Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

doi:10.1007/s40242-019-9223-1

高等学校化学研究 ›› 2019, Vol. 35 ›› Issue (6): 1119-1123.doi: 10.1007/s40242-019-9223-1

Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

ZHANG Bin^1,2, JIANG Jiquan^1,3, YUAN Ying¹, GUAN Yifu¹

1. Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, P. R. China;
2. Department of Plastic Surgery, School of Stomatology, China Medical University, Shenyang 110009, P. R. China;
3. Department of Biochemistry and Molecular Biology, College of Medical Laboratory and Technology, Harbin Medical University(Daqing), Daqing 163000, P. R. China

收稿日期:2019-08-19 修回日期:2019-09-08 出版日期:2019-12-01 发布日期:2019-11-29
通讯作者: GUAN Yifu E-mail:yfguan@cmu.edu.cn
基金资助:
Supported by the National Natural Science Foundation of China(No.31670821).

Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

ZHANG Bin^1,2, JIANG Jiquan^1,3, YUAN Ying¹, GUAN Yifu¹

1. Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110122, P. R. China;
2. Department of Plastic Surgery, School of Stomatology, China Medical University, Shenyang 110009, P. R. China;
3. Department of Biochemistry and Molecular Biology, College of Medical Laboratory and Technology, Harbin Medical University(Daqing), Daqing 163000, P. R. China

Received:2019-08-19 Revised:2019-09-08 Online:2019-12-01 Published:2019-11-29
Contact: GUAN Yifu E-mail:yfguan@cmu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China(No.31670821).

摘要/Abstract

摘要： The fluorescence dye SYBR Green II(SG II) has been frequently used in rolling circle amplification(RCA) based analyses of nucleic acids. However, a good amount of inconsistencies have been reported in regards the quality and reproducibility of RCA reactions. To properly examine this experimental issue, here we utilized a series of synthetic oligonucleotides and circular templates to investigate the impact of SG II in RCA reactions. The results indicate that SG II enables a strong fluorescence signal only when complexing with guanosine(G) residue. In RCA reactions, long single-stranded RCA products, enriched with G residues, result in higher fluorescence emission when compared with the addition of other nucleotide residues. These results suggest that the nucleotide composition of the reaction can affect the amplification results and, eventually, can lead to inconsistent fluorescence of the RCA products. This work indicates that particular attention should be given when circular templates are designed for the quantitative analysis of nucleic acids, to further allow the signal reproducibility of RCA-based experiments.

关键词: Rolling circle amplification, SYBR Green II, Nucleotide-biased, Fluorescence emission

Abstract: The fluorescence dye SYBR Green II(SG II) has been frequently used in rolling circle amplification(RCA) based analyses of nucleic acids. However, a good amount of inconsistencies have been reported in regards the quality and reproducibility of RCA reactions. To properly examine this experimental issue, here we utilized a series of synthetic oligonucleotides and circular templates to investigate the impact of SG II in RCA reactions. The results indicate that SG II enables a strong fluorescence signal only when complexing with guanosine(G) residue. In RCA reactions, long single-stranded RCA products, enriched with G residues, result in higher fluorescence emission when compared with the addition of other nucleotide residues. These results suggest that the nucleotide composition of the reaction can affect the amplification results and, eventually, can lead to inconsistent fluorescence of the RCA products. This work indicates that particular attention should be given when circular templates are designed for the quantitative analysis of nucleic acids, to further allow the signal reproducibility of RCA-based experiments.

Key words: Rolling circle amplification, SYBR Green II, Nucleotide-biased, Fluorescence emission

ZHANG Bin, JIANG Jiquan, YUAN Ying, GUAN Yifu. Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification[J]. 高等学校化学研究, 2019, 35(6): 1119-1123.

参考文献

[1] Dong H., Wang C., Xiong Y., Lu H., Ju H., Zhang X., Biosens. Bioelectron., 2013, 41, 348
[2] Ali M. M., Li F., Zhang Z., Zhang K., Kang D. K., Ankrum J. A., Le X. C., Zhao W., Chem. Soc. Rev., 2014, 43(10), 3324
[3] Xu W., Xie X., Li D., Yang Z., Li T., Liu X., Small, 2012, 8(12), 1846
[4] Polidoros A. N., Pasentsis K., Tsaftaris A. S., Biotechniques, 2006, 41(1), 35
[5] Kaocharoen S., Wang B., Tsui K. M., Trilles L., Kong F., Meyer W., Electrophoresis, 2008, 29(15), 3183
[6] Dahl F., Baner J., Gullberg M., Mendel-Hartvig M., Landegren U., Nilsson M., Proc. Natl. Acad. Sci. USA, 2004, 101(13), 4548
[7] Jin G., Wang C., Yang L., Li X., Guo L., Qiu B., Lin Z., Chen G., Biosens. Bioelectron., 2015, 63, 166
[8] Chen J., Tong P., Lin Y., Lu W., He Y., Lu M., Zhang L., Chen G., Analyst, 2015, 140(3), 907
[9] Stougaard M., Juul S., Andersen F. F., Knudsen B. R., Integr. Biol.(Camb.), 2011, 3(10), 982
[10] Wei H., Zhao G., Hu T., Tang S., Jiang J., Hu B., Guan Y., Sci. Rep., 2016, 6, 32560
[11] Wei H., Hu B., Tang S., Zhao G., Guan Y., Sci. Rep., 2016, 6, 37477
[12] Shi H., Mao X., Chen X., Wang Z., Wang K., Zhu X., Biosens. Bioelectron., 2017, 91, 136
[13] Chen Z., Duan X., Wei H., Tang S., Xu C., Li Y., Guan Y., Zhao G., Acta Biochim. Biophys. Sin.(Shanghai), 2018, 50(5), 507
[14] Meng F., Miao P., Wang B., Tang Y., Yin J., Anal. Chim. Acta, 2016, 943, 58
[15] Zhang Z., Ali M. M., Eckert M. A., Kang D. K., Chen Y. Y., Sender L. S., Fruman D. A., Zhao W., Biomaterials, 2013, 34(37), 9728
[16] Ciftci S., Neumann F., Hernandez-Neuta I., Hakhverdyan M., Balint A., Herthnek D., Madaboosi N., Nilsson M., Sci. Rep., 2019, 9(1), 2872
[17] Takahashi H., Ohkawachi M., Horio K., Kobori T., Aki T., Matsumura Y., Nakashimada Y., Okamura Y., Sci. Rep., 2018, 8(1), 7770
[18] Lee C. Y., Kang K. S., Park K. S., Park H. G., Mikrochim. Acta, 2017, 185(1), 53
[19] Battaglia C., Salani G., Consolandi C., Bernardi L. R., de Bellis G., Biotechniques, 2000, 29(1), 78
[20] Tuma R. S., Beaudet M. P., Jin X., Jones L. J., Cheung C. Y., Yue S., Singer V. L., Anal. Biochem., 1999, 268(2), 278
[21] Lane A. N., Chaires J. B., Gray R. D., Trent J. O., Nucleic. Acids Res., 2008, 36(17), 5482
[22] Chambers V. S., Marsico G., Boutell J. M., Di Antonio M., Smith G. P., Balasubramanian S., Nat. Biotechnol., 2015, 33(8), 877
[23] Searle M.S., Williams H. E., Gallagher C. T., Grant R. J., Stevens M. F., Org. Biomol. Chem., 2004, 2(6), 810

Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

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