ARTGEL: A temperature-regulated electrophoresis platform for quantitative studies of reversible association in gels

Title: ARTGEL: A temperature-regulated electrophoresis platform for quantitative studies of reversible association in gels Abstract: Here we present ARTGEL, an actively regulated-temperature gel electrophoresis platform designed for long-duration experiments under independently controlled thermal and electrical conditions. ARTGEL combines thermoelectric regulation of the gel temperature, a large heated and circulated buffer reservoir, and an automated electrode-wiping mechanism that stabilizes the voltage across the gel during runs exceeding 24 h. The platform was developed to address a limitation of conventional electrophoretic mobility shift assays, which are commonly used to analyze reversible biomolecular association but usually aim to suppress reaction during electrophoresis by dilution, competitors, or reduced temperature so that the gel reports a pre-equilibrated bulk solution. For temperature-sensitive systems, these strategies can alter the chemical state during loading and migration and obscure whether the measured band pattern reflects the original bulk sample or a re-equilibrated state inside the porous gel. Rather than attempting to quench reactions, ARTGEL enables electrophoresis to be performed at the same temperature as complementary bulk measurements, so that reversible association can be quantified directly in the gel and compared with matched measurements in solution. Using DNA origami assemblies, we show that ARTGEL preserves distinct temperature-dependent association states, resolves reaction-dependent distortions of migrating bands, and supports extraction of in-gel kinetic and thermodynamic parameters from reaction–diffusion–advection modeling. Authors (w/ORCID): Rupam Saha - 0009-0000-9567-3010 Seth Fraden* - 0000-0002-2420-9939 Funding: This work is supported by the Brandeis University Materials Research Science and Engineering Center, which is funded by the National Science Foundation under award number DMR-2011846. Description: This repository contains the files required to reproduce and operate the instrument ARTGEL. A detailed description of the instrument can be found in the publication: ARTGEL a temperature-regulated agarose gel electrophoresis platform for quantitative studies of reversible association in gels (https://arxiv.org/abs/2606.09597). The repository is organized as follows: Bill_of_Materials/ BOM.xlsx – Bill of materials listing the components required to build the ARTGEL instrument. Firmware/ TEC_control.ino – Arduino firmware for regulating the thermoelectric (Peltier) module used to control the gel temperature. Buffer_temp_control.ino – Arduino firmware for regulating the immersion heater used to control the buffer reservoir temperature. Software/ user_interface.mlapp – MATLAB graphical user interface (GUI) for operating the instrument. The GUI enables users to monitor and control the gel and buffer temperatures, configure proportional–integral (PI) controller parameters, set the electrophoresis voltage and experiment duration, and record experimental data. Hardware/ plug.stl – 3D-printable model of the well plugs used to block gel wells during long-duration electrophoresis, preventing electrochemical deposits from entering the wells. Documentation/ SI_material.pdf – Supplementary information accompanying the HardwareX manuscript, including additional experimental methods, calibration procedures, controller tuning, and supporting figures. Data/ Scanned gel images/ The raw laser-scanned images of the gels. The file name starts with the reference to the figure in the manuscript or supplementary.pdf. Use ImageJ to open the .gel files. Supplementary/ Movie_S1.mp4 – Supplementary video demonstrating the operation of the ARTGEL instrument during electrophoresis, including buffer circulation, automated electrode wiping, and real-time temperature regulation. Movie_S1_thumbnail.png – Thumbnail image corresponding to Supplementary Movie S1. For building instructions of ARTGEL, please follow the section 5 of the main manuscript.