1. ABOUT THE DATASET -------------------- Title: Data for Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale Creator(s): Chalmers C. C. Chau [1,2], Varun Gupta [2,3], George R. Heath [2,3,4], Christoph Wälti [1,2], Paolo Actis [1,2] Organisation(s): 1 School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK 2 Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK 3 School of Physics & Astronomy, University of Leeds, Leeds, LS2 9JT UK 4 School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT UK Rights-holder(s):Unless otherwise stated, Copyright 2026 University of Leeds Publication Year: 2026 Description: Data used for the associated manuscript "Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale". The repository contains 3 types of data, data associated with high-speed AFM, data associated with solid-state nanopore translocation data, and data associated with the DNA origami design. The high-speed AFM data contains video snapshots of the displacement reaction captured and associated raw image file. The nanopore readout data are in abf format, files can be opened through python with pyABF package or pClamp software. The DNA origami design file can be opened with Cadnano (free to use). Cite as: Chau, Chalmers C.C., Gupta, Varun, Heath, George R. Wälti, Christoph and Actis, Paolo (2026) Data for Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale. University of Leeds. [Dataset] https://doi.org/10.5518/1770 Related publication: C. C. C.Chau, V.Gupta, G. R.Heath, C.Wälti, and P.Actis, Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale, Angewandte Chemie International Edition (2026): e6443787, https://doi.org/10.1002/anie.6443787 Contact: c.c.chau@leeds.ac.uk, G.R.Heath@leeds.ac.uk, P.Actis@leeds.ac.uk 2. TERMS OF USE --------------- Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 3. PROJECT AND FUNDING INFORMATION ---------------------------------- Title: Multiplexed AKI biomarker detection with a single molecule biosensor Dates: Sept 21 - Apr 23 Funding organisation: EPSRC Grant no.: EP/W004933/1 Title: Unlocking the secrets of specialised ribosomes across eukaryotes Dates: Mar 23 - Mar 28 Funding organisation: BBSRC Grant no.: BB/X003086/1 Title: High Resolution Imaging Using Transient Binders Dates: Aug 23 - Aug 28 Funding organisation: EPSRC Grant no.: EP/W034735/1 4. CONTENTS ----------- File listing DNA Origami design_data: DNA Origami design_data.zip, you will find the cadnano design (4FST and 4FSF) and the monomer staple list used in this study as an excel file. high-speed AFM_data: high-speed AFM movies.zip, inside you will find a Statistic excel file that shows the calculation for figure 3 and the associated HS-AFM movies. Nanopore_data: all the nanopore files (.abf) is organised based on associated figure as a .zip file 5. METHODS ---------- Detail method can be found in the associated publication. For high-speed AFM, All high speed-atomic force microscopy (HS-AFM) measurements were performed using a NanoRacer HS-AFM (Bruker, Germany) instrument in amplitude modulation mode. All HS-AFM measurements were obtained in liquid and ambient temperature in an acoustic isolation housing on an active antivibration table using short cantilevers (USC-F1.2-k0.15, NanoWorld, Switzerland) with nominal spring constants of 0.15 N·m–1, resonance frequencies of ∼0.6 MHz and quality factors of ∼2. To prepare the sample for HS-AFM imagining of DNA Origami, freshly cleaved mica was treated with 5 µl of 10 mM Ni2+/Mg2+ salt solution, to promote the adsorption of DNA origami to the mica. Thereafter, 2-4 μl of DNA Origami sample was incubated on the mica and left for incubation for 2-3 minutes before rinsing, with 5 via fluid exchange with 5 µl of buffer solution. The sample holder was then filled with 1 ml with imaging buffer (5 mM Tris-HCl (pH 8.0), 1 mM EDTA, 20 mM MgCl2 and 5 mM NaCl). To visualize TMSD, 10 µl of the invader strands at a concentration of 1 µM were added to the imaging buffer. The images and videos were analysed with NanoLocz image analysis software (v1.30). For Nanopore, Quartz capillaries of 1.0 mm outer diameter and 0.5 mm inner diameter (QF100-50-7.5; Sutter Instrument) were used to fabricate the glass nanopores using the SU-P2000 laser puller (World Precision Instruments). A two-line protocol was used: line 1, HEAT 750/FIL 4/VEL 30/DEL 150/PUL 80, followed by line 2, HEAT 700/FIL 3/VEL 40/DEL 135/PUL 180. The pulling protocol was instrument specific, and these would vary between different laser pullers. The generation of the polymer electrolyte bath followed previously published method 41. To generate 40 ml of the polymer electrolyte with a composition of 50% (w/v) PEG 35K, 0.1 M KCl, 4 ml of 1 M KCl was mixed with 16 ml of ddH2O and 20 g of PEG 35K (81310; Sigma) inside a 50 ml centrifuge tube. The tube was then incubated at 85°C for 2 hours and left over night at 37°C, electrolyte was then aliquoted inside multiple 7 ml Bijou tubes, stored on shelves away from sunlight at room temperature (E1412-0710; Starlab), the aliquot would be discarded after 1 month since the first immersion of the nanopore and 6 months after the initial generation. The translocation experiment followed a similar procedure from the previous publications The glass nanopores were all filled with 9.4 ng/µl of origami (4 nM for monomers, 2 nM for dimer), all origami were diluted in the origami buffer without further addition of any salt. In each measurement, the glass nanopore was fitted with an Ag/AgCl working electrode and immersed into the polymer electrolyte bath with an Ag/AgCl reference electrode. The ionic current trace was recorded using a MultiClamp 700B patch-clamp amplifier (Molecular Devices) in voltage-clamp mode. The signal was filtered using a low-pass filter at 20 kHz unless specified, digitized with a Digidata 1550B at a 100 kHz (10 μs) sampling rate, and recorded using the software pClamp 10 (Molecular Devices). Unless otherwise specified, all translocations were carried out at -500 mV. The python code used to perform the translocation event detection could be accessed at https://github.com/chalmers4c/Nanopore_event_detection. For all events calling, a threshold line of 7 sigmas away from baseline is used. For DNA origami design, the Cadnano2 software was used to create the DNA nanostructure.