J. Lipfert

Accurate Drift-Invariant Single-Molecule Force Calibration Using the Hadamard Variance

This paper introduces a drift-invariant force calibration method for multiplexed magnetic tweezers using Hadamard variance, showing higher precision and accuracy than existing techniques.

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

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.

HIV integrase compacts viral DNA into biphasic condensates

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

Epigenetic histone modifications H3K36me3 and H4K5/8/12/16ac induce open polynucleosome conformations via different mechanisms

This study examines how H3K36me3 and H4K5/8/12/16ac histone modifications affect nucleosome structure and interactions in tri-nucleosome arrays, revealing distinct mechanisms for inducing open conformations.

Determination of Absolute Intramolecular Distances in Proteins by Anomalous X-ray Scattering Interferometry

This study introduces AXSI for measuring absolute intramolecular distances in proteins, validated against single-molecule FRET, showing its effectiveness under various solution conditions.

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

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

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.

Labelizer: systematic selection of protein residues for covalent fluorophore labeling

Labelizer systematically selects protein residues for covalent fluorophore labeling using a naive Bayes classifier and provides a tool and webserver for this purpose.

Temperature-dependent twist of double-stranded RNA probed by magnetic tweezers experiments and molecular dynamics simulations

This study investigates how temperature affects the twist of double-stranded RNA using magnetic tweezers and molecular dynamics simulations, finding RNA unwinds more than DNA with increasing temperature.

Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility

This study examines how mutations in SARS-CoV-2 variants affect the force-stability of the SARS-CoV-2:ACE2 interface and virus transmissibility.

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

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.

A DNA origami fiducial for accurate 3D AFM imaging

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

DNA fluctuations reveal the size and dynamics of topological domains

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

A Conformational Transition of Von Willebrand Factor's D'D3 Domain Primes It For Multimerization

This study uses single-molecule force spectroscopy to show that a conformational change in VWF's DD3 domain, triggered by pH changes and stabilized by FVIII, primes it for multimerization.

A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions

This paper introduces a tethered ligand assay to study SARS-CoV-2:ACE2 interactions under mechanical force, showing higher stability and lower dissociation rates compared to SARS-CoV-1.

Twisting DNA by Salt

This study investigates how DNA twist changes with ion concentration and identity using single-molecule experiments and simulations, revealing trends in cation-specific effects on DNA structure.

A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force

This paper introduces a tethered ligand assay to study SARS-CoV-2 ACE2 interactions under constant force and finds that the interaction is more mechanically stable and has a slower off-rate compared to SARS-CoV-1.

Intercalative DNA binding governs fluorescence enhancement of SYBR Gold

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

Designed Anchoring Geometries Determine Lifetimes of Biotin-Streptavidin Bonds under Constant Load and Enable Ultra-Stable Coupling

The paper investigates engineered streptavidin variants under constant force to determine how anchoring geometries affect biotin-streptavidin bond lifetimes, identifying a geometry that enables ultra-stable single molecule force spectroscopy.

High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes

The paper uses high-throughput atomic force microscopy to analyze nucleosome unwrapping pathways, revealing differences between H3 and CENP-A nucleosomes.

Cellular and Molecular Probing of Intact Transparent Human Organs

The paper introduces SHANEL, a method to clear and label stiff human organs for 3D histology, revealing structural details in intact adult human brain, kidney, and pig pancreas.

Modular, ultra-stable, and highly parallel protein force spectroscopy in magnetic tweezers using peptide linkers

This paper introduces a modular magnetic tweezers approach using peptide linkers to enable ultra-stable, parallel protein force spectroscopy in the low force regime, revealing new insights into protein unfolding and activation mechanisms.

The Dynamics and Energy Landscape of DNA Plectoneme Nucleation

The paper quantifies DNA buckling dynamics using magnetic tweezers and reconstructs energy landscapes revealing asymmetry and a bend transition state.