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GelGreen™在氯化铯密度梯度中用于DNA稳定同位素探测实验的应用。

Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments.

作者信息

Gao Jingfeng, Pan Kailing, Li Hongyu, Fan Xiaoyan, Sun Lixin, Zhang Shujun, Gao Yongqing

机构信息

National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, College of Environmental and Energy Engineering, Beijing University of Technology, Beijing, China.

Research and Development Center of Beijing Drainage Group Co., Ltd., Beijing, China.

出版信息

PLoS One. 2017 Jan 5;12(1):e0169554. doi: 10.1371/journal.pone.0169554. eCollection 2017.

DOI:10.1371/journal.pone.0169554
PMID:28056074
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5215936/
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.

摘要

在本研究中，对GelGreen™作为SYBR® Safe的替代品进行了研究，用于在氯化铯（CsCl）密度梯度中对DNA进行染色，以用于DNA稳定同位素探测（SIP）实验。使用环境DNA，与SYBR® Safe相比，对GelGreen™的使用进行了灵敏度优化，包括其最佳浓度、环境DNA的检测限及其在环境DNA-SIP分析中的应用。结果表明，GelGreen™比SYBR® Safe更灵敏，所需的最佳剂量（15倍浓度）约为SYBR® Safe的三分之一，这表明其灵敏度比SYBR® Safe高三倍。在这些最佳参数下，GelGreen™染色的环境DNA的检测限低至0.2μg，但建议使用0.5μg环境DNA以产生更一致的DNA条带。此外，开发了一种改良的针提取程序，通过将CsCl密度梯度分成四个或五个部分来有效地提取DNA。GelGreen™对富集活性污泥中13C标记的DNA染色的成功应用表明，这种染料是CsCl密度梯度中用于DNA-SIP分析的SYBR® Safe的极佳替代品。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/95c2b66cf7fc/pone.0169554.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/383338a5af9b/pone.0169554.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/c5064679a36e/pone.0169554.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/f92c6761ad83/pone.0169554.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/47ce677da0f6/pone.0169554.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/2df0d6af2b57/pone.0169554.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/05c968d4e497/pone.0169554.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/95c2b66cf7fc/pone.0169554.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/383338a5af9b/pone.0169554.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/c5064679a36e/pone.0169554.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/f92c6761ad83/pone.0169554.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/47ce677da0f6/pone.0169554.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/2df0d6af2b57/pone.0169554.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/05c968d4e497/pone.0169554.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e4e3/5215936/95c2b66cf7fc/pone.0169554.g007.jpg

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6
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10
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