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Magnetic tweezers are a high precision single-molecule manipulation instrument. A gradient magnetic field is used to generate a force on the order of pN, acting on biomolecule-tethered superparamagnetic beads and to manipulate them. By tracking the bead with an inverted microscope, an imaging system and an image process software, one can obtain the extension length information of the biomolecules, thus can study the mechanism and dynamics of the molecules at a single molecule level. Magnetic tweezers include transverse magnetic tweezers (TMT) which are cheap and simple, and longitudinal magnetic tweezers (LMT) which are expensive and complicated. As the traditional TMT can only track the long biomolecule-tethered beads and their spatial resolution is poorer than that of the LMT according to the error theory of magnetic tweezers and the experimental results, the TMT is not so widely used. To solve this problem, we utilize a light sheet to illuminate the beads only in TMT, and then observe the bead sticking on the lateral surface. The tracking error on the extension axis is 4 nm, which is very small. Then we track and obtain the “folding-unfolding” state transition trace of a hairpin DNA. The hairpin DNA is inserted into a 0.5 μm dsDNA. This experiment proves its ability to study short DNA, RNA or protein. Instead of the fully folded and unfolded state, we observe a semi-stable state at the 1/3 length of the hairpin. The semi-stable state is precisely at the place of the CG rich area of the hairpin, so the CG rich area should be the reason for the semi-stable state. Then we use the 16 μm λ -DNA to further test the novel TMT system. Having obtained the stretching curve of the dsDNA, we fit the length-force data with the worm-like-chain model. The fitted persistence length of the dsDNA is (47±2) nm, which is consistent with the result in the literature. Finally, we compare the noise of traditional TMT, novel TMT and LMT with that of short and long dsDNA at weak and strong force, and we find that at weak force, the novel TMT distinctly enhances the resolution to the LMT level; while at strong force, the resolution of the novel TMT is about half that of the LMT. The results above prove that (1) the short DNA, RNA or protein can be studied by the novel TMT, which extends the application scope of the instrument; (2) the resolution of TMT is enhanced distinctly under weak and strong force, making the novel TMT competent of more experiments.
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[2] Neuman K C, Nagy A 2008 Nat. Methods 5 491
[3] Wang S, Zheng H Z, Zhao Z Y, Lu Y, Xu C H 2013 Acta Phys. Sin. 62 168703 (in Chinese) [王爽, 郑海子, 赵振业, 陆越, 徐春华 2013 62 168703]
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[5] Madariaga-Marcos J, Hormeno S, Pastrana C L, Fisher G L M, Dillingham M S, Moreno-Herrero F 2018 Nanoscale 10 4579
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[7] Comstock M J, Whitley K D, Jia H, Sokoloski J, Lohman T M, Ha T, Chemla Y R 2015 Science 348 352
[8] Arslan S, Khafizov R, Thomas C D, Chemla Y R, Ha T 2015 Science 348 344
[9] Neupane K, Foster D A N, Dee D R, Yu H, Wang F, Woodside M T 2016 Science 352 239
[10] Righini M, Lee A, Canari-Chumpitaz C, Lionberger T, Gabizon R, Coello Y Tinoco I, Bustamante C 2018 Proc. Natl. Acad. Sci. USA 115 1286
[11] Sun B, Johnson D S, Patel G, Smith B Y, Pandey M, Patel S S, Wang M D 2011 Nature 478 132
[12] Yuan G, Le S, Yao M, Qian H, Zhou X, Yan J, Chen H 2017 Angew. Chem. Int. Edit. 56 5490
[13] Zhang X, Chen H, Fu H, Doyle P S, Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103
[14] Zhang X H, Chen H, Le S M, Rouzina I, Doyle P S, Yan J 2013 Proc. Natl. Acad. Sci. USA 110 3865
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[17] Lee C Y, Lou J Z, Wen K K, McKane M, Eskin S G, Ono S, Chien S, Rubenstein P A, Zhu C, McIntire L V 2013 Proc. Natl. Acad. Sci. USA 110 5022
[18] Lin W X, Ma J B, Nong D G, Xu C H, Zhang B, Li J H, Jia Q, Dou S X, Ye F F, Xi X G, Lu Y, Li M 2017 Phys. Rev. Lett. 119 138102
[19] Blosser T R, Yang J G, Stone M D, Narlikar G J, Zhuang X 2009 Nature 462 1022
[20] Yasuda R, Noji H, Kinosita K, Yoshida M 1998 Cell 93 1117
[21] Qi Z, Redding S, Lee J Y, Gibb B, Kwon Y, Niu H, Gaines W A, Sung P, Greene E C 2015 Cell 160 856
[22] Sun Y, Sato O, Ruhnow F, Arsenault M E, Ikebe M, Goldman Y E 2010 Nat. Struct. Mol. Biol. 17 485
[23] Lu H P, Xun L, Xie X S 1998 Science 282 1877
[24] Danilowicz C, Coljee V W, Bouzigues C, Lubensky D K, Nelson D R, Prentiss M 2003 Proc. Natl. Acad. Sci. USA 100 1694
[25] Smith S B, Finzi L, Bustamante C 1992 Science 258 1122
[26] Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[27] Marko J F, Siggia E D 1995 Macromolecules 28 8759
[28] Wang X L, Zhang X H, Wei K J, Sun B, Li M 2008 Acta Phys. Sin. 57 3905 (in Chinese) [王晓玲, 张兴华, 魏孔吉, 孙博, 李明 2008 57 3905]
[29] Sarkar R, Rybenkov V V 2016 Front. Phys. 4 48
[30] Li J H, Lin W X, Zhang B, Nong D G, Ju H P, Ma J B, Xu C H, Ye F F, Xi X G, Li M, Lu Y, Dou S X 2016 Nucleic Acids Res. 44 4330
[31] Kim K, Saleh O A 2009 Nucleic Acids Res. 37 e136
[32] Bosco A, Camunas-Soler J, Ritort F 2014 Nucleic Acids Res. 42 2064
[33] Strick T R, Allemand J F, Bensimon D, Bensimon A, Croquette V 1996 Science 271 1835
[34] Abels J A, Moreno-Herrero F, van der Heijden T, Veenhuizen P T M, Bruinink M M, Dekker C, Dekker N H 2005 Biophys. J. 88 2737
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[1] Ha T, Enderle T, Ogletree D F, Chemla D S, Selvin P R, Weiss S 1996 Proc. Natl. Acad. Sci. USA 93 6264
[2] Neuman K C, Nagy A 2008 Nat. Methods 5 491
[3] Wang S, Zheng H Z, Zhao Z Y, Lu Y, Xu C H 2013 Acta Phys. Sin. 62 168703 (in Chinese) [王爽, 郑海子, 赵振业, 陆越, 徐春华 2013 62 168703]
[4] Qian H, Chen H, Yan J 2016 Acta Phys. Sin. 65 188706 (in Chinese) [钱辉, 陈虎, 严洁 2016 65 188706]
[5] Madariaga-Marcos J, Hormeno S, Pastrana C L, Fisher G L M, Dillingham M S, Moreno-Herrero F 2018 Nanoscale 10 4579
[6] Cheng W, Arunajadai S G, Moffitt J R, Tinoco I J, Bustamante C 2011 Science 333 1746
[7] Comstock M J, Whitley K D, Jia H, Sokoloski J, Lohman T M, Ha T, Chemla Y R 2015 Science 348 352
[8] Arslan S, Khafizov R, Thomas C D, Chemla Y R, Ha T 2015 Science 348 344
[9] Neupane K, Foster D A N, Dee D R, Yu H, Wang F, Woodside M T 2016 Science 352 239
[10] Righini M, Lee A, Canari-Chumpitaz C, Lionberger T, Gabizon R, Coello Y Tinoco I, Bustamante C 2018 Proc. Natl. Acad. Sci. USA 115 1286
[11] Sun B, Johnson D S, Patel G, Smith B Y, Pandey M, Patel S S, Wang M D 2011 Nature 478 132
[12] Yuan G, Le S, Yao M, Qian H, Zhou X, Yan J, Chen H 2017 Angew. Chem. Int. Edit. 56 5490
[13] Zhang X, Chen H, Fu H, Doyle P S, Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103
[14] Zhang X H, Chen H, Le S M, Rouzina I, Doyle P S, Yan J 2013 Proc. Natl. Acad. Sci. USA 110 3865
[15] Sun B, Wei K J, Zhang B, Zhang X H, Dou S X, Li M, Xi X G 2008 EMBO J. 27 3279
[16] Li W, Chen P, Yu J, Dong L, Liang D, Feng J, Yan J, Wang P Y, Li Q, Zhang Z, Li M, Li G 2016 Mol. Cell 64 120
[17] Lee C Y, Lou J Z, Wen K K, McKane M, Eskin S G, Ono S, Chien S, Rubenstein P A, Zhu C, McIntire L V 2013 Proc. Natl. Acad. Sci. USA 110 5022
[18] Lin W X, Ma J B, Nong D G, Xu C H, Zhang B, Li J H, Jia Q, Dou S X, Ye F F, Xi X G, Lu Y, Li M 2017 Phys. Rev. Lett. 119 138102
[19] Blosser T R, Yang J G, Stone M D, Narlikar G J, Zhuang X 2009 Nature 462 1022
[20] Yasuda R, Noji H, Kinosita K, Yoshida M 1998 Cell 93 1117
[21] Qi Z, Redding S, Lee J Y, Gibb B, Kwon Y, Niu H, Gaines W A, Sung P, Greene E C 2015 Cell 160 856
[22] Sun Y, Sato O, Ruhnow F, Arsenault M E, Ikebe M, Goldman Y E 2010 Nat. Struct. Mol. Biol. 17 485
[23] Lu H P, Xun L, Xie X S 1998 Science 282 1877
[24] Danilowicz C, Coljee V W, Bouzigues C, Lubensky D K, Nelson D R, Prentiss M 2003 Proc. Natl. Acad. Sci. USA 100 1694
[25] Smith S B, Finzi L, Bustamante C 1992 Science 258 1122
[26] Smith S B, Cui Y, Bustamante C 1996 Science 271 795
[27] Marko J F, Siggia E D 1995 Macromolecules 28 8759
[28] Wang X L, Zhang X H, Wei K J, Sun B, Li M 2008 Acta Phys. Sin. 57 3905 (in Chinese) [王晓玲, 张兴华, 魏孔吉, 孙博, 李明 2008 57 3905]
[29] Sarkar R, Rybenkov V V 2016 Front. Phys. 4 48
[30] Li J H, Lin W X, Zhang B, Nong D G, Ju H P, Ma J B, Xu C H, Ye F F, Xi X G, Li M, Lu Y, Dou S X 2016 Nucleic Acids Res. 44 4330
[31] Kim K, Saleh O A 2009 Nucleic Acids Res. 37 e136
[32] Bosco A, Camunas-Soler J, Ritort F 2014 Nucleic Acids Res. 42 2064
[33] Strick T R, Allemand J F, Bensimon D, Bensimon A, Croquette V 1996 Science 271 1835
[34] Abels J A, Moreno-Herrero F, van der Heijden T, Veenhuizen P T M, Bruinink M M, Dekker C, Dekker N H 2005 Biophys. J. 88 2737
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