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Agarose Gel Purification of PCR Products for Denaturing Gradient Gel Electrophoresis Results in GC-Clamp Deletion

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Abstract

The 16S ribosomal RNA (rRNA) gene of marine archaeal samples was amplified using a nested PCR approach, and the V3 region of 16S rRNA gene of crab gut microbiota (CGM) was amplified using the V3 universal primer pair with a guanine and cytosine (GC)-clamp. Unpurified PCR products (UPPs), products purified from reaction solution (PPFSs), and products purified from gel (PPFGs) of above two DNA samples were used for denaturing gradient gel electrophoresis (DGGE) analysis, respectively. In contrast to almost identical band patterns shared by both the UPP and PPFS, the PPFGs were barely observed on the DGGE gel for both the marine archaea and CGM samples. Both PPFS and PPFG of CGM V3 regions were subjected to cloning. A small amount of positive clones was obtained for PPFS, but no positive clones were observed for PPFG. The melt curve and direct sequencing analysis of PPFS and PPFG of E. coli V3 region indicated that the Tm value of PPFG (82.35 ± 0.19 °C) was less than that of PPFS (83.81 ± 0.11 °C), and the number of shorter GC-clamps was significant higher in PPFG than in PPFS. The ultraviolet exposure experiment indicated that the ultraviolet was not responsible for the deletion of the GC-clamps. We conclude that the gel purification method is not suitable for DGGE PCR products or even other GC-rich DNA samples.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 41376135), Doctoral Fund of Ministry of Education of China (20133104110006), Innovation Program of Shanghai Municipal Education Commission (14ZZ144), China, and Construction Program of Shanghai Committee of Science and Technology (11DZ2280300), China.

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Authors and Affiliations

  1. College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China

    Guowei Sun, Jinzhou Xiao, Man Lu, Hongming Wang, Xiaobing Chen, Yongxin Yu, Yingjie Pan & Yongjie Wang

  2. Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, 201306, China

    Guowei Sun, Jinzhou Xiao, Man Lu, Hongming Wang, Xiaobing Chen, Yongxin Yu, Yingjie Pan & Yongjie Wang

  3. Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, China

    Guowei Sun, Jinzhou Xiao, Man Lu, Hongming Wang, Xiaobing Chen, Yongxin Yu, Yingjie Pan & Yongjie Wang

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  1. Guowei Sun
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  2. Jinzhou Xiao
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Correspondence to Yongjie Wang.

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Sun, G., Xiao, J., Lu, M. et al. Agarose Gel Purification of PCR Products for Denaturing Gradient Gel Electrophoresis Results in GC-Clamp Deletion. Appl Biochem Biotechnol 175, 400–409 (2015). https://doi.org/10.1007/s12010-014-1282-7

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  • DOI: https://doi.org/10.1007/s12010-014-1282-7

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