Knotting of linear DNA in nano-slits and nano-channels: a numerical study

Marenduzzo, D., Micheletti, C., Orlandini, E.: Biopolymer organization upon confinement. J. Phys. Condens. Matter 22(28), 283102 (2010)

Micheletti, C., Marenduzzo, D., Orlandini, E.: Polymers with spatial or topological constraints: theoretical and computational results. Phys. Rep. 504(1), 1–73 (2011)

Muthukumar, M.: Polymers under confinement. Adv. Chem. Phys. 149, Ch. 4 (2012)

Forrey, C., Muthukumar, M.: Langevin dynamics simulations of genome packing in bacteriophage. Biophys. J. 91(1), 25–41 (2006)

Leforestier, A., Livolant, F.: Structure of toroidal DNA collapsed inside the phage capsid. Proc. Natl. Acad. Sci. U.S.A. 106(23), 9157–9162 (2009)

Leforestier, A., Siber, A., Livolant, F., Podgornik, R.: Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids. Biophys. J. 100(9), 2209–2216 (2011)

Petrov, A., Boz, M., Harvey, S.: The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. J. Struct. Biol. 160(2), 241–248 (2007)

Arsuaga, J., Tan, R.K., Vazquez, M., Sumners, D.W., Harvey, S.C.: Investigation of viral DNA packaging using molecular mechanics models. Biophys. Chem. 101–102, 475–484 (2002)

Arsuaga, J., Vázquez, M., McGuirk, P., Trigueros, S., Sumners, D.W., Roca, J.: DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl. Acad. Sci. U.S.A. 102, 9165–9169 (2005)

Kindt, J., Tzlil, S., Ben-Shaul, A., Gelbart, W.M.: DNA packaging and ejection forces in bacteriophage. Proc. Natl. Acad. Sci. U.S.A. 98(24), 13,671–13,674 (2001)

Marenduzzo, D., Micheletti, C.: Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness. J. Mol. Biol. 330, 485–492 (2003)

Purohit, P.K., Kondev, J., Phillips, R.: Mechanics of DNA packaging in viruses. Proc. Natl. Acad. Sci. U.S.A. 100(6), 3173–3178 (2003)

Marenduzzo, D., Orlandini, E., Stasiak, A., Sumners, D.W., Tubiana, L., Micheletti, C.: DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting. Proc. Natl. Acad. Sci. U.S.A. 106(52), 22,269–22,274 (2009)

Matthews, R., Louis, A.A., Yeomans, J.M.: Knot-controlled ejection of a polymer from a virus capsid. Phys. Rev. Lett. 102, 088101 (2009)

Rosa, A., Di Ventra, M., Micheletti, C.: Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore. Phys. Rev. Lett. 109(11), 118301 (2012)

Bouligand, Y., Livolant, F.: The organization of cholesteric spherulites. J. Physique 45, 1899–1923 (1984)

Stanley, C.B., Hong, H., Strey, H.H.: DNA cholesteric pitch as a function of density and ionic strength. Biophys. J. 89, 2552–2557 (2005)

Bonthuis, D.J., Meyer, C., Stein, D., Dekker, C.: Conformation and dynamics of DNA confined in slitlike nanofluidic channels. Phys. Rev. Lett. 101, 108303 (2008)

Dai, L., Ng, S.Y., Doyle, P.S., van der Maarel, J.R.C.: Conformation model of back-folding and looping of a single DNA molecule confined inside a nanochannel. ACS Macro Lett. 1(8), 1046–1050 (2012)

Reisner, W., Beech, J.P., Larsen, N.B., Flyvbjerg, H., Kristensen, A., Tegenfeldt, J.O.: Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment. Phys. Rev. Lett. 99, 058302 (2007)

Reisner, W., Morton, K.J., Riehn, R., Wang, Y.M., Yu, Z., Rosen, M., Sturm, J.C., Chou, S.Y., Frey, E., Austin, R.H.: Statics and dynamics of single DNA molecules confined in nanochannels. Phys. Rev. Lett. 94, 196101 (2005)

Stein, D., van der Heyden, F.H.J., Koopmans, W.J.A., Dekker, C.: Pressure-driven transport of confined DNA polymers in fluidic channels. Proc. Natl. Acad. Sci. U.S.A. 103, 15853–15858 (2006)

Tegenfeldt, J.O., Prinz, C., Cao, H., Chou, S., Reisner, W.W., Riehn, R., Wang, Y.M., Cox, E.C., Sturm, J.C., Silberzan, P., Austin, R.H.: The dynamics of genomic-length DNA molecules in 100-nm channels. Proc. Natl. Acad. Sci. U.S.A. 101, 10979–10983 (2004)

Wang, Y.M., Tegenfeldt, J.O., Reisner, W.W., Wang X.J.: Single-molecule studies of repressor DNA interactions show long-range interactions. Proc. Natl. Acad. Sci. U.S.A. 102, 9796–9801 (2005)

Zwolak, M., Di Ventra, M.: Colloquium: physical approaches to DNA sequencing and detection. Rev. Mod. Phys. 80, 141–165 (2008)

Millett, K., Dobay, A., Stasiak, A.: Linear random knots and their scaling behavior. Macromol. 38, 601–606 (2005)

Tubiana, L., Orlandini, E., Micheletti, C.: Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes. Prog. Theor. Phys. 191, 192–204 (2011)

Virnau, P., Kantor, Y., Kardar, M.: Knots in globule and coil phases of a model polyethylene. Phys. Rev. E 127, 15102–15106 (2005)

Micheletti, C., Orlandini, E.: Knotting and metric scaling properties of DNA confined in nano-channels: a Monte Carlo study. Soft Matter 8, 10959–10968 (2012)

Micheletti, C., Orlandini, E.: Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties. Macromol. 45, 2113–2121 (2012)

Rybenkov, V.V., Cozzarelli, N.R., Vologodskii, A.V.: Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. U.S.A. 90, 5307–5311 (1993)

Strey, H.H., Podgornik, R., Rau, D.C., Parsegian, V.A.: DNA–DNA interactions. Curr. Opin. Struct. Biol. 8(3), 309–313 (1998)

Micheletti, C., Marenduzzo, D., Orlandini, E., Sumners D.W.: Simulations of knotting in confined circular DNA. Biophys. J. 95, 3591–3599 (2008)

Farago, O., Kantor, Y., Kardar, M.: Pulling knotted polymers. Europhys. Lett. 60, 53–59 (2002)

Marcone, B., Orlandini, E., Stella, A.L., Zonta, F.: What is the length of a knot in a polymer? J. Phys. A, Math. Gen. 38, L15–L21 (2005)

Marcone, B., Orlandini, E., Stella, A.L., Zonta, F.: Size of knots in ring polymers. Phys. Rev. E 75, 041105 (2007)

Tubiana, L., Orlandini, E., Micheletti, C.: Multiscale entanglement in ring polymers under spherical confinement. Phys. Rev. Lett. 107, 188302 (2011)