과제정보
This work was supported by the Creative-Pioneering Researchers Program of Seoul National University and NRF-2020R1A5A1019141 and NRF-2019R1A2C2090896 of the National Research Foundation of Korea.
참고문헌
- Ashkin, A. (1997). Optical trapping and manipulation of neutral particles usinglasers. Proc. Natl. Acad. Sci. U. S. A. 94, 4853-4860. https://doi.org/10.1073/pnas.94.10.4853
- Ashkin, A., Dziedzic, J.M., Bjorkholm, J.E., and Chu, S. (1986). Observation of a single-beam gradient force optical trap for dielectric particles. Opt. Lett. 11, 288-290. https://doi.org/10.1364/OL.11.000288
- Basu, A., Bobrovnikov, D.G., and Ha, T. (2021a). DNA mechanics and its biological impact. J. Mol. Biol. 433, 166861. https://doi.org/10.1016/j.jmb.2021.166861
- Basu, A., Bobrovnikov, D.G., Qureshi, Z., Kayikcioglu, T., Ngo, T.T.M., Ranjan, A., Eustermann, S., Cieza, B., Morgan, M.T., Hejna, M., et al. (2021b). Measuring DNA mechanics on the genome scale. Nature 589, 462-467. https://doi.org/10.1038/s41586-020-03052-3
- Baumann, C.G., Bloomfield, V.A., Smith, S.B., Bustamante, C., Wang, M.D., and Block, S.M. (2000). Stretching of single collapsed DNA molecules. Biophys. J. 78, 1965-1978. https://doi.org/10.1016/S0006-3495(00)76744-0
- Ben-Shaul, A. (2013). Entropy, energy, and bending of DNA in viral capsids. Biophys. J. 104, L15-L17. https://doi.org/10.1016/j.bpj.2013.04.006
- Bhairosing-Kok, D., Groothuizen, F.S., Fish, A., Dharadhar, S., Winterwerp, H.H.K., and Sixma, T.K. (2019). Sharp kinking of a coiled-coil in MutS allows DNA binding and release. Nucleic Acids Res. 47, 8888-8898. https://doi.org/10.1093/nar/gkz649
- Binnig, G., Quate, C.F., and Gerber, C. (1986). Atomic force microscope. Phys. Rev. Lett. 56, 930-933. https://doi.org/10.1103/PhysRevLett.56.930
- Brahmachari, S. and Marko, J.F. (2018). DNA mechanics and topology. In Biomechanics in Oncology, C. Dong, N. Zahir, and K. Konstantopoulos, eds. (Cham: Springer International Publishing), pp. 11-39.
- Brinkers, S., Dietrich, H.R.C., de Groote, F.H., Young, I.T., and Rieger, B. (2009). The persistence length of double stranded DNA determined using dark field tethered particle motion. J. Chem. Phys. 130, 215105. https://doi.org/10.1063/1.3142699
- Brunet, A., Chevalier, S., Destainville, N., Manghi, M., Rousseau, P., Salhi, M., Salome, L., and Tardin, C. (2015a). Probing a label-free local bend in DNA by single molecule tethered particle motion. Nucleic Acids Res. 43, e72. https://doi.org/10.1093/nar/gkv201
- Brunet, A., Salome, L., Rousseau, P., Destainville, N., Manghi, M., and Tardin, C. (2018). How does temperature impact the conformation of single DNA molecules below melting temperature? Nucleic Acids Res. 46, 2074-2081. https://doi.org/10.1093/nar/gkx1285
- Brunet, A., Tardin, C., Salome, L., Rousseau, P., Destainville, N., and Manghi, M. (2015b). Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: a joint theory-experiment study. Macromolecules 48, 3641-3652. https://doi.org/10.1021/acs.macromol.5b00735
- Cai, X., Arias, D.S., Velazquez, L.R., Vexler, S., Bevier, A.L., and Fygenson, D.K. (2020). DNA nunchucks: nanoinstrumentation for single-molecule measurement of stiffness and bending. Nano Lett. 20, 1388-1395. https://doi.org/10.1021/acs.nanolett.9b04980
- Cassina, V., Manghi, M., Salerno, D., Tempestini, A., Iadarola, V., Nardo, L., Brioschi, S., and Mantegazza, F. (2016). Effects of cytosine methylation on DNA morphology: an atomic force microscopy study. Biochim. Biophys. Acta 1860(1 Pt A), 1-7. https://doi.org/10.1016/j.bbagen.2015.10.006
- Chen, H., Fu, H., Zhou, Z., and Yan, J. (2010). Non-harmonic DNA bending elasticity is revealed by statistics of DNA minicircle shapes. Int. J. Mod. Phys. B 24, 5475-5485. https://doi.org/10.1142/S0217979210056682
- Cloutier, T.E. and Widom, J. (2004). Spontaneous sharp bending of double-stranded DNA. Mol. Cell 14, 355-362. https://doi.org/10.1016/S1097-2765(04)00210-2
- Driessen, R.P.C., Sitters, G., Laurens, N., Moolenaar, G.F., Wuite, G.J.L., Goosen, N., and Dame, R.T. (2014). Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry 53, 6430-6438. https://doi.org/10.1021/bi500344j
- Du, Q., Smith, C., Shiffeldrim, N., Vologodskaia, M., and Vologodskii, A. (2005). Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. U. S. A. 102, 5397-5402. https://doi.org/10.1073/pnas.0500983102
- Fan, H.F., Ma, C.H., and Jayaram, M. (2018). Single-molecule tethered particle motion: stepwise analyses of site-specific DNA recombination. Micromachines (Basel) 9, 216. https://doi.org/10.3390/mi9050216
- Fields, A.P., Meyer, E.A., and Cohen, A.E. (2013). Euler buckling and nonlinear kinking of double-stranded DNA. Nucleic Acids Res. 41, 9881-9890. https://doi.org/10.1093/nar/gkt739
- Forster, T. (1946). [Energiewanderung und Fluoreszenz]. Naturwissenschaften 33, 166-175. German. https://doi.org/10.1007/BF00585226
- Forties, R.A., Bundschuh, R., and Poirier, M.G. (2009). The flexibility of locally melted DNA. Nucleic Acids Res. 37, 4580-4586. https://doi.org/10.1093/nar/gkp442
- Garcia, H.G., Grayson, P., Han, L., Inamdar, M., Kondev, J., Nelson, P.C., Phillips, R., Widom, J., and Wiggins, P.A. (2007). Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers 85, 115-130. https://doi.org/10.1002/bip.20627
- Geggier, S., Kotlyar, A., and Vologodskii, A. (2011). Temperature dependence of DNA persistence length. Nucleic Acids Res. 39, 1419-1426. https://doi.org/10.1093/nar/gkq932
- Geggier, S. and Vologodskii, A. (2010). Sequence dependence of DNA bending rigidity. Proc. Natl. Acad. Sci. U. S. A. 107, 15421-15426. https://doi.org/10.1073/pnas.1004809107
- Guilbaud, S., Salome, L., Destainville, N., Manghi, M., and Tardin, C. (2019). Dependence of DNA persistence length on ionic strength and ion type. Phys. Rev. Lett. 122, 028102. https://doi.org/10.1103/PhysRevLett.122.028102
- Ha, T., Enderle, T., Ogletree, D.F., Chemla, D.S., Selvin, P.R., and Weiss, S. (1996). Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl. Acad. Sci. U. S. A. 93, 6264-6268. https://doi.org/10.1073/pnas.93.13.6264
- Hagerman, P.J. (1988). Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17, 265-286. https://doi.org/10.1146/annurev.bb.17.060188.001405
- Han, L., Garcia, H.G., Blumberg, S., Towles, K.B., Beausang, J.F., Nelson, P.C., and Phillips, R. (2009). Concentration and length dependence of DNA looping in transcriptional regulation. PLoS One 4, e5621. https://doi.org/10.1371/journal.pone.0005621
- Harrington, R.E. (1993). Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis 14, 732-746. https://doi.org/10.1002/elps.11501401116
- Hellenkamp, B., Schmid, S., Doroshenko, O., Opanasyuk, O., Kuhnemuth, R., Rezaei Adariani, S., Ambrose, B., Aznauryan, M., Barth, A., Birkedal, V., et al. (2018). Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nat. Methods 15, 669-676. https://doi.org/10.1038/s41592-018-0085-0
- Hildebrandt, L.L., Preus, S., and Birkedal, V. (2015). Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discuss. 184, 131-142. https://doi.org/10.1039/c5fd00100e
- Jeong, J. and Kim, H.D. (2019). Base-pair mismatch can destabilize small DNA loops through cooperative kinking. Phys. Rev. Lett. 122, 218101. https://doi.org/10.1103/physrevlett.122.218101
- Jeong, J. and Kim, H.D. (2020). Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res. 48, 5147-5156. https://doi.org/10.1093/nar/gkaa207
- Kang, J., Jung, J., and Kim, S.K. (2014). Flexibility of single-stranded DNA measured by single-molecule FRET. Biophys. Chem. 195, 49-52. https://doi.org/10.1016/j.bpc.2014.08.004
- Kang, Y., Cho, C., Lee, K.S., Song, J.J., and Lee, J.Y. (2021). Single-molecule imaging reveals the mechanism underlying histone loading of Schizosaccharomyces pombe AAA+ ATPase Abo1. Mol. Cells 44, 79-87. https://doi.org/10.14348/molcells.2021.2242
- Kapanidis, A.N., Lee, N.K., Laurence, T.A., Doose, S., Margeat, E., and Weiss, S. (2004). Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc. Natl. Acad. Sci. U. S. A. 101, 8936-8941. https://doi.org/10.1073/pnas.0401690101
- Kim, C., Lee, O.C., Kim, J.Y., Sung, W., and Lee, N.K. (2015). Dynamic release of bending stress in short dsDNA by formation of a kink and forks. Angew. Chem. Int. Ed. Engl. 54, 8943-8947. https://doi.org/10.1002/anie.201502055
- Kim, S., Song, H.S., Yu, J., and Kim, Y.M. (2021a). MiT family transcriptional factors in immune cell functions. Mol. Cells 44, 342-355. https://doi.org/10.14348/molcells.2021.0067
- Kim, S.H., Kim, H., Jeong, H., and Yoon, T.Y. (2021b). Encoding multiple virtual signals in DNA barcodes with single-molecule FRET. Nano Lett. 21, 1694-1701. https://doi.org/10.1021/acs.nanolett.0c04502
- Kratky, O. and Porod, G. (1949). [Rontgenuntersuchung geloster Fadenmolekule]. Recl. Trav. Chim. Pays Bas 68, 1106-1122. German. https://doi.org/10.1002/recl.19490681203
- Le, T.T. and Kim, H.D. (2014). Probing the elastic limit of DNA bending. Nucleic Acids Res. 42, 10786-10794. https://doi.org/10.1093/nar/gku735
- Lee, D.H. and Schleif, R.F. (1989). In vivo DNA loops in araCBAD: size limits and helical repeat. Proc. Natl. Acad. Sci. U. S. A. 86, 476-480. https://doi.org/10.1073/pnas.86.2.476
- Lee, N.K., Kapanidis, A.N., Wang, Y., Michalet, X., Mukhopadhyay, J., Ebright, R.H., and Weiss, S. (2005). Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys. J. 88, 2939-2953. https://doi.org/10.1529/biophysj.104.054114
- Lee, O.C., Kim, C., Kim, J.Y., Lee, N.K., and Sung, W. (2016). Two conformational states in D-shaped DNA: effects of local denaturation. Sci. Rep. 6, 28239. https://doi.org/10.1038/srep28239
- Lerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, S.C., Borner, R., Sung Chung, H., Cordes, T., Craggs, T.D., et al. (2021). FRET-based dynamic structural biology: challenges, perspectives and an appeal for open-science practices. Elife 10, e60416. https://doi.org/10.7554/eLife.60416
- Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., and Richmond, T.J. (1997). Crystal structure of the nucleosome core particle at 2.8A resolution. Nature 389, 251-260. https://doi.org/10.1038/38444
- Marko, J.F. and Siggia, E.D. (1995). Stretching DNA. Macromolecules 28, 8759-8770. https://doi.org/10.1021/ma00130a008
- Murphy, M.C., Rasnik, I., Cheng, W., Lohman, T.M., and Ha, T. (2004). Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys. J. 86, 2530-2537. https://doi.org/10.1016/S0006-3495(04)74308-8
- Napoli, A., Zivanovic, Y., Bocs, C., Buhler, C., Rossi, M., Forterre, P., and Ciaramella, M. (2002). DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus. Nucleic Acids Res. 30, 2656-2662. https://doi.org/10.1093/nar/gkf377
- Nathan, D. and Crothers, D.M. (2002). Bending and flexibility of methylated and unmethylated EcoRI DNA. J. Mol. Biol. 316, 7-17. https://doi.org/10.1006/jmbi.2001.5247
- Ngo, T.T.M., Yoo, J., Dai, Q., Zhang, Q., He, C., Aksimentiev, A., and Ha, T. (2016). Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nat. Commun. 7, 10813. https://doi.org/10.1038/ncomms10813
- Pavlicek, J.W., Oussatcheva, E.A., Sinden, R.R., Potaman, V.N., Sankey, O.F., and Lyubchenko, Y.L. (2004). Supercoiling-induced DNA bending. Biochemistry 43, 10664-10668. https://doi.org/10.1021/bi0362572
- Peters, J.P. and Maher, L.J. (2018). Approaches for determining DNA persistence length using atomic force microscopy. In Bacterial Chromatin: Methods and Protocols, R.T. Dame, ed. (New York: Springer New York), pp. 211-256.
- Pongor, C.I., Bianco, P., Ferenczy, G., Kellermayer, R., and Kellermayer, M. (2017). Optical trapping nanometry of hypermethylated CpG-island DNA. Biophys. J. 112, 512-522. https://doi.org/10.1016/j.bpj.2016.12.029
- Prinsen, P. and Schiessel, H. (2010). Nucleosome stability and accessibility of its DNA to proteins. Biochimie 92, 1722-1728. https://doi.org/10.1016/j.biochi.2010.08.008
- Privalov, P.L., Dragan, A.I., and Crane-Robinson, C. (2009). The cost of DNA bending. Trends Biochem. Sci. 34, 464-470. https://doi.org/10.1016/j.tibs.2009.05.005
- Protozanova, E., Yakovchuk, P., and Frank-Kamenetskii, M.D. (2004). Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775-785. https://doi.org/10.1016/j.jmb.2004.07.075
- Purohit, P.K., Kondev, J., and Phillips, R. (2003). Mechanics of DNA packaging in viruses. Proc. Natl. Acad. Sci. U. S. A. 100, 3173-3178. https://doi.org/10.1073/pnas.0737893100
- Pyne, A.L.B., Noy, A., Main, K.H.S., Velasco-Berrelleza, V., Piperakis, M.M., Mitchenall, L.A., Cugliandolo, F.M., Beton, J.G., Stevenson, C.E.M., Hoogenboom, B.W., et al. (2021). Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat. Commun. 12, 1053. https://doi.org/10.1038/s41467-021-21243-y
- Qu, H., Wang, Y., Tseng, C.Y., and Zocchi, G. (2011). Critical torque for kink formation in double-stranded DNA. Phys. Rev. X 1, 021008.
- Ray, P.C., Fan, Z., Crouch, R.A., Sinha, S.S., and Pramanik, A. (2014). Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications. Chem. Soc. Rev. 43, 6370-6404. https://doi.org/10.1039/C3CS60476D
- Richmond, T.J. and Davey, C.A. (2003). The structure of DNA in the nucleosome core. Nature 423, 145-150. https://doi.org/10.1038/nature01595
- Roth, E., Glick Azaria, A., Girshevitz, O., Bitler, A., and Garini, Y. (2018). Measuring the conformation and persistence length of single-stranded DNA using a DNA origami structure. Nano Lett. 18, 6703-6709. https://doi.org/10.1021/acs.nanolett.8b02093
- Saran, R., Wang, Y., and Li, I.T.S. (2020). Mechanical flexibility of DNA: a quintessential tool for DNA nanotechnology. Sensors (Basel) 20, 7019. https://doi.org/10.3390/s20247019
- Sarangi, M.K., Zvoda, V., Holte, M.N., Becker, N.A., Peters, J.P., Maher, L.J., III, and Ansari, A. (2019). Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A. Nucleic Acids Res. 47, 2871-2883. https://doi.org/10.1093/nar/gkz022
- Satange, R., Chang, C.K., and Hou, M.H. (2018). A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res. 46, 6416-6434. https://doi.org/10.1093/nar/gky561
- Schafer, D.A., Gelles, J., Sheetz, M.P., and Landick, R. (1991). Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352, 444-448. https://doi.org/10.1038/352444a0
- Shon, M.J., Rah, S.H., and Yoon, T.Y. (2019). Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers. Sci. Adv. 5, eaav1697. https://doi.org/10.1126/sciadv.aav1697
- Shore, D., Langowski, J., and Baldwin, R.L. (1981). DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. U. S. A. 78, 4833-4837. https://doi.org/10.1073/pnas.78.8.4833
- Shroff, H., Reinhard, B.M., Siu, M., Agarwal, H., Spakowitz, A., and Liphardt, J. (2005). Biocompatible force sensor with optical readout and dimensions of 6 nm3. Nano Lett. 5, 1509-1514. https://doi.org/10.1021/nl050875h
- Shroff, H., Sivak, D., Siegel, J.J., McEvoy, A.L., Siu, M., Spakowitz, A., Geissler, P.L., and Liphardt, J. (2008). Optical measurement of mechanical forces inside short DNA loops. Biophys. J. 94, 2179-2186. https://doi.org/10.1529/biophysj.107.114413
- Slutsky, M. (2005). Diffusion in a half-space: from Lord Kelvin to path integrals. Am. J. Phys. 73, 308-314. https://doi.org/10.1119/1.1842734
- Smith, S.B., Cui, Y., and Bustamante, C. (1996). Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795-799. https://doi.org/10.1126/science.271.5250.795
- Smith, S.B., Finzi, L., and Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122-1126. https://doi.org/10.1126/science.1439819
- Strick, T.R., Allemand, J.F., Bensimon, D., Bensimon, A., and Croquette, V. (1996). The elasticity of a single supercoiled DNA molecule. Science 271, 1835-1837. https://doi.org/10.1126/science.271.5257.1835
- Tan, C., Terakawa, T., and Takada, S. (2016). Dynamic coupling among protein binding, sliding, and DNA bending revealed by molecular dynamics. J. Am. Chem. Soc. 138, 8512-8522. https://doi.org/10.1021/jacs.6b03729
- Vafabakhsh, R. and Ha, T. (2012). Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337, 1097-1101. https://doi.org/10.1126/science.1224139
- van der Vliet, P.C. and Verrijzer, C.P. (1993). Bending of DNA by transcription factors. Bioessays 15, 25-32. https://doi.org/10.1002/bies.950150105
- van Mameren, J., Gross, P., Farge, G., Hooijman, P., Modesti, M., Falkenberg, M., Wuite, G.J.L., and Peterman, E.J.G. (2009). Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. Proc. Natl. Acad. Sci. U. S. A. 106, 18231-18236. https://doi.org/10.1073/pnas.0904322106
- Vologodskii, A. and Frank-Kamenetskii, M.D. (2013). Strong bending of the DNA double helix. Nucleic Acids Res. 41, 6785-6792. https://doi.org/10.1093/nar/gkt396
- Wang, D.X., Wang, J., Wang, Y.X., Du, Y.C., Huang, Y., Tang, A.N., Cui, Y.X., and Kong, D.M. (2021). DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem. Sci. 12, 7602-7622. https://doi.org/10.1039/D1SC00587A
- Waters, J.T. and Kim, H.D. (2013). Equilibrium statistics of a surface-pinned semiflexible polymer. Macromolecules 46, 6659-6666. https://doi.org/10.1021/ma4011704
- Wiggins, P.A., van der Heijden, T., Moreno-Herrero, F., Spakowitz, A., Phillips, R., Widom, J., Dekker, C., and Nelson, P.C. (2006). High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol. 1, 137-141. https://doi.org/10.1038/nnano.2006.63
- Yakovchuk, P., Protozanova, E., and Frank-Kamenetskii, M.D. (2006). Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564-574. https://doi.org/10.1093/nar/gkj454
- Yeou, S. and Lee, N.K. (2021). Contribution of a DNA nick to DNA bendability depending on the bending force. Bull. Korean Chem. Soc. 2021 Jul 4 [Epub]. https://doi.org/10.1002/bkcs.12351
- Yoo, J. (2021). On the stability of protein-DNA complexes in molecular dynamics simulations using the CUFIX corrections. J. Korean Phys. Soc. 78, 461-466. https://doi.org/10.1007/s40042-021-00063-9
- Yoo, J., Kim, H., Aksimentiev, A., and Ha, T. (2016). Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Nat. Commun. 7, 11045. https://doi.org/10.1038/ncomms11045
- Zlatanova, J. and van Holde, K. (2006). Single-molecule biology: what is it and how does it work? Mol. Cell 24, 317-329. https://doi.org/10.1016/j.molcel.2006.10.017