C. Dekker

Compliant DNA Origami Nanoactuators as Size-Selective Nanopores

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

Cohesin supercoils DNA during loop extrusion

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

All eukaryotic SMC proteins induce a twist of -0.6 at each DNA-loop-extrusion step

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.

Prospects and Challenges for Graphene Drums As Sensors Of Individual Bacteria

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.

Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

This paper introduces an optical method to rapidly assess antibiotic susceptibility of single bacteria within one hour by analyzing light intensity fluctuations.

Single-molecule visualization of twin-supercoiled domains generated during transcription

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

Topology-dependent DNA binding

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

Zero-mode waveguide nanowells for single-molecule detection in living 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.

Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation

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

Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical Nanopores

The paper studies transport selectivity through NPC mimics by measuring translocation rates of Kap95 and BSA across varying pore sizes and observes a decrease in selectivity for larger pores.

Direct observation of a crescent-shape chromosome in Bacillus subtilis

The paper visualizes the crescent shape of the Bacillus subtilis chromosome in live cells and identifies key proteins involved in its structure.

Mapping phosphorylation post-translational modifications along single peptides with nanopores

This paper develops a nanopore sequencing method to detect phosphorylation PTMs on single immunopeptides with high accuracy.

Orientation-locked DNA origami for stable trapping of small proteins in the NEOtrap

This paper improves the NEOtrap by orienting DNA origami to enhance trapping of small proteins, achieving longer observation times and reduced noise.

CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion

The paper shows CTCF blocks cohesin-mediated DNA loop extrusion and regulates its direction and loop size, revealing it as an active regulator rather than a passive barrier.

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

This study presents the first high-resolution single-molecule analysis of kDNA network topology using AFM and simulations, revealing heterogeneous structure and buckling behavior.

Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size?

This study evaluates pseudotopological models of SMC-driven DNA loop extrusion and finds they conflict with experimental data on roadblock traversal.

MukBEF-dependent chromosomal organization in widened Escherichia coli

This study investigates the role of MukBEF in E. coli chromosome organization, showing its ATP-dependent translocation and non-uniform distribution, and its importance for sister chromosome decatenation.

Extracting and characterizing protein-free megabasepair DNA for in vitro experiments

The paper presents a method to isolate megabasepair-long deproteinated DNA for in vitro studies, enabling the investigation of chromosome organization using long DNA substrates.

Quantitative analysis of surface wave patterns of Min proteins

This paper introduces a methodology for quantitatively analyzing Min protein surface wave patterns, providing tools for reproducible and user-independent analysis.

Directing Min protein patterns with advective bulk flow

The paper shows that hydrodynamic bulk flow can control the direction of Min protein pattern propagation in vitro, with downstream propagation at low MinE:MinD ratios and upstream propagation at high ratios.

Transport receptor occupancy in Nuclear Pore Complex mimics

This study investigates Kap95 binding in Nsp1-coated nanopores, showing two Kap populations and limited Kap occupancy due to steric constraints.

ParS-independent recruitment of the bacterial chromosome-partitioning protein ParB

This study shows ParB can recruit itself to DNA independently of parS, enabling long-distance chromosome segregation in bacteria.

The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC

This study shows that CdvB1 forms filamentous polymers that are depolymerized by CdvC, and that polymerization and membrane binding are mutually exclusive.

Probing nanomotion of single bacteria with graphene drums

This study measures nanomotion of single E. coli cells using graphene drums, identifies flagella as the source, and demonstrates single-cell antibiotic susceptibility testing.

SMC complexes can traverse physical roadblocks bigger than their ring size

The paper shows that SMC complexes can extrude DNA loops around large DNA-bound obstacles, suggesting a nontopological mechanism for loop extrusion.

Infinite re-reading of single proteins at single-amino-acid resolution using nanopore sequencing

This paper presents proof-of-concept experiments and simulations of a nanopore-based approach to sequencing individual proteins.

Condensin-driven loop extrusion on supercoiled DNA

This study investigates how condensin-driven DNA loop extrusion is influenced by supercoiling using single-molecule imaging and atomic force microscopy.

A designer FG-Nup that reconstitutes the selective transport barrier of the Nuclear Pore Complex

This study designs an artificial FG-Nup that mimics natural Nups and demonstrates selective transport behavior similar to native NPCs.

Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations

This paper introduces NEOtrap, a method to trap and observe single proteins for hours with high time resolution, enabling label-free analysis of protein conformations and dynamics.

Reconstitution of ultrawide DNA origami pores in liposomes for transmembrane transport of macromolecules

This study creates ultrawide DNA origami pores in lipid membranes, enabling transmembrane transport of large macromolecules and demonstrating size selectivity.