Publications
Explore Stefan Howorka’s research papers on DNA nanotechnology, protein nanopores, nanopore sequencing and single-molecule sensing.
125 publications
2026
A guide to securing your first research fellowship: what reviewers are looking for
Published 25 August 2026
The Power of Tiny Spaces
6(8), 4353-4366
Sequencing peptides by reversing translation
10.1038/s41587-026-03108-1
Preprint
Autonomous Homeostatic Synthetic Cells via Self-Gating DNA Nanopores
2025
Molecular Interactions within Nanoconfinement of Model DNA Nanostructures Controlled by Compensatory Kinetics as Revealed by Single-Molecule Fluorescence Analysis
5(9), 4427-4438
2024
Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics
16(3), 314-334
Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes
20(35), e2207585
DNA Origami – Lipid Membrane Interactions Controlled by Nanoscale Sterics
20(42), e2404720
2023
Creating complex protocells and prototissues using simple DNA building blocks
14(1), 1314
Unfolding the path to nanopore protein sequencing
18(11), 1259-1260
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations
14(1), 3630
Nanopores: synergy from DNA sequencing to industrial filtration – small holes with big impact
52(6), 1983-1994
Multi‐Stimuli‐Responsive and Mechano‐Actuated Biomimetic Membrane Nanopores Self‐Assembled from DNA
35(29), e2300589
Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy
23(10), 4439-4447
Functional Nanopores Enabled with DNA
62(33), e202303103
Preprint
DNA Origami – Lipid Membrane Interactions Defined at Single-Molecular Resolution
2022
Triggered Assembly of a DNA-Based Membrane Channel
144(10), 4333-4344
Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility
13(1), 3610
Rebuilding research
6(2), 81-82
Highly shape- and size-tunable membrane nanopores made with DNA
17(7), 708-713
A reversibly gated protein-transporting membrane channel made of DNA
13(1), 2271
A Light‐Triggered Synthetic Nanopore for Controlling Molecular Transport Across Biological Membranes
61(52), e202210886
2021
Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations
15(6), 9900-9912
Principles of Small-Molecule Transport through Synthetic Nanopores
15(10), 16194-16206
Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes
143(22), 8305-8313
DNA Nanodevices with Selective Immune Cell Interaction and Function
15(3), 4394-4404
Design, assembly, and characterization of membrane-spanning DNA nanopores
16(1), 86-130
A Biomimetic DNA‐Based Membrane Gate for Protein‐Controlled Transport of Cytotoxic Drugs
60(4), 1903-1908
2020
Exploring the Relationship between BODIPY Structure and Spectroscopic Properties to Design Fluorophores for Bioimaging
26(4), 863–872
Reading amino acids in a nanopore
38(2), 159-160
2019
Synthetic protein-conductive membrane nanopores built with DNA
10(1), 5018
Structural and Functional Stability of DNA Nanopores in Biological Media
9(4), 490
Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions
141(2), 1100-1108
Solvent-dependent photophysics of a red-shifted, biocompatible coumarin photocage
17(25), 6178-6183
Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures
30(7), 1836-1844
A Temperature-Gated Nanovalve Self-Assembled from DNA to Control Molecular Transport across Membranes
13(3), 3334-3340
A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation
58(20), 6620-6624
2018
Comparing proteins and nucleic acids for next-generation biomolecular engineering
2(7), 113–130
Tunable DNA Hybridization Enables Spatially and Temporally Controlled Surface-Anchoring of Biomolecular Cargo
34(49), 15021-15027
Nucleic Acids Nanoscience at Interfaces Special Issue
34(49), 14691
Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials.
9(1), 1521
Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes
34(49), 15084-15092
Defined Bilayer Interactions of DNA Nanopores Revealed with a Nuclease-Based Nanoprobe Strategy
12(4), 3263-3271
2017
Stability and dynamics of membrane-spanning DNA nanopores.
8, 14784
DNA nanotechnology: Bringing lipid bilayers into shape.
9(7), 611-613
Building membrane nanopores.
12(7), 619-630
Arrays of Individual DNA Molecules on Nanopatterned Substrates.
7, 42075
2016
NANOTECHNOLOGY. Changing of the guard.
352(6288), 890-1
Nanopores and Nanochannels: From Gene Sequencing to Genome Mapping.
10(11), 9768-9771
Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.
12(21), 2877-84
Biomimetic Hybrid Nanocontainers with Selective Permeability
55(37), 11106-9
A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane.
11(2), 152-6
2015
Nanopore-based electrical and label-free sensing of enzyme activity in blood serum.
87(18), 9149-54
Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations.
9(11), 11209-17
Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance.
15(7), 4822-8
Broadening students' minds.
10(11), 992
Bilayer-spanning DNA nanopores with voltage-switching between open and closed state.
9(2), 1117-26
2014
Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG
516(7530), 250-3
Nanomicrobiology: Physiological and Environmental Characteristics
S-layer structure in bacteria and archaea
Microarrays and single molecules: an exciting combination.
10(7), 931-41
Membrane-spanning DNA nanopores with cytotoxic effect.
53(46), 12466-70
DNA-modified polymer pores allow pH- and voltage-gated control of channel flux.
136(28), 9902-5
2013
Self-assembled DNA nanopores that span lipid bilayers.
13(6), 2351-6
Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor.
52(46), 12069-72
DNA nanoarchitectonics: assembled DNA at interfaces.
29(24), 7344-53
Disentangling steric and electrostatic factors in nanoscale transport through confined space.
13(8), 3890-6
2012
SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly.
487(7405), 119-22
Painting with biomolecules at the nanoscale: biofunctionalization with tunable surface densities.
12(4), 1983-9
Nanoscale DNA tetrahedra improve biomolecular recognition on patterned surfaces.
8(1), 89-97
Nanopores as protein sensors.
30(6), 506-7
2011
Progress in Molecular Biology and Translational Science
The structure of bacterial S-layer proteins.
103, 73-130
Single-molecule AFM characterization of individual chemically tagged DNA tetrahedra.
5(9), 7048-54
Rationally engineering natural protein assemblies in nanobiotechnology.
22(4), 485-91
Scanning Probe Microscopy in Nanoscience and Nanotechnology
Nanoimaging, molecular interaction, and Nanotemplating of human rhinovirus
pp. 589–643
Progress in Molecular Biology and Translational Science
Molecular assembly in natural and engineered systems. Preface.
103, xi-xii
DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics.
239(1-2), 105-13
2010
Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns.
5(11), 788-91
Interfacial dipole dynamics of light-emitting diodes incorporating a poly(amidoamine) dendrimer monolayer
Improved Kelvin probe force microscopy for imaging individual DNA molecules on insulating surfaces
Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus.
395(4), 742-53
Engineered voltage-responsive nanopores.
39(3), 1115-32
Electrically sensing protease activity with nanopores.
22(45), 454103
Chemical tags mediate the orthogonal self-assembly of DNA duplexes into supramolecular structures.
6(16), 1732-5
Biosensors and biofuel cells with engineered proteins.
6(9), 1548-56
2009
Topography and recognition imaging of protein-patterned surfaces generated by AFM nanolithography.
10(9-10), 1478-81
Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates.
7(18), 3826-35
Semipermeable poly(ethylene glycol) films: The relationship between permeability and molecular structure of polymer chains
Selective protein and DNA adsorption on PLL-PEG films modulated by ionic strength
Receptor arrays for the selective and efficient capturing of viral particles.
20(3), 466-75
Handbook of Single-Molecule Biophysics
Nanopores: Generation, engineering and single-molecule applications
Nanopore analytics: sensing of single molecules.
38(8), 2360-84
Imaging surface charges of individual biomolecules.
9(7), 2769-73
Engineering and exploiting protein assemblies in synthetic biology.
5(7), 723-32
Diene-modified nucleotides for the Diels-Alder-mediated functional tagging of DNA.
37(5), 1477-85
Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations.
5(8), 2135-48
Chemically labeled nucleotides and oligonucleotides encode DNA for sensing with nanopores.
131(22), 7530-1
A DNA nanostructure for the functional assembly of chemical groups with tunable stoichiometry and defined nanoscale geometry.
48(3), 525-7
2008
The surface location of individual residues in a bacterial S-layer protein.
377(2), 589-604
Self-assembled monolayers of protonated poly(amidoamine) dendrimers on indium tin oxide
Chemical tags facilitate the sensing of individual DNA strands with nanopores.
47(30), 5565-8
Atomic force microscopy-derived nanoscale chip for the detection of human pathogenic viruses.
4(6), 847-54
2007
Stochastic detection of motor protein-RNA complexes by single-channel current recording.
8(15), 2189-94
Sizing trinucleotide repeat sequences by single-molecule analysis of fluorescence brightness.
8(11), 1618-21
Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement.
19(5), 675-84
Preparation and characterization of dense films of poly(amidoamine) dendrimers on indium tin oxide.
23(17), 8916-24
Nanoscale protein pores modified with PAMAM dendrimers.
129(31), 9640-9
Dense passivating poly(ethylene glycol) films on indium tin oxide substrates.
23(20), 10244-53
Creating regular arrays of nanoparticles with self-assembling protein building blocks
2006
RNA expression profiling at the single molecule level.
16(8), 1041-5
Glass surfaces grafted with high-density poly(ethylene glycol) as substrates for DNA oligonucleotide microarrays.
22(1), 277-85
2005
Protein components for nanodevices.
9(6), 576-84
Nanopatterning of biomolecules with microscale beads.
6(5), 900-3
2004
Stochastic detection of monovalent and bivalent protein-ligand interactions.
43(7), 842-6
2002
Probing distance and electrical potential within a protein pore with tethered DNA.
83(6), 3202-10
Methods in Molecular Biology
High-throughput scanning mutagenesis by recombination polymerase chain reaction.
182, 139-47
2001
Sequence-specific detection of individual DNA strands using engineered nanopores.
19(7), 636-9
Location of a constriction in the lumen of a transmembrane pore by targeted covalent attachment of polymer molecules.
117(3), 239-52
Kinetics of duplex formation for individual DNA strands within a single protein nanopore.
98(23), 12996-3001
2000
Surface-accessible residues in the monomeric and assembled forms of a bacterial surface layer protein.
275(48), 37876-86
Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore.
18(10), 1091-5
A protein pore with a single polymer chain tethered within the lumen
1999
Self-assembly product formation of the Bacillus stearothermophilus PV72/p6 S-layer protein SbsA in the course of autolysis of Bacillus subtilis.
172(2), 187-96
1998
Improved protocol for high-throughput cysteine scanning mutagenesis.
25(5), 764-6, 768, 770 passim
1997
Biotechnological applications of recombinant S-layer proteins rSbsA and rSbsB from B. stearothermophilus PV72.
1996
2-D protein crystals as an immobilization matrix for producing reaction zones in dipstick-style immunoassays.
21(5), 918-25
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