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Kinetically Trapped Ligand Binding in DNA Tandem Repeats.
Rabia Tahir1, Shankar Pandey1, Jacob Haller1
1Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, United States.
Biochemistry
|February 17, 2026
Summary
Ligand binding to DNA tandem repeats can lead to kinetically trapped states, not just stable ones. This groundbreaking finding reveals a new mechanism in molecular interactions within the genome.
Area of Science:
- Genomics
- Molecular Biology
- Biophysics
Background:
- Tandem DNA repeats are prevalent in the human genome, influencing gene regulation.
- Investigating ligand binding to these repeats is difficult with traditional methods like NMR and X-ray crystallography due to ensemble averaging.
Purpose of the Study:
- To investigate the binding mechanism between netropsin and adenine-thymine (A-T) DNA repeats using single-molecule techniques.
- To explore the potential for kinetically trapped states in ligand-DNA interactions within tandem repeats.
Main Methods:
- Utilized optical tweezers, a single-molecule technique with high sensitivity and temporal resolution.
- Interrogated the binding of netropsin, a DNA minor groove binder, to individual recognition sites in A-T DNA repeats.
Main Results:
- Discovered that netropsin binding to A-T DNA repeats favors kinetically trapped states over thermodynamically stable ones.
- Provided the first direct demonstration of kinetically trapped misbinding between a ligand and DNA tandem repeats.
Conclusions:
- Ligand binding to DNA tandem repeats can result in kinetically trapped states, a novel finding in molecular interactions.
- This mechanism may be fundamental to ligand-receptor interactions in biological systems and influence biological activities.
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