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Items: 1 to 50 of 150

1.

How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation.

Erbaş A, Marko JF.

Curr Opin Chem Biol. 2019 Oct 2;53:118-124. doi: 10.1016/j.cbpa.2019.08.007. [Epub ahead of print] Review.

PMID:
31586479
2.

Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force.

Renn JP, Bhattacharyya S, Bai H, He C, Li H, Oberhauser AF, Marko JF, Makarov DE, Matouschek A.

Sci Rep. 2019 Jul 31;9(1):11101. doi: 10.1038/s41598-019-46525-w.

3.

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation.

Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF.

Mol Biol Cell. 2019 Aug 1;30(17):2320-2330. doi: 10.1091/mbc.E19-05-0286.

PMID:
31365328
4.

Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation.

Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF.

Mol Biol Cell. 2019 Jun 19:mbcE19050286T. doi: 10.1091/mbc.E19-05-0286-T. [Epub ahead of print]

PMID:
31216230
5.

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes.

Marko JF, De Los Rios P, Barducci A, Gruber S.

Nucleic Acids Res. 2019 Jul 26;47(13):6956-6972. doi: 10.1093/nar/gkz497.

6.

Receptor-Ligand Rebinding Kinetics in Confinement.

Erbaş A, Olvera de la Cruz M, Marko JF.

Biophys J. 2019 May 7;116(9):1609-1624. doi: 10.1016/j.bpj.2019.02.033. Epub 2019 Apr 5.

PMID:
31029377
7.

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.

Nomidis SK, Skoruppa E, Carlon E, Marko JF.

Phys Rev E. 2019 Mar;99(3-1):032414. doi: 10.1103/PhysRevE.99.032414.

PMID:
30999490
8.

Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm.

Gladstein S, Almassalha LM, Cherkezyan L, Chandler JE, Eshein A, Eid A, Zhang D, Wu W, Bauer GM, Stephens AD, Morochnik S, Subramanian H, Marko JF, Ameer GA, Szleifer I, Backman V.

Nat Commun. 2019 Apr 10;10(1):1652. doi: 10.1038/s41467-019-09717-6.

9.

Chromatin's physical properties shape the nucleus and its functions.

Stephens AD, Banigan EJ, Marko JF.

Curr Opin Cell Biol. 2019 Jun;58:76-84. doi: 10.1016/j.ceb.2019.02.006. Epub 2019 Mar 16. Review.

PMID:
30889417
10.

Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics.

Biggs R, Liu PZ, Stephens AD, Marko JF.

Mol Biol Cell. 2019 Mar 21;30(7):820-827. doi: 10.1091/mbc.E18-09-0592. Epub 2019 Jan 9.

11.

DNA Mechanics and Topology.

Brahmachari S, Marko JF.

Adv Exp Med Biol. 2018;1092:11-39. doi: 10.1007/978-3-319-95294-9_2. Review.

PMID:
30368746
12.

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.

Skoruppa E, Nomidis SK, Marko JF, Carlon E.

Phys Rev Lett. 2018 Aug 24;121(8):088101. doi: 10.1103/PhysRevLett.121.088101.

13.

Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold.

Sun M, Biggs R, Hornick J, Marko JF.

Chromosome Res. 2018 Dec;26(4):277-295. doi: 10.1007/s10577-018-9584-1. Epub 2018 Aug 24.

PMID:
30143891
14.

Effects of electrostatic interactions on ligand dissociation kinetics.

Erbaş A, de la Cruz MO, Marko JF.

Phys Rev E. 2018 Feb;97(2-1):022405. doi: 10.1103/PhysRevE.97.022405.

15.

Defect-facilitated buckling in supercoiled double-helix DNA.

Brahmachari S, Dittmore A, Takagi Y, Neuman KC, Marko JF.

Phys Rev E. 2018 Feb;97(2-1):022416. doi: 10.1103/PhysRevE.97.022416.

16.

Separate roles for chromatin and lamins in nuclear mechanics.

Stephens AD, Banigan EJ, Marko JF.

Nucleus. 2018 Jan 1;9(1):119-124. doi: 10.1080/19491034.2017.1414118. Epub 2017 Dec 28.

17.

Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices.

Brahmachari S, Gunn KH, Giuntoli RD, Mondragón A, Marko JF.

Phys Rev Lett. 2017 Nov 3;119(18):188103. doi: 10.1103/PhysRevLett.119.188103. Epub 2017 Oct 31.

18.

Single-Molecule Magnetic Tweezer Analysis of Topoisomerases.

Gunn KH, Marko JF, Mondragón A.

Methods Mol Biol. 2018;1703:139-152. doi: 10.1007/978-1-4939-7459-7_10.

19.

Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins.

Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF.

Mol Biol Cell. 2018 Jan 15;29(2):220-233. doi: 10.1091/mbc.E17-06-0410. Epub 2017 Nov 15.

20.

Oligomerization and ATP stimulate condensin-mediated DNA compaction.

Keenholtz RA, Dhanaraman T, Palou R, Yu J, D'Amours D, Marko JF.

Sci Rep. 2017 Oct 27;7(1):14279. doi: 10.1038/s41598-017-14701-5.

21.

Supercoiling DNA Locates Mismatches.

Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC.

Phys Rev Lett. 2017 Oct 6;119(14):147801. doi: 10.1103/PhysRevLett.119.147801. Epub 2017 Oct 3.

22.

Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei.

Banigan EJ, Stephens AD, Marko JF.

Biophys J. 2017 Oct 17;113(8):1654-1663. doi: 10.1016/j.bpj.2017.08.034.

23.

Torque and buckling in stretched intertwined double-helix DNAs.

Brahmachari S, Marko JF.

Phys Rev E. 2017 May;95(5-1):052401. doi: 10.1103/PhysRevE.95.052401. Epub 2017 May 1.

24.

A comparison of nucleosome organization in Drosophila cell lines.

Martin RL, Maiorano J, Beitel GJ, Marko JF, McVicker G, Fondufe-Mittendorf YN.

PLoS One. 2017 Jun 1;12(6):e0178590. doi: 10.1371/journal.pone.0178590. eCollection 2017.

25.

An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases.

Gunn KH, Marko JF, Mondragón A.

Nat Struct Mol Biol. 2017 May;24(5):484-490. doi: 10.1038/nsmb.3401. Epub 2017 Apr 17.

26.

Facilitated dissociation of transcription factors from single DNA binding sites.

Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, Marko JF.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3251-E3257. doi: 10.1073/pnas.1701884114. Epub 2017 Mar 31.

27.

Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus.

Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF.

Mol Biol Cell. 2017 Jul 7;28(14):1984-1996. doi: 10.1091/mbc.E16-09-0653. Epub 2017 Jan 5.

28.

Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase.

Keenholtz RA, Grindley ND, Hatfull GF, Marko JF.

Nucleic Acids Res. 2016 Oct 14;44(18):8921-8932. Epub 2016 Aug 22.

29.

Cell division: A sticky problem for chromosomes.

Brangwynne CP, Marko JF.

Nature. 2016 Jul 14;535(7611):234-5. doi: 10.1038/nature18904. Epub 2016 Jun 29. No abstract available.

PMID:
27362225
30.

An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates.

Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A.

Anal Biochem. 2016 Sep 15;509:50-59. doi: 10.1016/j.ab.2016.05.026. Epub 2016 Jun 11.

31.

Chromosome Compaction by Active Loop Extrusion.

Goloborodko A, Marko JF, Mirny LA.

Biophys J. 2016 May 24;110(10):2162-8. doi: 10.1016/j.bpj.2016.02.041.

32.

Compaction and segregation of sister chromatids via active loop extrusion.

Goloborodko A, Imakaev MV, Marko JF, Mirny L.

Elife. 2016 May 18;5. pii: e14864. doi: 10.7554/eLife.14864.

33.

Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)].

Banigan EJ, Marko JF.

Phys Rev E. 2016 Apr;93(4-2):049904. Epub 2016 Apr 20.

PMID:
27182590
34.

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines.

Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JF.

Chromosome Res. 2016 Sep;24(3):339-53. doi: 10.1007/s10577-016-9528-6. Epub 2016 May 5.

35.

Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome.

Hadizadeh N, Johnson RC, Marko JF.

J Bacteriol. 2016 May 27;198(12):1735-42. doi: 10.1128/JB.00225-16. Print 2016 Jun 15.

36.

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.

Xiao B, McLean MM, Lei X, Marko JF, Johnson RC.

Sci Rep. 2016 Apr 1;6:23697. doi: 10.1038/srep23697.

37.

Corrigendum: Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.

Kharerin H, Bhat PJ, Marko JF, Padinhateeri R.

Sci Rep. 2016 Mar 4;6:22220. doi: 10.1038/srep22220. No abstract available.

38.

Self-propulsion and interactions of catalytic particles in a chemically active medium.

Banigan EJ, Marko JF.

Phys Rev E. 2016 Jan;93(1):012611. doi: 10.1103/PhysRevE.93.012611. Epub 2016 Jan 25.

39.

Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.

Kharerin H, Bhat PJ, Marko JF, Padinhateeri R.

Sci Rep. 2016 Feb 4;6:20319. doi: 10.1038/srep20319. Erratum in: Sci Rep. 2016;6:22220.

40.

Forces, fluctuations, and self-organization in the nucleus.

Pederson T, King MC, Marko JF.

Mol Biol Cell. 2015 Nov 5;26(22):3915-9. doi: 10.1091/mbc.E15-06-0357.

41.

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response.

Giuntoli RD, Linzer NB, Banigan EJ, Sing CE, de la Cruz MO, Graham JS, Johnson RC, Marko JF.

J Mol Biol. 2015 Sep 25;427(19):3123-36. doi: 10.1016/j.jmb.2015.07.015. Epub 2015 Jul 26.

42.

Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg.

Hornick JE, Duncan FE, Sun M, Kawamura R, Marko JF, Woodruff TK.

J Assist Reprod Genet. 2015 May;32(5):765-9. doi: 10.1007/s10815-015-0453-y. Epub 2015 Mar 11.

43.
44.

Nuclear physics (of the cell, not the atom).

Pederson T, Marko JF.

Mol Biol Cell. 2014 Nov 5;25(22):3466-9. doi: 10.1091/mbc.E14-03-0790.

45.

Single-molecule analysis uncovers the difference between the kinetics of DNA decatenation by bacterial topoisomerases I and III.

Terekhova K, Marko JF, Mondragón A.

Nucleic Acids Res. 2014 Oct;42(18):11657-67. doi: 10.1093/nar/gku785. Epub 2014 Sep 17.

46.

Torque correlation length and stochastic twist dynamics of DNA.

Banigan EJ, Marko JF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jun;89(6):062706. Epub 2014 Jun 13. Erratum in: Phys Rev E. 2016 Apr;93(4-2):049904.

47.

Stochastic ratchet mechanisms for replacement of proteins bound to DNA.

Cocco S, Marko JF, Monasson R.

Phys Rev Lett. 2014 Jun 13;112(23):238101. Epub 2014 Jun 11.

48.

Global force-torque phase diagram for the DNA double helix: structural transitions, triple points, and collapsed plectonemes.

Marko JF, Neukirch S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062722. Epub 2013 Dec 27.

49.

Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins.

Sing CE, Olvera de la Cruz M, Marko JF.

Nucleic Acids Res. 2014 Apr;42(6):3783-91. doi: 10.1093/nar/gkt1327. Epub 2014 Jan 6.

50.

Binding-rebinding dynamics of proteins interacting nonspecifically with a long DNA molecule.

Parsaeian A, de la Cruz MO, Marko JF.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Oct;88(4):040703. Epub 2013 Oct 23.

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