De Paepe B, De Mey M
ACS Synth Biol. 2024; 14(1):72-86.
PMID: 39709556
PMC: 11745168.
DOI: 10.1021/acssynbio.4c00689.
Verma A, Roy B, Dwivedi Y
Heliyon. 2024; 10(21):e39036.
PMID: 39524798
PMC: 11550049.
DOI: 10.1016/j.heliyon.2024.e39036.
van der Valk R, van Erp B, Qin L, Moolenaar G, Dame R
Methods Mol Biol. 2024; 2819:443-454.
PMID: 39028518
DOI: 10.1007/978-1-0716-3930-6_20.
Dubrovin E
Biophys Rev. 2023; 15(5):1015-1033.
PMID: 37974971
PMC: 10643717.
DOI: 10.1007/s12551-023-01111-3.
Vilar J, Saiz L
Sci Rep. 2023; 13(1):10835.
PMID: 37407625
PMC: 10322939.
DOI: 10.1038/s41598-023-37140-x.
DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions.
Yi J, Yeou S, Lee N
J Am Chem Soc. 2022; 144(29):13137-13145.
PMID: 35839423
PMC: 9335521.
DOI: 10.1021/jacs.2c02466.
Small DNA circles as bacterial topoisomerase I inhibitors.
Li D, Wang Q, Zhou B, Zhuge Q, Lv B
RSC Adv. 2022; 9(32):18415-18419.
PMID: 35515216
PMC: 9064831.
DOI: 10.1039/c9ra02398d.
CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy.
Mawhinney M, Liu R, Lu F, Maksimoska J, DAmico K, Marmorstein R
J Mol Biol. 2018; 430(6):759-776.
PMID: 29409905
PMC: 5860984.
DOI: 10.1016/j.jmb.2018.01.012.
Protein-mediated looping of DNA under tension requires supercoiling.
Yan Y, Leng F, Finzi L, Dunlap D
Nucleic Acids Res. 2018; 46(5):2370-2379.
PMID: 29365152
PMC: 5861448.
DOI: 10.1093/nar/gky021.
A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands.
Foreman K
PLoS One. 2017; 12(11):e0188134.
PMID: 29166663
PMC: 5699851.
DOI: 10.1371/journal.pone.0188134.
Supercoiling Effects on Short-Range DNA Looping in E. coli.
Mogil L, Becker N, Maher 3rd L
PLoS One. 2016; 11(10):e0165306.
PMID: 27783696
PMC: 5081198.
DOI: 10.1371/journal.pone.0165306.
Optical Pushing: A Tool for Parallelized Biomolecule Manipulation.
Sitters G, Laurens N, de Rijk E, Kress H, Peterman E, Wuite G
Biophys J. 2016; 110(1):44-50.
PMID: 26745408
PMC: 4805865.
DOI: 10.1016/j.bpj.2015.11.028.
A complex genetic switch involving overlapping divergent promoters and DNA looping regulates expression of conjugation genes of a gram-positive plasmid.
Ramachandran G, Singh P, Luque-Ortega J, Yuste L, Alfonso C, Rojo F
PLoS Genet. 2014; 10(10):e1004733.
PMID: 25340403
PMC: 4207663.
DOI: 10.1371/journal.pgen.1004733.
DNA supercoiling: a regulatory signal for the λ repressor.
Ding Y, Manzo C, Fulcrand G, Leng F, Dunlap D, Finzi L
Proc Natl Acad Sci U S A. 2014; 111(43):15402-7.
PMID: 25319264
PMC: 4217475.
DOI: 10.1073/pnas.1320644111.
Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins.
Driessen R, Sitters G, Laurens N, Moolenaar G, Wuite G, Goosen N
Biochemistry. 2014; 53(41):6430-8.
PMID: 25291500
PMC: 5451147.
DOI: 10.1021/bi500344j.
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit.
Razo-Mejia M, Boedicker J, Jones D, DeLuna A, Kinney J, Phillips R
Phys Biol. 2014; 11(2):026005.
PMID: 24685590
PMC: 4051709.
DOI: 10.1088/1478-3975/11/2/026005.
A multi-scale model of hepcidin promoter regulation reveals factors controlling systemic iron homeostasis.
Casanovas G, Banerji A, DAlessio F, Muckenthaler M, Legewie S
PLoS Comput Biol. 2014; 10(1):e1003421.
PMID: 24391488
PMC: 3879105.
DOI: 10.1371/journal.pcbi.1003421.
Multiple interferon regulatory factor and NF-κB sites cooperate in mediating cell-type- and maturation-specific activation of the human CD83 promoter in dendritic cells.
Stein M, Lang S, Winkler T, Deinzer A, Erber S, Nettelbeck D
Mol Cell Biol. 2013; 33(7):1331-44.
PMID: 23339870
PMC: 3624272.
DOI: 10.1128/MCB.01051-12.
DNA looping in prokaryotes: experimental and theoretical approaches.
Cournac A, Plumbridge J
J Bacteriol. 2013; 195(6):1109-19.
PMID: 23292776
PMC: 3591992.
DOI: 10.1128/JB.02038-12.
Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway.
Dubois E, Bischerour J, Marmignon A, Mathy N, Regnier V, Betermier M
Int J Evol Biol. 2012; 2012:436196.
PMID: 22888464
PMC: 3408717.
DOI: 10.1155/2012/436196.