Liu2, Rita Evangelisti1, Giandomenico Russo3, Jorge M Santos46, Carlo M Croce2 and Stefano Volinia12*

Author Affiliations

1 Dipartimento di Morfologia ed Embriologia and DAMA, Data Mining for Analysis of DNA Microarrays, Telethon Facility, Università degli Studi di Ferrara, Ferrara, Italy

2 Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA

3 Nucleic Acid Facility, IDI – IRCCS, Roma, Italy

4 STAB VIDA Lda, Oeiras, Portugal

5 Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden

6 ECBio S.A., Oeiras, Portugal

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BMC Biotechnology 2007, 7:82  doi:10.1186/1472-6750-7-82

Published: 23 November 2007

Abstract

Background

DNA microarrays are among the most widely used technical platforms for DNA and RNA studies, and issues related to microarrays sensitivity and specificity are therefore of general importance in life sciences. Compatible solutes are derived from hyperthermophilic microorganisms and allow such microorganisms to survive in environmental and stressful conditions. Compatible solutes show stabilization effects towards biological macromolecules, including DNA.

Results

We report here that compatible solutes from hyperthermophiles increased the performance of the hybridization buffer for Affymetrix GeneChip® arrays. The experimental setup included independent hybridizations with constant RNA over a wide range of compatible solute concentrations. The dependence of array quality and compatible solute was assessed using specialized statistical tools provided by both the proprietary Affymetrix quality control system and the open source Bioconductor suite.

Conclusion

Low concentration (10 to 25 mM) of hydroxyectoine, potassium mannosylglycerate and potassium diglycerol phosphate in hybridization buffer positively affected hybridization parameters and enhanced microarrays outcome. This finding harbours a strong potential for the improvement of DNA microarray experiments.