Chemistry
Document Type
Article
Abstract
Homeodomain transcription factors (TFs) bind to specific DNA sequences to regulate the expression of target genes. Structural work has provided insight into molecular identities and aided in unraveling structural features of these TFs. However, the detailed affinity and specificity by which these TFs bind to DNA sequences is still largely unknown. Qualitative methods, such as DNA footprinting, Electrophoretic Mobility Shift Assays (EMSAs), Systematic Evolution of Ligands by Exponential Enrichment (SELEX), Bacterial One Hybrid (B1H) systems, Surface Plasmon Resonance (SPR), and Protein Binding Microarrays (PBMs) have been widely used to investigate the biochemical characteristics of TF-DNA binding events. In addition to these qualitative methods, bioinformatic approaches have also assisted in TF binding site discovery. Here we discuss the advantages and limitations of these different approaches, as well as the benefits of utilizing more quantitative approaches, such as Mechanically Induced Trapping of Molecular Interactions (MITOMI), Microscale Thermophoresis (MST) and Isothermal Titration Calorimetry (ITC), in determining the biophysical basis of binding specificity of TF-DNA complexes and improving upon existing computational approaches aimed at affinity predictions.
Publication Title
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms
Publication Date
3-2025
Volume
1868
Issue
1
ISSN
1874-9399
DOI
10.1016/j.bbagrm.2024.195074
Keywords
binding affinity; biophysics, Drosophila, homeodomain, protein-DNA, transcription factor
Repository Citation
Mekkaoui, Fadwa; Drewell, Robert A.; Dresch, Jacqueline M.; and Spratt, Donald E., "Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA" (2025). Chemistry. 44.
https://commons.clarku.edu/chemistry/44
Cross Post Location
Student Publications
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright Conditions
Mekkaoui, F., Drewell, R. A., Dresch, J. M., & Spratt, D. E. (2024). Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 195074.
