Probing high-affinity 11-mer DNA aptamer against Lup an 1 (β-conglutin)

Area of Science:

• Biotechnology
• Molecular Biology
• Allergen Detection

Background:

• Aptamers are synthetic nucleic acids with analytical potential.
• Full-length aptamers (60-100 bases) may contain non-essential bases, impacting affinity.
• Truncation is crucial for developing high-affinity, specific, and cost-effective aptamers.

Purpose of the Study:

• To truncate an aptamer that specifically binds to β-conglutin (Lup an 1), a major allergenic protein.
• To identify the minimal binding domain responsible for high affinity and specificity.
• To characterize the structure and stability of the truncated aptamer.

Main Methods:

• Comparative analysis of predicted secondary structures to identify binding motifs.
• Sequence truncation and affinity testing (K D determination).
• Specificity assays against related proteins and NMR for structural elucidation.

Main Results:

• A hairpin structure with a G-rich loop was identified as the binding motif.
• An 11-mer truncated aptamer exhibited the highest affinity (K D = 1.7 × 10⁻⁹ M).
• The 11-mer showed high specificity for β-conglutin, with no cross-reactivity to other conglutins or gliadin.
• Structural analysis predicted and confirmed a stable G-quadruplex structure.

Conclusions:

• Truncation effectively generated a high-affinity, specific aptamer for β-conglutin.
• The 11-mer aptamer, featuring a G-quadruplex, is a stable and potent tool for allergen detection.
• This work advances aptamer technology for improved diagnostics and reduced allergen detection costs.