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Single-molecule investigation of the impacts of fluorescent DNA-binding proteins on DNA mechanical properties |
| Yaxi Cheng(成雅茜)1,2, Shang Gao(高上)1,2, Xianqi Ye(叶贤其)1,2, Chuang Tan(谭创)1,2,†, and Jie Ma(马杰)1,2,‡ |
1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China |
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Abstract DNA imaging and visualization techniques are crucial in biological experiments and have also emerged as a powerful method for single-molecule studies. Traditional intercalating dyes (e.g., SYTOX, EtBr, GelRed) can stain DNA but may alter its structure and mechanical properties, and cause photocleavage. Recently, a novel fluorescent DNA-binding protein (FP-DBP) was introduced, which can stain DNA without sequence preference and without inducing photocleavage. In this study, using a custom-built magnetic tweezers system, we performed DNA stretching, twisting and unzipping experiments to compare the mechanical properties of DNA with and without two kinds of intercalating dyes (SYTOX Orange and GelRed) and mCherry FP-DBP. Our results show that mCherry FP-DBP does not affect DNA structure or mechanics, unlike SYTOX Orange and GelRed, making FP-DBP a promising tool for DNA visualization in single-molecule experiments.
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Received: 15 March 2025
Revised: 07 May 2025
Accepted manuscript online: 23 May 2025
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PACS:
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87.80.Nj
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(Single-molecule techniques)
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82.37.Rs
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(Single molecule manipulation of proteins and other biological molecules)
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87.14.gk
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(DNA)
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87.15.La
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(Mechanical properties)
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| Fund: This project was supported by the National Natural Science Foundation of China (Grant No. 32371284) and the Open Fund of the State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University (Grant No. OEMT-2024-ZTS-04). We also wish to thank for the support from the Physical Research Platform in the School of Physics, Sun Yat-sen University (Grant No. PRPSP, SYSU). |
Corresponding Authors:
Chuang Tan, Jie Ma
E-mail: tanch26@mail.sysu.edu.cn;majie6@mail.sysu.edu.cn
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Cite this article:
Yaxi Cheng(成雅茜), Shang Gao(高上), Xianqi Ye(叶贤其), Chuang Tan(谭创), and Jie Ma(马杰) Single-molecule investigation of the impacts of fluorescent DNA-binding proteins on DNA mechanical properties 2025 Chin. Phys. B 34 088702
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[1] Seeman N C, Chen J H and Kallenbach N R 1989 Electrophoresis 10 345
[2] Stellwagen N C 2009 Electrophoresis 30 S188
[3] Chrzanowska N M, Kowalewski J and Lewandowska M A 2020 Molecules 25 1864
[4] Matsumoto K and Hirose S 2004 J. Cell Sci. 117 3797
[5] Finkelstein I J, Visnapuu M L and Greene E C 2010 Nature 468 983
[6] King G A, Gross P, Bockelmann U, Modesti M, Wuite G J L and Peterman E J G 2013 Proc. Natl. Acad. Sci. USA 110 3859
[7] Zou Z, Liang J, Jia Q, Bai D, Xie W, Wu W, Tan C and Ma J 2023 Nanoscale 15 17443
[8] van Loenhout M T, de Grunt M V and Dekker C 2012 Science 338 94
[9] Ganji M, Kim S H, van der Torre J, Abbondanzieri E and Dekker C 2016 Nano Lett. 16 4699
[10] Almaqwashi A A, Paramanathan T, Rouzina I and Williams M C 2016 Nucleic Acids Res. 44 3971
[11] Biebricher A S, Heller I, Roijmans R F, Hoekstra T P, Peterman E J and Wuite G J 2015 Nat. Commun. 6 7304
[12] Celedon A, Wirtz D and Sun S 2010 J. Phys. Chem. B 114 16929
[13] Lee S, Oh Y, Lee J, Choe S, Lim S, Lee H S, Jo K and Schwartz D C 2015 Nucleic Acids Res. 44 e6
[14] Gao S, Liang J, Tan C and Ma J 2025 Nanoscale 17 3236
[15] Crisafuli F A, Ramos E B and Rocha M S 2015 Eur. Biophys. J. 44 1
[16] Kopuštas A, Ivanovait·e S, Rakickas T, Počevičiut·e E, Paksait·e J, Karvelis T, Zaremba M, Manakova E and Tutkus M 2021 Langmuir 37 3428
[17] Janissen R, Barth R, Polinder M, van der Torre J and Dekker C 2024 Nucleic Acids Res. 52 1677
[18] Odijk T 1995 Macromolecules 28 7016
[19] Fu H, Zhang C, Qiang X W, Yang Y J, Dai L, Tan Z J and Zhang X H 2020 Phys. Rev. Lett. 124 058101
[20] Bouchiat C, Wang M D, Allemand J F, Strick T, Block S M and Croquette V 1999 Biophys. J. 76 409
[21] Shon M J, Rah S H and Yoon T Y 2019 Sci. Adv. 5 eaav1697
[22] Yardimci H, Wang X, Loveland A B, Tappin I, Rudner D Z, Hurwitz J, van Oijen A M and Walter J C 2012 Nature 492 205
[23] Liu L F and Wang J C 1987 Proc. Natl. Acad. Sci. USA 84 7024
[24] Ma J, Bai L and Wang M D 2013 Science 340 1580
[25] Ma J, Tan C, Gao X, Fulbright R M Jr, Roberts J W and Wang M D 2019 Proc. Natl. Acad. Sci. USA 116 2583
[26] Ma J and Wang M D 2016 Biophys. Rev. 8 75 |
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