Functional DNA Superstructures Exhibit Positive Homotropic Allostery in Ligand Binding

Area of Science:

• Biochemistry
• Molecular Biology
• Biotechnology

Background:

• Intrinsically disordered proteins inspire DNA aptamers with cooperative ligand binding.
• This cooperative binding is useful for biosensing, imaging, and drug delivery.
• A key challenge is the reduced binding affinity associated with intrinsic disorder.

Purpose of the Study:

• To address the reduced binding affinity of disordered aptamers.
• To design and build multivalent supramolecular aptamers.
• To create functional DNA superstructures (3D DNA) with enhanced binding properties.

Main Methods:

• Constructed long-chain DNA with tandem repeating DNA aptamers (concatemeric aptamers).
• Developed functional DNA superstructures denoted as 3D DNA.
• Tested the binding cooperativity and affinity of 3D DNA systems for small molecules and proteins.

Main Results:

• 3D DNA systems demonstrated highly cooperative binding to both small molecules and proteins.
• The binding affinity of the parent aptamers was preserved in the 3D DNA constructs.
• Developed a responsive sensor for fluorescence imaging of adenosine triphosphate (ATP) release in neurons and astrocytes.

Conclusions:

• Multivalent supramolecular aptamers, specifically 3D DNA, can overcome the affinity limitations of intrinsically disordered aptamers.
• 3D DNA exhibits strong cooperative binding without compromising individual aptamer affinities.
• This approach enables sensitive biosensing applications, such as imaging neurotransmitter release in neural cells.