The Power of Tiny Spaces

Andrieu-Brunsen A, Azzaroni O, Binyaminov H, Danil de Namor A, Fyta M, García-Martínez J, Guldin S, Howorka S, Lamotte S, Lemay SG, Lotsch BV, Magdassi S, Nakanishi K, Plueg C, Polarz S, Pozzo L, Rafti M, Rehahn M, Roth AG, Sanchez C, Scherlis DA, Soler-Illia GJAA, Szleifer I, Tschulik K, Thommes M, Toimil-Molares E

JACS Au, 6(8), 4353-4366

Sequencing peptides by reversing translation

Howorka S

Nat Biotechnol, 10.1038/s41587-026-03108-1

Autonomous Homeostatic Synthetic Cells via Self-Gating DNA Nanopores

Molecular Interactions within Nanoconfinement of Model DNA Nanostructures Controlled by Compensatory Kinetics as Revealed by Single-Molecule Fluorescence Analysis

Hagleitner-Ertuğrul N, Xing Y, Pfeffermann J, Rottensteiner A, Gaugutz A, Knyazev DG, Pohl P, Howorka S

JACS Au, 5(9), 4427-4438

Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics

Dorey A, Howorka S

Nat Chem, 16(3), 314-334

Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes

Bennett ID, Burns JR, Ryadnov MG, Howorka S, Pyne ALB

Small, 20(35), e2207585

DNA Origami – Lipid Membrane Interactions Controlled by Nanoscale Sterics

Georgiou E, Cabello-Garcia J, Xing Y, Howorka S

Small, 20(42), e2404720

Unfolding the path to nanopore protein sequencing

Dorey A, Howorka S

Nat Nanotechnol, 18(11), 1259-1260

Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

Ahmad K, Javed A, Lanphere C, Coveney PV, Orlova EV, Howorka S

Nat Commun, 14(1), 3630

Nanopores: synergy from DNA sequencing to industrial filtration – small holes with big impact

Siwy ZS, Bruening ML, Howorka S

Chem Soc Rev, 52(6), 1983-1994

Multi‐Stimuli‐Responsive and Mechano‐Actuated Biomimetic Membrane Nanopores Self‐Assembled from DNA

Xing Y, Dorey A, Howorka S

Adv Mater, 35(29), e2300589

Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy

Suh SH, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P

Nano Lett, 23(10), 4439-4447

Functional Nanopores Enabled with DNA

Xing Y, Rottensteiner A, Ciccone J, Howorka S

Angew Chem Int Ed Engl, 62(33), e202303103

DNA Origami – Lipid Membrane Interactions Defined at Single-Molecular Resolution

Triggered Assembly of a DNA-Based Membrane Channel

Lanphere C, Ciccone J, Dorey A, Hagleitner-Ertuğrul N, Knyazev D, Haider S, Howorka S

J Am Chem Soc, 144(10), 4333-4344

Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility

van Dyck JF, Burns JR, Le Huray KIP, Konijnenberg A, Howorka S, Sobott F

Nat Commun, 13(1), 3610

Rebuilding research

Howorka S

Nat Rev Chem, 6(2), 81-82

Highly shape- and size-tunable membrane nanopores made with DNA

Xing Y, Dorey A, Jayasinghe L, Howorka S

Nat Nanotechnol, 17(7), 708-713

A reversibly gated protein-transporting membrane channel made of DNA

Dey S, Dorey A, Abraham L, Xing Y, Zhang I, Zhang F, Howorka S, Yan H

Nat Commun, 13(1), 2271

A Light‐Triggered Synthetic Nanopore for Controlling Molecular Transport Across Biological Membranes

Offenbartl-Stiegert D, Rottensteiner A, Dorey A, Howorka S

Angew Chem Int Ed Engl, 61(52), e202210886

Protein Transport through Nanopores Illuminated by Long-Time-Scale Simulations

Mitscha-Baude G, Stadlbauer B, Howorka S, Heitzinger C

ACS Nano, 15(6), 9900-9912

Principles of Small-Molecule Transport through Synthetic Nanopores

Diederichs T, Ahmad K, Burns JR, Nguyen QH, Siwy ZS, Tornow M, Coveney PV, Tampé R, Howorka S

ACS Nano, 15(10), 16194-16206

Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes

Jones SF, Joshi H, Terry SJ, Burns JR, Aksimentiev A, Eggert US, Howorka S

J Am Chem Soc, 143(22), 8305-8313

DNA Nanodevices with Selective Immune Cell Interaction and Function

Arulkumaran N, Lanphere C, Gaupp C, Burns JR, Singer M, Howorka S

ACS Nano, 15(3), 4394-4404

Design, assembly, and characterization of membrane-spanning DNA nanopores

Lanphere C, Offenbartl-Stiegert D, Dorey A, Pugh G, Georgiou E, Xing Y, Burns JR, Howorka S

Nat Protoc, 16(1), 86-130

A Biomimetic DNA‐Based Membrane Gate for Protein‐Controlled Transport of Cytotoxic Drugs

Lanphere C, Arnott PM, Jones SF, Korlova K, Howorka S

Angew Chem Int Ed Engl, 60(4), 1903-1908

Reading amino acids in a nanopore

Howorka S, Siwy ZS

Nat Biotechnol, 38(2), 159-160

Synthetic protein-conductive membrane nanopores built with DNA

Diederichs T, Pugh G, Dorey A, Xing Y, Burns JR, Hung Nguyen Q, Tornow M, Tampé R, Howorka S

Nat Commun, 10(1), 5018

Structural and Functional Stability of DNA Nanopores in Biological Media

Burns JR, Howorka S

Nanomaterials (Basel), 9(4), 490

Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions

Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF

J Am Chem Soc, 141(2), 1100-1108

Solvent-dependent photophysics of a red-shifted, biocompatible coumarin photocage

Offenbartl-Stiegert D, Clarke TM, Bronstein H, Nguyen HP, Howorka S

Org Biomol Chem, 17(25), 6178-6183

Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures

Whitehouse WL, Noble JE, Ryadnov MG, Howorka S

Bioconjug Chem, 30(7), 1836-1844

A Temperature-Gated Nanovalve Self-Assembled from DNA to Control Molecular Transport across Membranes

Arnott PM, Howorka S

ACS Nano, 13(3), 3334-3340

A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation

Nguyen HP, Stewart S, Kukwikila MN, Jones SF, Offenbartl-Stiegert D, Mao S, Balasubramanian S, Beck S, Howorka S

Angew Chem Int Ed Engl, 58(20), 6620-6624

Tunable DNA Hybridization Enables Spatially and Temporally Controlled Surface-Anchoring of Biomolecular Cargo

Hager R, Arnold A, Sevcsik E, Schütz GJ, Howorka S

Langmuir, 34(49), 15021-15027

Nucleic Acids Nanoscience at Interfaces Special Issue

Zuilhof H, Albada B, Armitage B, Howorka S

Langmuir, 34(49), 14691

Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials.

Birkholz O, Burns JR, Richter CP, Psathaki OE, Howorka S, Piehler J

Nat Commun, 9(1), 1521

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes

Arnott PM, Joshi H, Aksimentiev A, Howorka S

Langmuir, 34(49), 15084-15092

Defined Bilayer Interactions of DNA Nanopores Revealed with a Nuclease-Based Nanoprobe Strategy

Burns JR, Howorka S

ACS Nano, 12(4), 3263-3271

Stability and dynamics of membrane-spanning DNA nanopores.

Maingi V, Burns JR, Uusitalo JJ, Howorka S, Marrink SJ, Sansom MS

Nat Commun, 8, 14784

DNA nanotechnology: Bringing lipid bilayers into shape.

Howorka S

Nat Chem, 9(7), 611-613

Building membrane nanopores.

Howorka S

Nat Nanotechnol, 12(7), 619-630

Arrays of Individual DNA Molecules on Nanopatterned Substrates.

Hager R, Halilovic A, Burns JR, Schäffler F, Howorka S

Sci Rep, 7, 42075

NANOTECHNOLOGY. Changing of the guard.

Howorka S

Science, 352(6288), 890-1

Nanopores and Nanochannels: From Gene Sequencing to Genome Mapping.

Howorka S, Siwy Z

ACS Nano, 10(11), 9768-9771

Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

Hager R, Burns JR, Grydlik MJ, Halilovic A, Haselgrübler T, Schäffler F, Howorka S

Small, 12(21), 2877-84

Biomimetic Hybrid Nanocontainers with Selective Permeability

Messager L, Burns JR, Kim J, Cecchin D, Hindley J, Pyne AL, Gaitzsch J, Battaglia G, Howorka S

Angew Chem Int Ed Engl, 55(37), 11106-9

A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane.

Burns JR, Seifert A, Fertig N, Howorka S

Nat Nanotechnol, 11(2), 152-6

Nanopore-based electrical and label-free sensing of enzyme activity in blood serum.

Kukwikila M, Howorka S

Anal Chem, 87(18), 9149-54

Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations.

Maingi V, Lelimousin M, Howorka S, Sansom MS

ACS Nano, 9(11), 11209-17

Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance.

Ficici E, Andricioaei I, Howorka S

Nano Lett, 15(7), 4822-8

Broadening students' minds.

Lukeman PS, Howorka S

Nat Nanotechnol, 10(11), 992

Bilayer-spanning DNA nanopores with voltage-switching between open and closed state.

Seifert A, Göpfrich K, Burns JR, Fertig N, Keyser UF, Howorka S

ACS Nano, 9(2), 1117-26

Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG

Goyal P, Krasteva PV, Van Gerven N, Gubellini F, Van den Broeck I, Troupiotis-Tsaïlaki A, Jonckheere W, Péhau-Arnaudet G, Pinkner JS, Chapman MR, Hultgren SJ, Howorka S, Fronzes R, Remaut H

Nature, 516(7530), 250-3

S-layer structure in bacteria and archaea

Nanomicrobiology: Physiological and Environmental Characteristics

Microarrays and single molecules: an exciting combination.

Howorka S, Hesse J

Soft Matter, 10(7), 931-41

Membrane-spanning DNA nanopores with cytotoxic effect.

Burns JR, Al-Juffali N, Janes SM, Howorka S

Angew Chem Int Ed Engl, 53(46), 12466-70

DNA-modified polymer pores allow pH- and voltage-gated control of channel flux.

Buchsbaum SF, Nguyen G, Howorka S, Siwy ZS

J Am Chem Soc, 136(28), 9902-5

Self-assembled DNA nanopores that span lipid bilayers.

Burns JR, Stulz E, Howorka S

Nano Lett, 13(6), 2351-6

Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor.

Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S

Angew Chem Int Ed Engl, 52(46), 12069-72

DNA nanoarchitectonics: assembled DNA at interfaces.

Howorka S

Langmuir, 29(24), 7344-53

Disentangling steric and electrostatic factors in nanoscale transport through confined space.

Buchsbaum SF, Mitchell N, Martin H, Wiggin M, Marziali A, Coveney PV, Siwy Z, Howorka S

Nano Lett, 13(8), 3890-6

SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly.

Baranova E, Fronzes R, Garcia-Pino A, Van Gerven N, Papapostolou D, Péhau-Arnaudet G, Pardon E, Steyaert J, Howorka S, Remaut H

Nature, 487(7405), 119-22

Painting with biomolecules at the nanoscale: biofunctionalization with tunable surface densities.

Schlapak R, Danzberger J, Haselgrübler T, Hinterdorfer P, Schäffler F, Howorka S

Nano Lett, 12(4), 1983-9

Nanoscale DNA tetrahedra improve biomolecular recognition on patterned surfaces.

Schlapak R, Danzberger J, Armitage D, Morgan D, Ebner A, Hinterdorfer P, Pollheimer P, Gruber HJ, Schäffler F, Howorka S

Small, 8(1), 89-97

Nanopores as protein sensors.

Howorka S, Siwy ZS

Nat Biotechnol, 30(6), 506-7

The structure of bacterial S-layer proteins.

Pavkov-Keller T, Howorka S, Keller W

Prog Mol Biol Transl Sci, 103, 73-130

Single-molecule AFM characterization of individual chemically tagged DNA tetrahedra.

Leitner M, Mitchell N, Kastner M, Schlapak R, Gruber HJ, Hinterdorfer P, Howorka S, Ebner A

ACS Nano, 5(9), 7048-54

Rationally engineering natural protein assemblies in nanobiotechnology.

Howorka S

Curr Opin Biotechnol, 22(4), 485-91

Nanoimaging, molecular interaction, and Nanotemplating of human rhinovirus

NanoScience and Technology

Molecular assembly in natural and engineered systems. Preface.

Howorka S

Prog Mol Biol Transl Sci, 103, xi-xii

DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics.

Nguyen G, Howorka S, Siwy ZS

J Membr Biol, 239(1-2), 105-13

Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns.

Zhu R, Howorka S, Pröll J, Kienberger F, Preiner J, Hesse J, Ebner A, Pastushenko VP, Gruber HJ, Hinterdorfer P

Nat Nanotechnol, 5(11), 788-91

Interfacial dipole dynamics of light-emitting diodes incorporating a poly(amidoamine) dendrimer monolayer

Applied Physics Letters

Improved Kelvin probe force microscopy for imaging individual DNA molecules on insulating surfaces

Applied Physics Letters

Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus.

Kinns H, Badelt-Lichtblau H, Egelseer EM, Sleytr UB, Howorka S

J Mol Biol, 395(4), 742-53

Engineered voltage-responsive nanopores.

Siwy ZS, Howorka S

Chem Soc Rev, 39(3), 1115-32

Electrically sensing protease activity with nanopores.

Kukwikila M, Howorka S

J Phys Condens Matter, 22(45), 454103

Chemical tags mediate the orthogonal self-assembly of DNA duplexes into supramolecular structures.

Mitchell N, Ebner A, Hinterdorfer P, Tampé R, Howorka S

Small, 6(16), 1732-5

Biosensors and biofuel cells with engineered proteins.

Caruana DJ, Howorka S

Mol Biosyst, 6(9), 1548-56

Topography and recognition imaging of protein-patterned surfaces generated by AFM nanolithography.

Zhu R, Ebner A, Kastner M, Preiner J, Howorka S, Hinterdorfer P

Chemphyschem, 10(9-10), 1478-81

Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates.

Borsenberger V, Kukwikila M, Howorka S

Org Biomol Chem, 7(18), 3826-35

Semipermeable poly(ethylene glycol) films: The relationship between permeability and molecular structure of polymer chains

Soft Matter

Selective protein and DNA adsorption on PLL-PEG films modulated by ionic strength

Soft Matter

Receptor arrays for the selective and efficient capturing of viral particles.

Pollheimer PD, Kastner M, Ebner A, Blaas D, Hinterdorfer P, Gruber HJ, Howorka S

Bioconjug Chem, 20(3), 466-75

Nanopores: Generation, engineering and single-molecule applications

Handbook of Single-Molecule Biophysics

Nanopore analytics: sensing of single molecules.

Howorka S, Siwy Z

Chem Soc Rev, 38(8), 2360-84

Imaging surface charges of individual biomolecules.

Leung C, Kinns H, Hoogenboom BW, Howorka S, Mesquida P

Nano Lett, 9(7), 2769-73

Engineering and exploiting protein assemblies in synthetic biology.

Papapostolou D, Howorka S

Mol Biosyst, 5(7), 723-32

Diene-modified nucleotides for the Diels-Alder-mediated functional tagging of DNA.

Borsenberger V, Howorka S

Nucleic Acids Res, 37(5), 1477-85

Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations.

Martin HS, Jha S, Howorka S, Coveney PV

J Chem Theory Comput, 5(8), 2135-48

Chemically labeled nucleotides and oligonucleotides encode DNA for sensing with nanopores.

Borsenberger V, Mitchell N, Howorka S

J Am Chem Soc, 131(22), 7530-1

A DNA nanostructure for the functional assembly of chemical groups with tunable stoichiometry and defined nanoscale geometry.

Mitchell N, Schlapak R, Kastner M, Armitage D, Chrzanowski W, Riener J, Hinterdorfer P, Ebner A, Howorka S

Angew Chem Int Ed Engl, 48(3), 525-7

The surface location of individual residues in a bacterial S-layer protein.

Kinns H, Howorka S

J Mol Biol, 377(2), 589-604

Self-assembled monolayers of protonated poly(amidoamine) dendrimers on indium tin oxide

Applied Physics Letters

Chemical tags facilitate the sensing of individual DNA strands with nanopores.

Mitchell N, Howorka S

Angew Chem Int Ed Engl, 47(30), 5565-8

Atomic force microscopy-derived nanoscale chip for the detection of human pathogenic viruses.

Artelsmair H, Kienberger F, Tinazli A, Schlapak R, Zhu R, Preiner J, Wruss J, Kastner M, Saucedo-Zeni N, Hoelzl M, Rankl C, Baumgartner W, Howorka S, Blaas D, Gruber HJ, Tampé R, Hinterdorfer P

Small, 4(6), 847-54

Stochastic detection of motor protein-RNA complexes by single-channel current recording.

Astier Y, Kainov DE, Bayley H, Tuma R, Howorka S

Chemphyschem, 8(15), 2189-94

Sizing trinucleotide repeat sequences by single-molecule analysis of fluorescence brightness.

Schlapak R, Kinns H, Wechselberger C, Hesse J, Howorka S

Chemphyschem, 8(11), 1618-21

Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement.

Drbal K, Moertelmaier M, Holzhauser C, Muhammad A, Fuertbauer E, Howorka S, Hinterberger M, Stockinger H, Schütz GJ

Int Immunol, 19(5), 675-84

Preparation and characterization of dense films of poly(amidoamine) dendrimers on indium tin oxide.

Schlapak R, Armitage D, Saucedo-Zeni N, Latini G, Gruber HJ, Mesquida P, Samotskaya Y, Hohage M, Cacialli F, Howorka S

Langmuir, 23(17), 8916-24

Nanoscale protein pores modified with PAMAM dendrimers.

Martin H, Kinns H, Mitchell N, Astier Y, Madathil R, Howorka S

J Am Chem Soc, 129(31), 9640-9

Dense passivating poly(ethylene glycol) films on indium tin oxide substrates.

Schlapak R, Armitage D, Saucedo-Zeni N, Hohage M, Howorka S

Langmuir, 23(20), 10244-53

Creating regular arrays of nanoparticles with self-assembling protein building blocks

Journal of Materials Chemistry

RNA expression profiling at the single molecule level.

Hesse J, Jacak J, Kasper M, Regl G, Eichberger T, Winklmayr M, Aberger F, Sonnleitner M, Schlapak R, Howorka S, Muresan L, Frischauf AM, Schütz GJ

Genome Res, 16(8), 1041-5

Glass surfaces grafted with high-density poly(ethylene glycol) as substrates for DNA oligonucleotide microarrays.

Schlapak R, Pammer P, Armitage D, Zhu R, Hinterdorfer P, Vaupel M, Frühwirth T, Howorka S

Langmuir, 22(1), 277-85

Protein components for nanodevices.

Astier Y, Bayley H, Howorka S

Curr Opin Chem Biol, 9(6), 576-84

Nanopatterning of biomolecules with microscale beads.

Pammer P, Schlapak R, Sonnleitner M, Ebner A, Zhu R, Hinterdorfer P, Höglinger O, Schindler H, Howorka S

Chemphyschem, 6(5), 900-3

Stochastic detection of monovalent and bivalent protein-ligand interactions.

Howorka S, Nam J, Bayley H, Kahne D

Angew Chem Int Ed Engl, 43(7), 842-6

Probing distance and electrical potential within a protein pore with tethered DNA.

Howorka S, Bayley H

Biophys J, 83(6), 3202-10

High-throughput scanning mutagenesis by recombination polymerase chain reaction.

Howorka S, Bayley H

Methods Mol Biol, 182, 139-47

Sequence-specific detection of individual DNA strands using engineered nanopores.

Howorka S, Cheley S, Bayley H

Nat Biotechnol, 19(7), 636-9

Location of a constriction in the lumen of a transmembrane pore by targeted covalent attachment of polymer molecules.

Movileanu L, Cheley S, Howorka S, Braha O, Bayley H

J Gen Physiol, 117(3), 239-52

Kinetics of duplex formation for individual DNA strands within a single protein nanopore.

Howorka S, Movileanu L, Braha O, Bayley H

Proc Natl Acad Sci U S A, 98(23), 12996-3001

Surface-accessible residues in the monomeric and assembled forms of a bacterial surface layer protein.

Howorka S, Sára M, Wang Y, Kuen B, Sleytr UB, Lubitz W, Bayley H

J Biol Chem, 275(48), 37876-86

Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore.

Movileanu L, Howorka S, Braha O, Bayley H

Nat Biotechnol, 18(10), 1091-5

A protein pore with a single polymer chain tethered within the lumen

Journal of the American Chemical Society

Self-assembly product formation of the Bacillus stearothermophilus PV72/p6 S-layer protein SbsA in the course of autolysis of Bacillus subtilis.

Howorka S, Sára M, Lubitz W, Kuen B

FEMS Microbiol Lett, 172(2), 187-96

Improved protocol for high-throughput cysteine scanning mutagenesis.

Howorka S, Bayley H

Biotechniques, 25(5), 764-6, 768, 770 passim

Biotechnological applications of recombinant S-layer proteins rSbsA and rSbsB from B. stearothermophilus PV72.

FMES Molecular Biology Reviews

2-D protein crystals as an immobilization matrix for producing reaction zones in dipstick-style immunoassays.

Breitwieser A, Küpcü S, Howorka S, Weigert S, Langer C, Hoffmann-Sommergruber K, Scheiner O, Sleytr UB, Sára M

Biotechniques, 21(5), 918-25