嗜热菌中的相容性溶质可提高DNA微阵列的质量。

Compatible solutes from hyperthermophiles improve the quality of DNA microarrays.

作者信息

Mascellani Nicoletta, Liu Xiuping, Rossi Simona, Marchesini Jlenia, Valentini Davide, Arcelli Diego, Taccioli Cristian, Helmer Citterich Mauro, Liu Chang-Gong, Evangelisti Rita, Russo Giandomenico, Santos Jorge M, Croce Carlo M, Volinia Stefano

机构信息

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

出版信息

BMC Biotechnol. 2007 Nov 23;7:82. doi: 10.1186/1472-6750-7-82.

DOI:10.1186/1472-6750-7-82

PMID:18036223

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2248183/

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(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.

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.

摘要

背景

DNA微阵列是DNA和RNA研究中使用最广泛的技术平台之一，因此与微阵列灵敏度和特异性相关的问题在生命科学中具有普遍重要性。相容性溶质源自嗜热微生物，可使此类微生物在环境压力条件下存活。相容性溶质对包括DNA在内的生物大分子具有稳定作用。

结果

我们在此报告，嗜热微生物产生的相容性溶质提高了Affymetrix GeneChip(R)阵列杂交缓冲液的性能。实验设置包括在广泛的相容性溶质浓度范围内对恒定RNA进行独立杂交。使用Affymetrix专有质量控制系统和开源Bioconductor套件提供的专门统计工具评估阵列质量与相容性溶质的相关性。