Abstract
Adding ethidium bromide (EtBr) at low concentrations to RNA samples before running formaldehyde–agarose gels affords the advantages of checking RNA integrity and evaluating the quality of size-separation at any time during electrophoresis or immediately after either electrophoresis or blotted the separated RNA onto the membrane without significantly compromising mobility, transfer, or hybridization. In this study, we systematically examined the factors that affect the sensitivity of RNA prestaining by heating RNA samples that include EtBr before electrophoresis under different denaturation conditions. We also examined the efficiency of the hybridization of EtBr-prestained RNA with heterologous DNA probes. The results showed that the fluorescent intensity of EtBr-prestained RNA was affected not only by the EtBr concentration as previously reported but also by the RNA amount, denaturation time, and denaturation temperature. Prior staining of RNA with 40 μg/mL EtBr significantly decreased the efficiency of Northern blot hybridization with heterologous DNA probes. We propose that to best combine staining sensitivity and the efficiency of Northern blot hybridization with heterologous DNA probes, the concentration of EtBr used to prestain RNA should not exceed 30 μg/mL. The efficiency of the hybridization of EtBr-prestained RNA was affected not only by factors that affect staining sensitivity but also by the type of probe used.
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Acknowledgments
We thank Dr. Yusheng Zhu for generously providing us Lhcb1 gene probe, Dr. Chijun Li and Dr. Lefu Lan for help in preparation of the manuscript. This study was supported by grants from the National Natural Science Foundation of China (No. 31071334 and No. 30270124) and National Basic Research 973 Program (2009CB118502).
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Zhao, Y., Du, L. & Zhang, N. Sensitivity of Prestaining RNA with Ethidium Bromide Before Electrophoresis and Performance of Subsequent Northern Blots Using Heterologous DNA Probes. Mol Biotechnol 54, 204–210 (2013). https://doi.org/10.1007/s12033-012-9553-4
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DOI: https://doi.org/10.1007/s12033-012-9553-4