Evolving Aptamers with Unnatural Base Pairs

Area of Science:

• Biotechnology
• Molecular Biology
• Synthetic Biology

Background:

• Genetic alphabet expansion involves creating unnatural base pairs that function in DNA replication.
• DNA aptamers are valuable tools, often used as alternatives to antibodies for target binding.
• Unnatural base pairs can enhance the properties of biomolecules like DNA aptamers.

Purpose of the Study:

• To describe the ExSELEX method for generating DNA aptamers containing unnatural base pairs.
• To demonstrate the utility of the Ds-Px hydrophobic unnatural base pair in aptamer generation.
• To highlight how genetic alphabet expansion can improve DNA aptamer binding affinity.

Main Methods:

• Application of the hydrophobic unnatural base pair, Ds-Px, within the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process.
• Utilizing genetic alphabet expansion to incorporate unnatural bases into DNA aptamer sequences.
• The ExSELEX (genetic alphabet Expansion for SELEX) protocol for evolving high-affinity aptamers.

Main Results:

• The Ds-Px base pair exhibits high fidelity during replication as a third base pair.
• Incorporation of Ds bases into DNA aptamers significantly increases their binding affinity to targets.
• The ExSELEX method successfully generates DNA aptamers with enhanced binding capabilities.

Conclusions:

• Genetic alphabet expansion, specifically using the Ds-Px base pair, is a powerful tool for generating high-affinity DNA aptamers.
• The ExSELEX method provides a robust protocol for creating novel DNA aptamers with improved target recognition.
• Ds-containing DNA aptamers represent a promising alternative to antibody-based therapeutics and diagnostics.