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Updated: Mar 9, 2026

DNA Stable-Isotope Probing DNA-SIP
Published on: August 2, 2010
Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments
Jingfeng Gao1, Kailing Pan1, Hongyu Li1
1National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, China.
Abstract:
In this study, GelGreen™ was investigated as a replacement for SYBR® Safe to stain DNA in cesium chloride (CsCl) density gradients for DNA-stable isotope probing (SIP) experiments. Using environmental DNA, the usage of GelGreen™ was optimized for sensitivity compared to SYBR® Safe, its optimal concentration, detection limit for environmental DNA and its application in environmental DNA-SIP assay. Results showed that GelGreen™ was more sensitive than SYBR® Safe, while the optimal dosage (15X concentration) needed was approximately one-third of SYBR® Safe, suggesting that its sensitivity was three times more superior than SYBR® Safe. At these optimal parameters, the detection limit of GelGreen™-stained environmental DNA was as low as 0.2 μg, but the usage of 0.5 μg environmental DNA was recommended to produce a more consistent DNA band. In addition, a modified needle extraction procedure was developed to withdraw DNA effectively by fractionating CsCl density gradients into four or five fractions. The successful application of GelGreen™ staining with 13C-labeled DNA from enriched activated sludge suggests that this stain was an excellent alternative of SYBR® Safe in CsCl density gradients for DNA-SIP assays.
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