Institute of Fundamental Technological Research
Polish Academy of Sciences


Maciej Lisicki

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)
2.  Lisicki M., Cichocki B., Wajnryb E., Near-wall diffusion tensor of an axisymmetric colloidal particle, JOURNAL OF CHEMICAL PHYSICS, ISSN: 0021-9606, DOI: 10.1063/1.4958727, Vol.145, pp.034904-1-8, 2016

Hydrodynamic interactions with confining boundaries often lead to drastic changes in the diffusive behaviour of microparticles in suspensions. For axially symmetric particles, earlier numerical studies have suggested a simple form of the near-wall diffusion matrix which depends on the distance and orientation of the particle with respect to the wall, which is usually calculated numerically. In this work, we derive explicit analytical formulae for the dominant correction to the bulk diffusion tensor of an axially symmetric colloidal particle due to the presence of a nearby no-slip wall. The relative correction scales as powers of inverse wall-particle distance and its angular structure is represented by simple functions in sines and cosines of the particle’s inclination angle to the wall. We analyse the correction for translational and rotational motion, as well as the translation-rotation coupling. Our findings provide a simple approximation to the anisotropic diffusion tensor near a wall, which completes and corrects relations known from earlier numerical and theoretical findings.

Lisicki M. - other affiliation
Cichocki B. - University of Warsaw (PL)
Wajnryb E. - IPPT PAN
3.  Liu Y., Bławzdziewicz J., Cichocki B., Dhont J.K.G., Lisicki M., Wajnryb E., Youngf Y.N., Lang P.R., Near-wall dynamics of concentrated hard-sphere suspensions: comparison of evanescent wave DLS experiments, virial approximation and simulations, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c5sm01624j, Vol.11, pp.7316-7327, 2015

In this article we report on a study of the near-wall dynamics of suspended colloidal hard spheres over a broad range of volume fractions. We present a thorough comparison of experimental data with predictions based on a virial approximation and simulation results. We find that the virial approach describes the experimental data reasonably well up to a volume fraction of ϕ ≈ 0.25 which provides us with a fast and non-costly tool for the analysis and prediction of evanescent wave DLS data. Based on this we propose a new method to assess the near-wall self-diffusion at elevated density. Here, we qualitatively confirm earlier results [Michailidou, et al., Phys. Rev. Lett., 2009, 102, 068302], which indicate that many-particle hydrodynamic interactions are diminished by the presence of the wall at increasing volume fractions as compared to bulk dynamics. Beyond this finding we show that this diminishment is different for the particle motion normal and parallel to the wall.

Liu Y. - Forschugszentrum Jülich, Institute of Complex Systems (DE)
Bławzdziewicz J. - Texas Tech University (US)
Cichocki B. - University of Warsaw (PL)
Dhont J.K.G. - Forschugszentrum Jülich, Institute of Complex Systems (DE)
Lisicki M. - other affiliation
Wajnryb E. - IPPT PAN
Youngf Y.N. - New Jersey Institute of Technology (US)
Lang P.R. - Forschugszentrum Jülich, Institute of Complex Systems (DE)

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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