Professor Alice Pyne

• Journal articles
• Chapters
• Conference proceedings papers
• Software / Code
• Datasets
• Other
• Preprints

Journal articles

• Poole S, Aning OA, McKee V, Catley T, Nielsen AY, Thisgaard H, Johansson P, Menounou G, Hennessy J, Slator C , Gibney A et al (2025) Design and in vitr o anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease. Nucleic Acids Research, 53(1).
• Smith QM, Aramayo RJ, Rollins DE, Pyne ALB, Morris KL & Rueda DS (2024) Structural basis of negative supercoiling induced Cas9 off-targeting. Biophysical Journal, 123(3), 320a-320a.
• Newton MD, Lewis JS, Anand R, Holmes EP, Pyne ALB & Boulton SJ (2023) Direct observation of Shelterin dynamics and T-loop formation at telomeres. Biophysical Journal, 122(3), 9a-10a.
• Haynes PJ, Main KHS, Akpinar B & Pyne ALB (2022) Atomic Force Microscopy of DNA and DNA-Protein Interactions.. Methods Mol Biol, 2476, 43-62.
• Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA & Pyne ALB (2021) Atomic force microscopy—a tool for structural and translational DNA research. APL Bioengineering, 5.
• Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW , Bates AD et al (2021) Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature Communications, 12. View this article in WRRO
• Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB (2021) TopoStats – A program for automated tracing of biomolecules from AFM images. Methods. View this article in WRRO
• Hammond K, Benn G, Bennett I, Parsons ES, Ryadnov MG, Hoogenboom BW & Pyne ALB (2021) Imaging the Effects of Peptide Materials on Phospholipid Membranes by Atomic Force Microscopy, 225-235.
• Bennett I, Pyne ALB & McKendry RA (2020) Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing. ACS Sensors, 5(10), 3133-3139. View this article in WRRO
• Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW (2019) Imaging live bacteria at the nanoscale: comparison of immobilisation strategies. The Analyst, 144(23), 6944-6952. View this article in WRRO
• Parsons ES, Stanley GJ, Pyne ALB, Hodel AW, Nievergelt AP, Menny A, Yon AR, Rowley A, Richter RP, Fantner GE , Bubeck D et al (2019) Single-molecule kinetics of pore assembly by the membrane attack complex. Nature Communications, 10(1), ---. View this article in WRRO
• Akpinar B, Haynes PJ, Bell NAW, Brunner K, Pyne ALB & Hoogenboom BW (2019) PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy. Nanoscale, 11(42), 20072-20080. View this article in WRRO
• Heesterbeek DAC, Bardoel BW, Parsons ES, Bennett I, Ruyken M, Doorduijn DJ, Gorham RD, Berends ETM, Pyne ALB, Hoogenboom BW & Rooijakkers SHM (2019) Bacterial killing by complement requires membrane attack complex formation via surface‐bound C5 convertases. The EMBO Journal, 38(4).
• Pfeil M-P, Pyne ALB, Losasso V, Ravi J, Lamarre B, Faruqui N, Alkassem H, Hammond K, Judge PJ, Winn M , Martyna GJ et al (2018) Author Correction: Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms. Scientific Reports, 8(1).
• Pfeil M-P, Pyne ALB, Losasso V, Ravi J, Lamarre B, Faruqui N, Alkassem H, Hammond K, Judge PJ, Winn M , Martyna GJ et al (2018) Tuneable poration : host defense peptides as sequence probes for antimicrobial mechanisms. Scientific Reports, 8(1). View this article in WRRO
• Burns JR, Lamarre B, Pyne ALB, Noble JE & Ryadnov MG (2018) DNA Origami Inside-Out Viruses. ACS Synthetic Biology, 7(3), 767-773.
• Heesterbeek DAC, Bardoel BW, Bennett I, Pyne A, Berends ETM, Ruyken M, Hoogenboom B & Rooijakkers SHM (2017) The role of C5 convertases in membrane attack complex dependent killing of Gram-negative bacteria. Molecular Immunology, 89, 154-154.
• Pyne A, Pfeil M-P, Bennett I, Ravi J, Iavicoli P, Lamarre B, Roethke A, Ray S, Jiang H, Bella A , Reisinger B et al (2017) Engineering monolayer poration for rapid exfoliation of microbial membranes. Chemical Science, 8(2), 1105-1115.
• Messager L, Burns JR, Kim J, Cecchin D, Hindley J, Pyne ALB, Gaitzsch J, Battaglia G & Howorka S (2016) Biomimetic Hybrid Nanocontainers with Selective Permeability. Angewandte Chemie, 128(37), 11272-11275.
• Messager L, Burns JR, Kim J, Cecchin D, Hindley J, Pyne ALB, Gaitzsch J, Battaglia G & Howorka S (2016) Biomimetic Hybrid Nanocontainers with Selective Permeability. Angewandte Chemie International Edition, 55(37), 11106-11109.
• Pyne A, Thompson R, Leung C, Roy D & Hoogenboom BW (2014) Single-Molecule Reconstruction of Oligonucleotide Secondary Structure by Atomic Force Microscopy. Small, 10(16), 3257-3261. View this article in WRRO
• Rakowska PD, Jiang H, Ray S, Pyne A, Lamarre B, Carr M, Judge PJ, Ravi J, M. Gerling UI, Koksch B , Martyna GJ et al (2013) Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers. Proceedings of the National Academy of Sciences, 110(22), 8918-8923.
• Leung C, Bestembayeva A, Thorogate R, Stinson J, Pyne A, Marcovich C, Yang J, Drechsler U, Despont M, Jankowski T , Tschöpe M et al (2012) Atomic Force Microscopy with Nanoscale Cantilevers Resolves Different Structural Conformations of the DNA Double Helix. Nano Letters, 12(7), 3846-3850.
• Pyne A, Marks W, M. Picco L, G. Dunton P, Ulcinas A, E. Barbour M, B. Jones S, Gimzewski J & J. Miles M (2009) High-speed atomic force microscopy of dental enamel dissolution in citric acid. Archives of Histology and Cytology, 72(4/5), 209-215.
• Holmes EP, Gamill MC, Provan JI, Wiggins L, Rusková R, Whittle S, Catley TE, Main KHS, Shephard N, Bryant HE , Gilhooly NS et al () Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy. Nature Communications, 16(1).
• Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW () Complement-mediated killing of Escherichia coli by mechanical destabilization of the cell envelope. The EMBO Journal.
• Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne A () Multiscale topological analysis of kinetoplast DNA via high resolution AFM. Physical Chemistry Chemical Physics.
• Bennett ID, Burns JR, Ryadnov MG, Howorka S & Pyne ALB () Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes. Small.
• dos Santos Á, Rollins DE, Hari-Gupta Y, McArthur H, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Lambert D , Brown I et al () Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription. Nature Communications, 14(1).
• Klejevskaja B, Pyne ALB, Reynolds M, Shivalingam A, Thorogate R, Hoogenboom BW, Ying L & Vilar R () Studies of G-quadruplexes formed within self-assembled DNA mini-circles. Chemical Communications, 52(84), 12454-12457.

Chapters

• Tor Y, Gehring K, Fabris D, Egli M, Korostelev AA, Craggs TD, Pyne A, Gagnon KT, Watts JK, Cheatham III TE & Richards NGJ (2022) Online Content: Physical and Structural Techniques Applied to Nucleic Acids, Nucleic Acids in Chemistry and Biology (pp. E1-E50). The Royal Society of Chemistry
• Pyne ALB & Hoogenboom BW (2016) Imaging DNA Structure by Atomic Force Microscopy, Methods in Molecular Biology (pp. 47-60). Springer New York
• Egli M, Flavell A, Pyle AM, Wilson WD, Haq SI, Luisi B, Fisher J, Laughton C, Allen S, Engels J , Grasby JA et al (2006) Nucleic Acids in Chemistry and Biology In Blackburn GM, Gait MJ, Loakes D & Williams DM (Ed.) The Royal Society of Chemistry

Conference proceedings papers

• Ravi J, Pfeil MP & Pyne AL (2019) Probing antimicrobial mechanisms for effective strategies to overcome resistance. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 48 (pp S223-S223)
• Pyne ALB, Hoogenboom BW, Vilar R & Maxwell A (2017) Visualisation of DNA conformational changes in situ at nanometre resolution. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S369-S369)
• Yon AR, Pyne ALB, Kwakwa K, Lowe AR, Williams WA & Hoogenboom BW (2017) A combinatorial single-molecule study of ligand-gated ion channels and monoclonal antibodies. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S371-S371)
• Pyne ALB, Pfeil M-P, Bennett I, Ravi J, Lamarre B, Hoogenboom BW & Ryadnov MG (2017) Investigating the mechanism of action of a novel antimicrobial peptide on live E. coli cells. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S389-S389)

Software / Code

• Beton J, Pyne A, Joseph AP & Topf M TopoStats - an automated tracing program for AFM images.

Datasets

• J P, H K & Pyne A 2 Methods for DNA Adsorption on a Mica Substrate for AFM Imaging in Fluid v1 (protocols.io.bncjmaun).
• J P, H K & Pyne A Atomic Force Microscopy of DNA and DNA-Protein Interactions v1 (protocols.io.bncemate).
• J P, H K & Pyne A 3 Pre-imaging Setup for High Resolution AFM in Fluid v1 (protocols.io.bncnmave).
• J P, H K & Pyne A 5 Methods for DNA-protein imaging by AFM in fluid v1 (protocols.io.bncqmavw).
• J P, H K & Pyne A 1 Preparation of Mica Substrate v1 (protocols.io.bnb2maqe).
• J P, H K & Pyne A 4 Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA v1 (protocols.io.bncpmavn).

Other

• Pyne A () Protocol for AFM image processing using Gwyddion.

Preprints

• Holleman E, Catley TE, Sereiva T, Hartono SR, Pyne ALB & Chédin F (2025) Protein-mediated stabilization and nicking of the non-template DNA strand dramatically affect R-loop formationin vitro, Cold Spring Harbor Laboratory.
• Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS & Pyne ALB (2024) Multiscale topological analysis of kinetoplast DNA via high-resolution AFM, Cold Spring Harbor Laboratory.
• Gamill MC, Holmes EP, Provan JI, Wiggins L, Rusková R, Whittle S, Catley TE, Main KHS, Shephard N, Bryant HE , Račko D et al (2024) Under or Over? Tracing Complex DNA Topologies with High Resolution Atomic Force Microscopy, Cold Spring Harbor Laboratory.
• Benn G, Bortolini C, Roberts DM, Pyne ALB, Holden S & Hoogenboom BW (2023) Complement-mediated killing of bacteria by mechanical destabilization of the cell envelope, Cold Spring Harbor Laboratory.
• Parsons ES, Stanley GJ, Pyne ALB, Hodel AW, Nievergelt AP, Menny A, Yon AR, Rowley A, Richter RP, Fantner GE , Bubeck D et al (2018) Single-molecule kinetics of pore assembly by the membrane attack complex, bioRxiv.
• dos Santos Á, Rollins DE, Hari-Gupta Y, Reed HCW, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Brown I , Howland K et al () Autophagy receptor NDP52 alters DNA conformation to modulate RNA Polymerase II transcription, Cold Spring Harbor Laboratory.
• Beton JG, Moorehead R, Helfmann L, Gray R, Hoogenboom BW, Joseph AP, Topf M & Pyne ALB () TopoStats – a program for automated tracing of biomolecules from AFM images.
• Pyne ALB, Noy A, Main K, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW , Bates AD et al () Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.
• Benn G, Pyne ALB, Ryadnov MG & Hoogenboom BW () Imaging live bacteria at the nanoscale: comparison of immobilisation strategies.
• Akpinar B, Bell NAW, Pyne ALB & Hoogenboom BW () PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy.
• Bennett I, Pyne A & McKendry R () Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing.