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Updated: May 1, 2026

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides
Published on: November 29, 2016
Single molecule visualization and characterization of Sox2-Pax6 complex formation on a regulatory DNA element using a
Seigi Yamamoto1, Debojyoti De, Kumi Hidaka
1Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
Abstract:
We report the use of atomic force microscopy (AFM) to study Sox2-Pax6 complex formation on the regulatory DNA element at a single molecule level. Using an origami DNA scaffold containing two DNA strands with different levels of tensile force, we confirmed that DNA bending is necessary for Sox2 binding. We also demonstrated that two transcription factors bind cooperatively by observing the increased occupancy of Sox2-Pax6 on the DNA element compared to that of Sox2 alone.
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