Analysis of quadruplex propensity of aptamer sequences

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• Aptamers are nucleic acid molecules with high affinity for specific targets.
• G-quadruplex (G4) structures are a unique fold adopted by some aptamers.
• The frequency of G4 motif emergence during aptamer selection (SELEX) is not well understood.

Purpose of the Study:

• To investigate the prevalence of G-quadruplex (G4) forming motifs in aptamer sequences.
• To analyze G4 and i-motif propensity within a large aptamer database.
• To assess the experimental validation of predicted G4 structures in aptamers.

Main Methods:

• Analysis of over 1400 aptamer sequences from the UTexas Aptamer Database.
• Computational prediction of G4 and i-motif forming potentials using G4Hunter.
• Experimental validation of G4 formation for selected aptamer candidates.

Main Results:

• Nearly 1/4 of DNA aptamers and 1/6 of RNA aptamers were predicted to form G4 structures.
• Many G4 motifs were found in sequences not previously associated with quadruplex formation.
• Experimental validation confirmed G4 formation for all sequences with a G4Hunter score >= 1.31.

Conclusions:

• A significant proportion of aptamers contain G-quadruplex forming motifs.
• The potential for G4 formation in aptamers is frequently underestimated or unreported.
• These findings suggest a need to re-evaluate G4 propensity in aptamer sequence analysis and design.