Cees Dekker

The paper quantifies electro-osmotic flow in MspA nanopores using a dipolar peptide and finite-element simulations, finding charged mutations near the constriction site enhance EOF.

This study examines how intercalating dyes affect DNA loop extrusion by SMC proteins, finding they alter extrusion rates and SMC activity, and introduces a dye-free assay.

The paper introduces a modular DNA toolkit for creating long, customizable DNA molecules with user-defined sequences for single-molecule biophysics applications.

This study designs and tests artificial FG-Nups to show that spacing and charge-to-hydrophobicity ratio affect Kap95 binding and transport selectivity through NPCs.

This paper develops DNA origami nanopores that mimic nuclear pore complexes, showing tunable size and transport selectivity.

This paper demonstrates a minimal one-component abscission machinery for synthetic cells using dynamin A, enabling self-dividing synthetic cells.

This study shows how the glycocalyx regulates liposome interactions with membranes through charge and steric effects, enabling fusion and internalization.

This paper introduces lipid-conjugated DNA (LiNA) to enable programmable fusion between LUVs and GUVs, demonstrating efficient delivery of lipids and proteins to synthetic cells.

This paper develops chemical strategies for nanopore sequencing of natural peptides, showing that different peptide properties require tailored conjugation methods for successful sequencing.

The study identifies two CTCF N-terminal motifs that synergistically stall cohesin-mediated DNA loop extrusion through distinct mechanisms.

This study shows cohesin supercoils DNA during loop extrusion, influencing genome architecture through both looping and supercoiling.

This study shows that lipid flip flop regulates the shape of synthetic cells during growth and division by relaxing curvature stresses and enabling symmetric bud formation and scission.

This paper introduces a microfluidic platform for extracting and analyzing bacterial genomic DNA without fragmentation, demonstrating its use on B. subtilis cells.

The paper measures the twist induced by eukaryotic SMC proteins during DNA loop extrusion and finds all three SMC complexes induce a consistent -0.6 twist per step.

This study uses nanopore sequencing to accurately detect sulfation and phosphorylation on plant peptide hormones, demonstrating high sensitivity for identifying sulfotyrosine modifications.

This study shows DNA supercoiling enhances ParB-DNA condensation, forming partition complexes at lower ParB concentrations than on relaxed DNA.

The paper investigates how interactions among Cdv proteins drive their recruitment to membrane necks during crenarchaeal cell division.

This paper introduces a DNA origami-based nanopore that can adjust its size through molecular triggers, enabling size-selective transport of biomolecules.

This paper discusses the potential of graphene drums as nanomotion sensors for studying microbial processes at the single-cell level and explores their future applications in clinical settings.

This paper engineers ssRNA tiles to create cytoskeletal-like filaments with programmable assembly, disassembly, stiffness, membrane binding, and protein attachment capabilities.

The paper shows that all eukaryotic SMC complexes extrude DNA asymmetrically, with direction switches observed in cohesin and SMC5/6, linked to NIPBL turnover and stabilized by STAG1.

This study visualizes twin-supercoiled domains formed during transcription using single-molecule experiments, showing equal upstream and downstream supercoiling without requiring RNA transcript drag.

The paper shows that dense Rap1 arrays block DNA loop extrusion by condensin in yeast, acting as contact insulators and affecting dicentric chromosome resolution.

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

This study demonstrates that Dynamin A can split dumbbell-shaped liposomes, functioning as a one-component division machinery for synthetic cells.

This paper demonstrates the use of zero-mode waveguide nanowells to enable single-molecule detection in live cells by reducing observation volume and background fluorescence.

This study investigates how ParB-DNA interactions form a dynamic partition condensate for bacterial chromosome segregation using in vitro experiments and simulations.

This paper introduces a DNA-based tool called SMS to generate controlled liposome shapes like stomatocytes and dumbbells, compatible with protein reconstitution.

This paper introduces a Vortex PSF for simultaneous orientation and 3D localization of single-molecules, demonstrating its effectiveness on DNA intercalators.

This paper optimizes the cDICE method to produce high-quality, defect-free GUVs with efficient encapsulation of complex biochemical systems.