Compatible solutes from hyperthermophiles improve the quality of DNA microarrays.
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(R) 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.


CONCLUSIONS
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.
Mascellani
Nicoletta
N
Dipartimento di Morfologia ed Embriologia and DAMA, Data Mining for Analysis of DNA Microarrays, Telethon Facility, Università degli Studi di Ferrara, Ferrara, Italy. nicoletta.mascellani@gmail.com
Liu
Xiuping
X
Rossi
Simona
S
Marchesini
Jlenia
J
Valentini
Davide
D
Arcelli
Diego
D
Taccioli
Cristian
C
Helmer Citterich
Mauro
M
Liu
Chang-Gong
CG
Evangelisti
Rita
R
Russo
Giandomenico
G
Santos
Jorge M
JM
Croce
Carlo M
CM
Volinia
Stefano
S
D001105:Archaea / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012995:Solubility; D012997:Solvents / Q000737:chemistry*
D012997:Solvents; D004247:DNA