Janissen R, Barth R, Davidson I, Peters J, Dekker C
Sci Adv. 2024; 10(50):eadt1832.
PMID: 39671477
PMC: 11641105.
DOI: 10.1126/sciadv.adt1832.
Roldan-Pinero C, Luengo-Marquez J, Assenza S, Perez R
J Chem Theory Comput. 2024; 20(5):2261-2272.
PMID: 38411091
PMC: 10938644.
DOI: 10.1021/acs.jctc.3c01089.
Kolbeck P, Tisma M, Analikwu B, Vanderlinden W, Dekker C, Lipfert J
Nucleic Acids Res. 2023; 52(1):59-72.
PMID: 38000393
PMC: 10783501.
DOI: 10.1093/nar/gkad1055.
Gilbert B, Thornburg Z, Brier T, Stevens J, Grunewald F, Stone J
Front Cell Dev Biol. 2023; 11:1214962.
PMID: 37621774
PMC: 10445541.
DOI: 10.3389/fcell.2023.1214962.
Aldag P, Rutkauskas M, Madariaga-Marcos J, Songailiene I, Sinkunas T, Kemmerich F
Nat Commun. 2023; 14(1):3654.
PMID: 37339984
PMC: 10281945.
DOI: 10.1038/s41467-023-38790-1.
Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers.
Haghizadeh A, Iftikhar M, Dandpat S, Simpson T
Int J Mol Sci. 2023; 24(3).
PMID: 36768987
PMC: 9916863.
DOI: 10.3390/ijms24032668.
DNA fluctuations reveal the size and dynamics of topological domains.
Vanderlinden W, Skoruppa E, Kolbeck P, Carlon E, Lipfert J
PNAS Nexus. 2023; 1(5):pgac268.
PMID: 36712371
PMC: 9802373.
DOI: 10.1093/pnasnexus/pgac268.
Conformational deformation of a multi-jointed elastic loop.
Tanaka H, Seki Y, Ueno S, Shibutani Y
Sci Rep. 2022; 12(1):19984.
PMID: 36411324
PMC: 9678883.
DOI: 10.1038/s41598-022-24355-7.
Nucleus size and its effect on nucleosome stability in living cells.
Efremov A, Hovan L, Yan J
Biophys J. 2022; 121(21):4189-4204.
PMID: 36146936
PMC: 9675033.
DOI: 10.1016/j.bpj.2022.09.019.
Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.
Assenza S, Perez R
J Chem Theory Comput. 2022; 18(5):3239-3256.
PMID: 35394775
PMC: 9097290.
DOI: 10.1021/acs.jctc.2c00138.
Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops.
Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L
Nucleic Acids Res. 2022; 50(5):2826-2835.
PMID: 35188572
PMC: 8934669.
DOI: 10.1093/nar/gkac093.
Two-phase dynamics of DNA supercoiling based on DNA polymer physics.
Wan B, Yu J
Biophys J. 2022; 121(4):658-669.
PMID: 35016860
PMC: 8873955.
DOI: 10.1016/j.bpj.2022.01.001.
Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.
Qian J, Xu W, Dunlap D, Finzi L
Transcription. 2021; 12(4):219-231.
PMID: 34719335
PMC: 8632135.
DOI: 10.1080/21541264.2021.1997315.
Nanomechanics of negatively supercoiled diaminopurine-substituted DNA.
Salerno D, Marrano C, Cassina V, Cristofalo M, Shao Q, Finzi L
Nucleic Acids Res. 2021; 49(20):11778-11786.
PMID: 34718727
PMC: 8599871.
DOI: 10.1093/nar/gkab982.
Torsional Stiffness of Extended and Plectonemic DNA.
Gao X, Hong Y, Ye F, Inman J, Wang M
Phys Rev Lett. 2021; 127(2):028101.
PMID: 34296898
PMC: 9007542.
DOI: 10.1103/PhysRevLett.127.028101.
A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.
Sengar A, Ouldridge T, Henrich O, Rovigatti L, Sulc P
Front Mol Biosci. 2021; 8:693710.
PMID: 34235181
PMC: 8256390.
DOI: 10.3389/fmolb.2021.693710.
Spo11 generates gaps through concerted cuts at sites of topological stress.
Prieler S, Chen D, Huang L, Mayrhofer E, Zsoter S, Vesely M
Nature. 2021; 594(7864):577-582.
PMID: 34108684
DOI: 10.1038/s41586-021-03632-x.
A review on nonlinear DNA physics.
Chevizovich D, Michieletto D, Mvogo A, Zakiryanov F, Zdravkovic S
R Soc Open Sci. 2021; 7(11):200774.
PMID: 33391787
PMC: 7735367.
DOI: 10.1098/rsos.200774.
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems.
Maffeo C, Aksimentiev A
Nucleic Acids Res. 2020; 48(9):5135-5146.
PMID: 32232413
PMC: 7229838.
DOI: 10.1093/nar/gkaa200.
Dynamics of DNA nicking and unwinding by the RepC-PcrA complex.
Carrasco C, Pastrana C, Aicart-Ramos C, Leuba S, Khan S, Moreno-Herrero F
Nucleic Acids Res. 2020; 48(4):2013-2025.
PMID: 31930301
PMC: 7038956.
DOI: 10.1093/nar/gkz1200.