Institute of Fundamental Technological Research
Polish Academy of Sciences


Borries Demeler

Recent publications
1.  Waszkiewicz R., Ranasinghe M., Fogg J., Catanese Jr. Daniel J., Ekiel-Jeżewska M.L., Lisicki M., Demeler B., Zechiedrich L., Szymczak P., DNA supercoiling-induced shapes alter minicircle hydrodynamic properties, Nucleic Acids Research, ISSN: 0305-1048, DOI: 10.1093/nar/gkad183, Vol.51, No.8, pp.4027-4042, 2023

DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.

Waszkiewicz R. - other affiliation
Ranasinghe M. - other affiliation
Fogg J. - other affiliation
Catanese Jr. Daniel J. - other affiliation
Ekiel-Jeżewska M.L. - IPPT PAN
Lisicki M. - other affiliation
Demeler B. - other affiliation
Zechiedrich L. - other affiliation
Szymczak P. - University of Warsaw (PL)

Conference papers
1.  Waszkiewicz R., Lisicki M., Catanese D.J., Fogg J., Gruziel M., Ekiel-Jeżewska M.L., Demeler B., Zechiedrich E.L., Szymczak P., Shape and sedimentation coefficients of supercoiled DNA minicircles, BPS2021,Biophysical Society 65th Annual Meeting, DOI: 10.1016/j.bpj.2020.11.1482, Vol.120, No.3, pp.221a, 2021

Conference abstracts
1.  Waszkiewicz R., Lisicki M., Catanese D.J., Fogg J., Gruziel-Słomka M., Ekiel-Jeżewska M.L., Demeler B., Ranasinghe M., Zechiedrich E.L., Szymczak P., Looped DNA: supercoiling dependent shape and hydrodynamics, Bulletin of the American Physical Society, ISSN: 0003-0503, Vol.66, pp.M11.10, 2021

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