A computationally designed DNA aptamer template with specific binding to phosphatidylserine

Area of Science:

• Biochemistry and Molecular Biology
• Biotechnology
• Neuroscience

Background:

• Phosphatidylserine (PS) is an early indicator of apoptosis, evidenced by its externalization on the cell membrane.
• PS is implicated in amyloid plaque deposition in transmissible spongiform encephalopathies (TSEs), suggesting its role in neurodegenerative diseases.
• Aptamers, short nucleic acid sequences, are promising tools for targeted molecular therapies and diagnostics due to their specificity.

Purpose of the Study:

• To design and develop a DNA aptamer capable of specifically binding to phosphatidylserine (PS).
• To explore the potential of PS-targeting aptamers for diagnostic and therapeutic applications in diseases like TSEs.
• To identify a specific DNA sequence that serves as a template for further aptamer development.

Main Methods:

• Employed an entropy-based seed-and-grow strategy for DNA aptamer template design.
• Conducted computational investigations to predict and analyze aptamer binding properties.
• Performed experimental validation to confirm the binding affinity and specificity of the designed aptamers.

Main Results:

• Successfully designed DNA aptamer templates with the potential to bind specifically to phosphatidylserine.
• Identified the DNA sequence 5'-AAAGAC-3' as a preferred template for aptamer development.
• Demonstrated the feasibility of computational and experimental approaches in aptamer design and validation.

Conclusions:

• The identified DNA sequence 5'-AAAGAC-3' is a promising template for developing PS-specific aptamers.
• PS-targeting aptamers hold significant potential for the diagnosis and treatment of apoptosis-related and neurodegenerative diseases.
• Further modifications and studies of this aptamer template are warranted for practical clinical implementation.