Author

P. J. Kolbeck

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 7 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 7 Assay:DNA methylation· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:clustering· 1 Approach:comparative / phylogenetic analysis· 1 Approach:deep learning· 1

Frequent Co-Authors

J. Lipfert· 8 shared W. Vanderlinden· 7 shared M. de Jager· 2 shared T. Brouns· 2 shared T. Liedl· 2 shared A. Lak· 1 shared A. van Blaaderen· 1 shared B. Bekaert· 1 shared

Activity by Year

2020-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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8 shared papersBiophysics

J. Lipfert

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Author profile →

8 papers

Recent·Most cited

Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning

M. de Jager, P. J. Kolbeck, W. Vanderlinden, J. Lipfert, L. Filion

The paper uses coarse-grained simulations and unsupervised learning to study protein-mediated DNA compaction, finding that protein-protein interactions are critical for forming looped structures observed experimentally.

bioRxiv · Mar 28, 2024Biophysics

HIV integrase compacts viral DNA into biphasic condensates

P. J. Kolbeck, M. de Jager, M. Gallano, T. Brouns, B. Bekaert, W. Frederickx, S. F. Konrad, S. Van Belle, F. Christ, S. De Feyter, Z. Debyser, L. C. Filion, J. Lipfert, W. Vanderlinden

This study shows HIV integrase compacts viral DNA into biphasic condensates, with the core susceptible to inhibitors and the outer layer resistant.

bioRxiv · Mar 15, 2024 · PreprintBiophysics

Cooperative dynamics of DNA grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

A. Lak, Y. Wang, P. J. Kolbeck, C. Pauer, M. S. Chowdhury, M. Cassani, F. Ludwig, T. Viereck, F. Selbach, P. Tinnefeld, M. Schilling, T. Liedl, J. Tavacoli, J. Lipfert

This study shows that DNA grafting density on magnetic nanoparticles affects their dynamics and biosensing performance, with optimal sensitivity at intermediate densities.

Nanoscale · Jan 1, 2024Peer-reviewedBiochemistry

Topology-dependent DNA binding

P. J. Kolbeck, M. Tisma, B. T. Analikwu, W. Vanderlinden, C. Dekker, J. Lipfert

This study presents a quantitative model showing how DNA topology modulates binding, with experiments using fluorescent intercalators and psoralen to demonstrate topology-dependent effects.

bioRxiv · Jun 30, 2023Biophysics

High-yield, ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single molecule manipulation assays

Y.-Y. Lin, T. Brouns, P. J. Kolbeck, W. Vanderlinden, J. Lipfert

This paper describes a method for high-yield DNA construct assembly with nucleosome positioning sequences for single-molecule manipulation assays, demonstrating stable tethers and proof-of-concept measurements on nucleosome dynamics.

bioRxiv · Jan 5, 2023Biophysics

A DNA origami fiducial for accurate 3D AFM imaging

P. J. Kolbeck, M. Dass, I. Martynenko, R. van Dijk-Moes, K. J. H. Brouwer, A. van Blaaderen, W. Vanderlinden, T. Liedl, J. Lipfert

This paper introduces a DNA origami fiducial to correct AFM image distortions by enabling accurate tip shape reconstruction and improving imaging precision.

bioRxiv · Nov 11, 2022 · PreprintBiophysics

DNA fluctuations reveal the size and dynamics of topological domains

W. Vanderlinden, E. Skoruppa, P. J. Kolbeck, E. Carlon, J. Lipfert

This paper develops a method to measure topological domain size and dynamics in supercoiled DNA using magnetic tweezers and simulations.

bioRxiv · Dec 21, 2021Biophysics

Intercalative DNA binding governs fluorescence enhancement of SYBR Gold

P. J. Kolbeck, W. Vanderlinden, T. Nicolaus, C. Gebhardt, T. Cordes, J. Lipfert

This study quantifies SYBR Gold binding to DNA using mechanical and spectroscopic methods, revealing intercalative binding and providing guidelines for quantitative DNA sensing.

bioRxiv · May 23, 2020 · PreprintBiophysics