Single-molecule investigation of the impacts of fluorescent DNA-binding proteins on DNA mechanical properties

doi:10.1088/1674-1056/addcbd

中国物理B ›› 2025, Vol. 34 ›› Issue (8): 88702-088702.doi: 10.1088/1674-1056/addcbd

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

收稿日期:2025-03-15 修回日期:2025-05-07 接受日期:2025-05-23 出版日期:2025-07-17 发布日期:2025-08-05
通讯作者: Chuang Tan, Jie Ma E-mail:tanch26@mail.sysu.edu.cn;majie6@mail.sysu.edu.cn
基金资助:
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).

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

Received:2025-03-15 Revised:2025-05-07 Accepted:2025-05-23 Online:2025-07-17 Published:2025-08-05
Contact: Chuang Tan, Jie Ma E-mail:tanch26@mail.sysu.edu.cn;majie6@mail.sysu.edu.cn
Supported by:
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).

1. 2025-088702-SI.pdf(853KB)

摘要/Abstract

摘要： 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.

关键词: fluorescent DNA-binding protein, single-molecule, magnetic tweezers, DNA mechanical properties, intercalating dye

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.

Key words: fluorescent DNA-binding protein, single-molecule, magnetic tweezers, DNA mechanical properties, intercalating dye

中图分类号: (Single-molecule techniques)

87.80.Nj

82.37.Rs (Single molecule manipulation of proteins and other biological molecules) 87.14.gk (DNA) 87.15.La (Mechanical properties)

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[J]. 中国物理B, 2025, 34(8): 88702-088702.

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Single-molecule investigation of the impacts of fluorescent DNA-binding proteins on DNA mechanical properties

Single-molecule investigation of the impacts of fluorescent DNA-binding proteins on DNA mechanical properties

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