Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules

References

• Adams, D. E., Shekhtman, E. M., Zechiedrich, E. L., Schmid, M. B., & Cozzarelli, N. R. (1992). The role of topoisomerase-IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell, 71(2), 277–288. doi:10.1016/0092-8674(92)90356-H
   PubMed Web of Science ®Google Scholar
• Baldi, M. I., Benedetti, P., Mattoccia, E., & Tocchini-Valentini, G. P. (1980). In vitro catenation and decatenation of DNA and a novel eucaryotic ATP-dependent topoisomerase. Cell, 20(2), 461–467. doi:10.1016/0092-8674(80)90632-7
   PubMed Web of Science ®Google Scholar
• Burnier, Y., Dorier, J., & Stasiak, A. (2008). DNA supercoiling inhibits DNA knotting. Nucleic Acids Research, 36(15), 4956–4963. doi:10.1093/nar/gkn467
   PubMed Web of Science ®Google Scholar
• Cebrian, J., Castan, A., Martinez, V., Kadomatsu-Hermosa, M. J., Parra, C., Fernandez-Nestosa, M. J., Schaerer, C., Hernandez, P., Krimer, D. B., & Schvartzman, J. B. (2015). Direct evidence for the formation of precatenanes during DNA replication. Journal of Biological Chemistry, 290(22), 13725–13735. doi:10.1074/jbc.M115.642272
   PubMed Web of Science ®Google Scholar
• Champoux, J. J., & Been, M. D. (1980). Topoisomerases and the swivel problem. In B. Alberts (Ed.), Mechanistic studies of DNA replication and genetic recombination (pp. 809–815). Academic Press.
   Google Scholar
• Crisona, N. J., Strick, T. R., Bensimon, D., Croquette, V., & Cozzarelli, N. R. (2000). Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes & Development, 14(22), 2881–2892. doi:10.1101/gad.838900
   PubMed Web of Science ®Google Scholar
• de Vries, R. (2005). Evaluating changes of writhe in computer simulations of supercoiled DNA. Journal of Chemical Physics, 122(6), 064905. doi:10.1063/1.1846052
   PubMed Web of Science ®Google Scholar
• Frank-Kamenetskii, M. D., Lukashin, A. V., Anshelevich, V. V., & Vologodskii, A. V. (1985). Torsional and bending rigidity of the double helix from data on small DNA rings. Journal of Biomolecular Structure and Dynamics, 2(5), 1005–1012. doi:10.1080/07391102.1985.10507616
   PubMed Web of Science ®Google Scholar
• Fuller, F. B. (1971). The writhing number of a space curve. Proceedings of the National Academy of Sciences of Sciences, 68(4), 815–819. doi:10.1073/pnas.68.4.815
   PubMed Web of Science ®Google Scholar
• Funnell, B. E., Baker, T. A., & Kornberg, A. (1986). Complete enzymatic replication of plasmids containing the origin of the Escherichia coli chromosome. The Journal of Biological Chemistry, 261(12), 5616–5624.
   PubMed Web of Science ®Google Scholar
• Klenin, K., & Langowski, J. (2000). Computation of writhe in modeling of supercoiled DNA. Biopolymers, 54(5), 307–317. doi:10.1002/1097-0282(20001015)54:5<307::AID-BIP20>3.0.CO;2-Y
   PubMed Web of Science ®Google Scholar
• Kornberg, A., & Baker, T. A. (1992). DNA replication (2nd ed.). W.H. Freeman and Co.
   Google Scholar
• Kreuzer, K. N., & Cozzarelli, N. R. (1980). Formation and resolution of DNA catenanes by DNA gyrase. Cell, 20(1), 245–254. doi:10.1016/0092-8674(80)90252-4
   PubMed Web of Science ®Google Scholar
• Le, T. T., Gao, X., Park, S. H., Lee, J., Inman, J. T., Lee, J. H., Killian, J. L., Badman, R. P., Berger, J. M., & Wang, M. D. (2019). Synergistic coordination of chromatin torsional mechanics and topoisomerase activity. Cell, 179(3), 619–631. doi:10.1016/j.cell.2019.09.034
   PubMed Web of Science ®Google Scholar
• Liu, Z., Deibler, R. W., Chan, H. S., & Zechiedrich, L. (2009). The why and how of DNA unlinking. Nucleic Acids Research, 37(3), 661–671. doi:10.1093/nar/gkp041
   PubMed Web of Science ®Google Scholar
• Liu, Y., Perez, T., Li, W., Gunton, J. D., & Green, A. (2011). Statistical mechanics of helical wormlike chain model. Journal of Chemical Physics, 134(6), 065107. doi:10.1063/1.3548885
   PubMed Web of Science ®Google Scholar
• Marians, K. J., Minden, J. S., & Parada, C. (1986). Replication of superhelical DNAs in vitro. Prog Nucleic Acids Res Mol Biol, 33, 111–140.
   PubMed Web of Science ®Google Scholar
• Mariezcurrena, A., & Uhlmann, F. (2017). Observation of DNA intertwining along authentic budding yeast chromosomes. Genes & Development, 31(21), 2151–2161. doi:10.1101/gad.305557.117
   PubMed Web of Science ®Google Scholar
• Martinez-Robles, M. L., Witz, G., Hernandez, P., Schvartzman, J. B., Stasiak, A., & Krimer, D. B. (2009). Interplay of DNA supercoiling and catenation during the segregation of sister duplexes. Nucleic Acids Research, 37(15), 5126–5137. doi:10.1093/nar/gkp530
   PubMed Web of Science ®Google Scholar
• Nomidis, S. K., Skoruppa, E., Carlon, E., & Marko, J. F. (2019). Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. Physical Review. E, 99(3-1), 032414doi:10.1103/PhysRevE.99.032414
   PubMed Web of Science ®Google Scholar
• Peter, B. J., Ullsperger, C., Hiasa, H., Marians, K. J., & Cozzarelli, N. R. (1998). The structure of supercoiled intermediates in DNA replication. Cell, 94(6), 819–827. doi:10.1016/S0092-8674(00)81740-7
   PubMed Web of Science ®Google Scholar
• Racko, D., Benedetti, F., Dorier, J., Burnier, Y., & Stasiak, A. (2017). Molecular dynamics simulation of supercoiled, knotted, and catenated DNA molecules, including modeling of action of DNA gyrase. Methods in Molecular Biology, 1624, 339–372. doi:10.1007/978-1-4939-7098-8_24
   PubMedGoogle Scholar
• Rawdon, E. J., Dorier, J., Racko, D., Millett, K. C., & Stasiak, A. (2016). How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation. Nucleic Acids Research, 44(10), 4528–4538. doi:10.1093/nar/gkw311
   PubMed Web of Science ®Google Scholar
• Schalbetter, S. A., Mansoubi, S., Chambers, A. L., Downs, J. A., & Baxter, J. (2015). Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proceedings of the National Academy of Sciences, 112(33), E4565–4570. doi:10.1073/pnas.1505356112
   PubMed Web of Science ®Google Scholar
• Schvartzman, J. B., Hernandez, P., Krimer, D. B., Dorier, J., & Stasiak, A. (2019). Closing the DNA replication cycle: From simple circular molecules to supercoiled and knotted DNA catenanes. Nucleic Acids Research, 47(14), 7182–7198. doi:10.1093/nar/gkz586
   PubMed Web of Science ®Google Scholar
• Schvartzman, J. B., Martinez-Robles, M. L., Hernandez, P., & Krimer, D. B. (2013). The benefit of DNA supercoiling during replication. Biochemical Society Transactions, 41(2), 646–651. doi:10.1042/BST20120281
   PubMed Web of Science ®Google Scholar
• Schvartzman, J. B., & Stasiak, A. (2004). A topological view of the replicon. EMBO Reports, 5(3), 256–261. doi:10.1038/sj.embor.7400101
   PubMed Web of Science ®Google Scholar
• Stone, M. D., Bryant, Z., Crisona, N. J., Smith, S. B., Vologodskii, A., Bustamante, C., & Cozzarelli, N. R. (2003). Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proceedings of the National Academy of Sciences of Sciences , 100(15), 8654–8659. doi:10.1073/pnas.1133178100
   PubMed Web of Science ®Google Scholar
• Sundin, O., & Varshavsky, A. (1980). Terminal stages of SV40 DNA replication proceed via multiply intertwined catenated dimers. Cell, 21(1), 103–114. doi:10.1016/0092-8674(80)90118-X
   PubMed Web of Science ®Google Scholar
• Sundin, O., & Varshavsky, A. (1981). Arrest of segregation leads to accumulation of highly intertwined catenated dimers dissection of the final stages of SV40 DNA replication. Cell, 25(3), 659–669. doi:10.1016/0092-8674(81)90173-2
   PubMed Web of Science ®Google Scholar
• Ullsperger, C., Vologodskii, A. A., & Cozzarelli, N. R. (1995). Unlinking of DNA by topoisomerases during DNA replication. In D. M. J. Lilley & F. Eckstein (Eds.), Nucleic acids and molecular biology (pp. 115–142). Springer-Verlag.
   Google Scholar
• Vologodskii, A. (1992). Topology and physics of circular DNA. CRC Press.
   Google Scholar
• Vologodskii, A. (2011). Unlinking of supercoiled DNA catenanes by type IIA topoisomerases. Biophysical Journal, 101(6), 1403–1411. doi:10.1016/j.bpj.2011.08.011
   PubMed Web of Science ®Google Scholar
• Vologodskii, A. V., & Cozzarelli, N. R. (1993). Monte Carlo analysis of the conformation of DNA catenanes. Journal of Molecular Biology, 232(4), 1130–1140. doi:10.1006/jmbi.1993.1465
   PubMed Web of Science ®Google Scholar
• Vologodskii, A. V., Levene, S. D., Klenin, K. V., Frank-Kamenetskii, M., & Cozzarelli, N. R. (1992). Conformational and thermodynamic properties of supercoiled DNA. Journal of Molecular Biology, 227(4), 1224–1243. doi:10.1016/0022-2836(92)90533-P
   PubMed Web of Science ®Google Scholar
• Vologodskii, A., & Rybenkov, V. V. (2009). Simulation of DNA catenanes. Physical Chemistry Chemical Physics, 11(45), 10543–10552. doi:10.1039/b910812b
   PubMed Web of Science ®Google Scholar
• Wasserman, S. A., White, J. H., & Cozzarelli, N. R. (1988). The helical repeat of double-stranded DNA varies as a function of catenation and supercoiling. Nature, 334(6181), 448–450. doi:10.1038/334448a0
   PubMed Web of Science ®Google Scholar
• Witz, G., & Stasiak, A. (2010). DNA supercoiling and its role in DNA decatenation and unknotting. Nucleic Acids Research, 38(7), 2119–2133. doi:10.1093/nar/gkp1161
   PubMed Web of Science ®Google Scholar