1. Stodola, J. L. & Burgers, P. M. Mechanism of Lagging-Strand DNA Replication in Eukaryotes. in 117–133 (2017). doi:10.1007/978-981-10-6955-0_6.
2. Guilliam, T. A. & Yeeles, J. T. P. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Critical Reviews in Biochemistry and Molecular Biology 55, 469–481 (2020).
3. Prelich, G. et al. Functional identity of proliferating cell nuclear antigen and a DNA polymerase-δ auxiliary protein. Nature 326, 517–520 (1987).
4. Choe, K. N. & Moldovan, G. Review Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork. Molecular Cell 65, 380–392 (2017).
5. Stodola, J. L. & Burgers, P. M. Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nature Structural & Molecular Biology 23, 402–409 (2016).
6. Sallmyr, A., Rashid, I., Bhandari, S. K., Naila, T. & Tomkinson, A. E. Human DNA ligases in replication and repair. DNA Repair 93, 102908 (2020).
7. Howes, T. R. L. & Tomkinson, A. E. DNA Ligase I, the Replicative DNA Ligase. in 327–341 (2012). doi:10.1007/978-94-007-4572-8_17.
8. Johnson, A. & O’Donnell, M. DNA Ligase: Getting a Grip to Seal the Deal. Current Biology 15, R90–R92 (2005).
9. Pascal, J. M., O’Brien, P. J., Tomkinson, A. E. & Ellenberger, T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432, 473–478 (2004).
10. Levin, D. S., Bai, W., Yao, N., O’Donnell, M. & Tomkinson, A. E. An interaction between DNA ligase I and proliferating cell nuclear antigen: Implications for Okazaki fragment synthesis and joining. Proceedings of the National Academy of Sciences 94, 12863–12868 (1997).
11. Montecucco, A. et al. DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: identification of a common targeting mechanism for the assembly of replication factories. The EMBO Journal 17, 3786–3795 (1998).
12. Tom, S., Henricksen, L. A., Park, M. S. & Bambara, R. A. DNA Ligase I and Proliferating Cell Nuclear Antigen Form a Functional Complex. Journal of Biological Chemistry 276, 24817–24825 (2001).
13. Levin, D. S. et al. A conserved interaction between the replicative clamp loader and DNA ligase in eukaryotes: Implications for Okazaki fragment joining. Journal of Biological Chemistry 279, 55196–55201 (2004).
14. Levin, D. S., McKenna, A. E., Motycka, T. A., Matsumoto, Y. & Tomkinson, A. E. Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Current Biology 10, 919-S2 (2000).
15. Song, W., Pascal, J. M., Ellenberger, T. & Tomkinson, A. E. The DNA binding domain of human DNA ligase I interacts with both nicked DNA and the DNA sliding clamps, PCNA and hRad9-hRad1-hHus1. DNA Repair 8, 912–919 (2009).
16. Pascal, J. M. et al. A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA. Molecular Cell 24, 279–291 (2006).
17. Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. v. Improvement of cryo-EM maps by density modification. Nature Methods 17, 923–927 (2020).
18. Teraoka, H. et al. Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct. Journal of Biological Chemistry 268, 24156–24162 (1993).
19. Taylor, M. R., Conrad, J. A., Wahl, D. & O’Brien, P. J. Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency. Journal of Biological Chemistry 286, 23054–23062 (2011).
20. Prestel, A. et al. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cellular and Molecular Life Sciences 76, 4923–4943 (2019).
21. Boehm, E. M. & Washington, M. T. R.I.P. to the PIP: PCNA-binding motif no longer considered specific: PIP motifs and other related sequences are not distinct entities and can bind multiple proteins involved in genome maintenance. BioEssays 38, 1117–1122 (2016).
22. Nakane, T., Kimanius, D., Lindahl, E. & Scheres, S. H. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. eLIFE (2018) doi:10.7554/eLife.36861.001.
23. Balakrishnan, L. & Bambara, R. A. Flap Endonuclease 1. Annual Review of Biochemistry 82, 119–138 (2013).
24. Tsutakawa, S. E. et al. Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 145, 198–211 (2011).
25. Rashid, F. et al. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. (2017) doi:10.7554/eLife.21884.001.
26. Tsutakawa, S. E. et al. Phosphate steering by Flap Endonuclease 1 promotes 5′-flap specificity and incision to prevent genome instability. Nature Communications 8, (2017).
27. Rashid, F. et al. Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation. Nature Communications 10, (2019).
28. Sakurai, S. et al. Structural basis for recruitment of human flap endonuclease 1 to PCNA. The EMBO Journal 24, 683–693 (2005).
29. Craggs, T. D., Hutton, R. D., Brenlla, A., White, M. F. & Penedo, J. C. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Research 42, 1857–1872 (2014).
30. Zaher, M. S. et al. Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Nucleic Acids Research 46, 2956–2974 (2018).
31. Sobhy, M. A. et al. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Computational and Structural Biotechnology Journal vol. 19 4456–4471 (2021).
32. Nishida, H., Kiyonari, S., Ishino, Y. & Morikawa, K. The Closed Structure of an Archaeal DNA Ligase from Pyrococcus furiosus. Journal of Molecular Biology 360, 956–967 (2006).
33. Mayanagi, K. et al. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. PNAS 106, 4647–4652 (2009).
34. Sverzhinsky, A., Tomkinson, A. E. & Pascal, J. M. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure 30, 1–15 (2021).
35. Lancey, C. et al. Structure of the processive human Pol δ holoenzyme. Nature Communications 11, (2020).
36. Lancey, C. et al. Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA. Nature Communications 12, (2021).
37. Chen, X. et al. Human DNA Ligases I, III, and IV-Purification and New Specific Assays for These Enzymes. Methods in Enzymology vol. 409 39–52 (2006).
38. Kim, D. et al. DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging. Nucleic acids research 47, e107 (2019).
39. Jarmoskaite, I., Alsadhan, I., Vaidyanathan, P. P. & Herschlag, D. How to measure and evaluate binding affinities. eLife 9, 1–34 (2020).
40. Raducanu, V. S. et al. TSGIT: An N- and C-terminal tandem tag system for purification of native and intein-mediated ligation-ready proteins. Protein Science 30, 497–512 (2021).
41. Sassa, A., Beard, W. A., Shock, D. D. & Wilson, S. H. Steady-state, pre-steady-state, and single-turnover kinetic measurement for DNA glycosylase activity. Journal of visualized experiments : JoVE (2013) doi:10.3791/50695.
42. Schnell, S. & Mendoza, C. Closed Form Solution for Time-dependent Enzyme Kinetics. J. theor. Biol vol. 187 (1997).
43. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLIFE 7, (2018).
44. Zheng, S. Q. et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods vol. 14 331–332 (2017).
45. Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology 192, 216–221 (2015).
46. Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology 2, (2019).
47. Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nature Methods 18, 176–185 (2021).
48. Gulbis, J. M. & Kelman, Z. Structure of the C-Terminal Region of p21 WAF1/CIP1 Complexed with Human PCNA. Cell vol. 87 (1996).
49. Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605–1612 (2004).
50. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallographica Section D: Biological Crystallography 66, 486–501 (2010).
51. Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D: Biological Crystallography 66, 213–221 (2010).
52. Ishida, T. & Kinoshita, K. PrDOS: Prediction of disordered protein regions from amino acid sequence. Nucleic Acids Research 35, (2007).