Earnshaw, W. C. & Harrison, S. C. DNA arrangement in isometric phage heads. Nature 268, 598–602 (1977). The study provides a detailed insight into bacteriophage DNA packaging geometry and how this could be achieved.

Article  CAS  PubMed  Google Scholar 

Rao, V. B., Fokine, A., Fang, Q. & Shao, Q. Bacteriophage T4 head: structure, assembly, and genome packaging. Viruses 15, 527 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Catalano, C. E. & Morais, M. C. Viral genome packaging machines: structure and enzymology. Enzymes 50, 369–413 (2021).

Article  CAS  PubMed  Google Scholar 

Rao, V. B., Fokine, A. & Fang, Q. The remarkable viral portal vertex: structure and a plausible model for mechanism. Curr. Opin. Virol. 51, 65–73 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rao, V. B. & Feiss, M. Mechanisms of DNA packaging by large double-stranded DNA viruses. Annu. Rev. Virol. 2, 351–378 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jardine, P. J. Slow and steady wins the race: physical limits on the rate of viral DNA packaging. Curr. Opin. Virol. 36, 32–37 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tong, A. B. & Bustamante, C. Helical inchworming: a novel translocation mechanism for a ring ATPase. Biophys. Rev. 13, 885–888 (2021). The paper provides a model summary arising from a series of sophisticated single-molecule studies that dissected the mechanochemical properties of a bacteriophage motor.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gahlmann, A. & Moerner, W. E. Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging. Nat. Rev. Microbiol. 12, 9–22 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mäkelä, J. & Sherratt, D. SMC complexes organize the bacterial chromosome by lengthwise compaction. Curr. Genet. 66, 895–899 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Dame, R. T., Rashid, F.-Z. M. & Grainger, D. C. Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nat. Rev. Genet. 21, 227–242 (2020).

Article  CAS  PubMed  Google Scholar 

Badrinarayanan, A., Le, T. B. K. & Laub, M. T. Bacterial chromosome organization and segregation. Annu. Rev. Cell Dev. Biol. 31, 171–199 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yáñez-Cuna, F. O. & Koszul, R. Insights in bacterial genome folding. Curr. Opin. Struct. Biol. 82, 102679 (2023).

Article  PubMed  Google Scholar 

Paulson, J. R., Hudson, D. F., Cisneros-Soberanis, F. & Earnshaw, W. C. Mitotic chromosomes. Semin. Cell Dev. Biol. 117, 7–29 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yatskevich, S., Rhodes, J. & Nasmyth, K. Organization of chromosomal DNA by SMC complexes. Annu. Rev. Genet. 53, 445–482 (2019).

Article  CAS  PubMed  Google Scholar 

Banigan, E. J. & Mirny, L. A. Loop extrusion: theory meets single-molecule experiments. Curr. Opin. Cell Biol. 64, 124–138 (2020).

Article  CAS  PubMed  Google Scholar 

Corsi, F., Rusch, E. & Goloborodko, A. Loop extrusion rules: the next generation. Curr. Opin. Genet. Dev. 81, 102061 (2023).

Article  CAS  PubMed  Google Scholar 

Davidson, I. F. & Peters, J.-M. Genome folding through loop extrusion by SMC complexes. Nat. Rev. Mol. Cell Biol. 22, 445–464 (2021).

Article  CAS  PubMed  Google Scholar 

Kim, E., Barth, R. & Dekker, C. Looping the genome with SMC complexes. Annu. Rev. Biochem. 92, 15–41 (2023).

Article  CAS  PubMed  Google Scholar 

Gall, J. G. Kinetics of deoxyribonuclease action on chromosomes. Nature 198, 36–38 (1963). The paper demonstrates that chromosomes are unineme using a specially designed microscope.

Article  CAS  PubMed  Google Scholar 

Baumann, C. G., Smith, S. B., Bloomfield, V. A. & Bustamante, C. Ionic effects on the elasticity of single DNA molecules. Proc. Natl Acad. Sci. USA 94, 6185–6190 (1997).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nelson, P. Biological Physics: Energy, Information, Life (W. H. Freeman, 2003).

Garcia, H. G. et al. Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers 85, 115–130 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pollard, T. D., Earnshaw, W. C., Lippincott-Schwartz, J. & Johnson, G. Cell Biology (Elsevier, 2023).

Vafabakhsh, R. & Ha, T. Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337, 1097–1101 (2012). This single-molecule study shows that short naked DNA (<100 bp, well within the DNA persistence length) can efficiently form loops in vitro.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hahnfeldt, P., Hearst, J. E., Brenner, D. J., Sachs, R. K. & Hlatky, L. R. Polymer models for interphase chromosomes. Proc. Natl Acad. Sci. USA 90, 7854–7858 (1993).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cui, Y. & Bustamante, C. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl Acad. Sci. USA 97, 127–132 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bystricky, K., Heun, P., Gehlen, L., Langowski, J. & Gasser, S. M. Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc. Natl Acad. Sci. USA 101, 16495–16500 (2004).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Phillips, R., Kondev, J., Theriot, J. & Garcia, H. Physical Biology of the Cell (Garland Science, 2012).

Wennerström, H., Vallina Estrada, E., Danielsson, J. & Oliveberg, M. Colloidal stability of the living cell. Proc. Natl Acad. Sci. USA 117, 10113–10121 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Lorch, Y., Kornberg, R. D. & Maier-Davis, B. Role of the histone tails in histone octamer transfer. Nucleic Acids Res. 51, 3671–3678 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun, S., Rao, V. B. & Rossmann, M. G. Genome packaging in viruses. Curr. Opin. Struct. Biol. 20, 114–120 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Johnson, J. E. & Chiu, W. DNA packaging and delivery machines in tailed bacteriophages. Curr. Opin. Struct. Biol. 17, 237–243 (2007).

Article  CAS