A. Aksimentiev

RNA regulates cohesiveness and porosity of a biological condensate

This study uses molecular dynamics simulations to show RNA increases condensate cohesiveness but affects fluidity and permeability depending on RNA length.

Single molecule delivery into living cells

This paper introduces a nanoinjection platform using nanopipettes to deliver macromolecules into cells with single molecule resolution, showing phenotypic changes and enhanced detection through macromolecular crowding.

Real-Time Structural Biology of DNA and DNA-Protein Complexes on an Optical Microscope

This study develops a method to study DNA and DNA-protein interactions with high spatial and temporal resolution using graphene and energy transfer.

Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations

This study investigates how the length of poly(ADP-ribose) (PAR) affects its structural transitions in the presence of Mg2+ ions, revealing length-dependent compaction and bundle formation.

Nanopore translocation reveals electrophoretic force on non-canonical RNA:DNA double helix

The paper compares the electrophoretic translocation dynamics of RNA:DNA hybrids and DNA:DNA duplexes through nanopores, finding that RNA:DNA hybrids translocate faster despite similar contour lengths.

Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates

This study benchmarks molecular dynamics force fields for simulating biological condensates, finding that combined protein and RNA force fields with a common water model best describe RNA-protein interactions and protein conformations.

Long-Range Hopping Conductivity in Proteins

This paper explains how proteins without redox cofactors can conduct electricity efficiently by reducing the energy barrier for electron hopping through non-equilibrium states.

DNA double helix, a tiny electromotor

The paper demonstrates that a DNA or RNA duplex rotates unidirectionally at high speed under an electric field, driven by electro-osmotic flow, and shows potential for nanoscale engineering applications.

Percolation transition determines protein size limit for passive transport through the nuclear pore complex

The paper uses simulations and theory to show that protein size limits passive transport through the nuclear pore complex due to a percolation transition in the disordered mesh.

Single-molecule biophysics experiments in silico: Towards a physical model of a replisome

The paper develops a coarse-grained computational model of a DNA binding protein to mimic single-molecule experiments and simulates a replication fork's trombone loop.

Resolving isomeric posttranslational modifications using a nanopore

This paper demonstrates a nanopore-based method to distinguish positional isomers of PTMs in histone H4 by measuring ionic current modulations from whole-molecule sensing.

Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore

This paper demonstrates a method for unidirectional transport of full-length proteins through nanopores using guanidinium chloride and machine learning to identify protein orientation and identity.

DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity

The paper develops DNA origami-based voltage sensors with single-molecule sensitivity, showing a 5% FRET change for 100 mV transmembrane potential shifts.

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.

A nanoscale reciprocating rotary mechanism with coordinated mobility control

This paper describes a synthetic molecular mechanism that converts rotary motion into reciprocating structural transitions using DNA origami and mechanical deformation, demonstrating allosteric coupling and tunable free energy landscapes.

Electrical Unfolding of Cytochrome c During Translocation Through a Nanopore Constriction

This paper investigates how electric fields affect the translocation of cytochrome c through nanopores of different diameters, showing that electric fields can stabilize unfolded states and influence translocation modes.

Outperforming nature: synthetic enzyme built from DNA flips lipids of biological membranes at record rates

This paper describes a synthetic DNA enzyme that rapidly transports lipids between membrane leaflets, outperforming natural enzymes by three orders of magnitude.