Post-SELEX modification of quinine aptamers through neoacetalization

Area of Science:

• Chemical Biology
• Biochemistry
• Nucleic Acid Chemistry

Background:

• SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a powerful technique for aptamer discovery.
• Post-SELEX modification allows for the fine-tuning of aptamer properties and functionalities.
• Dynamic combinatorial chemistry offers novel approaches for molecular recognition and sensor development.

Purpose of the Study:

• To introduce a neoacetalization-based method for post-SELEX aptamer modification.
• To investigate the behavior of modified aptamers in the presence and absence of quinine.
• To explore the potential of dynamic combinatorial chemistry for aptamer functionalization.

Main Methods:

• Synthesis of modified aptamer scaffolds by incorporating a (2R,3S)-4-(methoxyamino)butane-1,2,3-triol residue.
• Incubation of aptamers with aldehyde mixtures and quinine to form N-methoxy-1,3-oxazinane (MOANA) nucleoside analogues.
• UHPLC-MS analysis to identify reacting aldehydes and ITC to determine binding affinities.

Main Results:

• Two aldehydes, methyl 4-formylbenzoate and 3-nitrobenzaldehyde, showed differential reactivity with a modified aptamer scaffold.
• The 3-nitrobenzaldehyde-derivatized aptamer unexpectedly dimerized upon quinine binding.
• Quinine binding induced N-O bond cleavage in the modified residue of another aptamer.

Conclusions:

• Neoacetalization provides a versatile platform for post-SELEX aptamer modification.
• Dynamic combinatorial chemistry can be employed to create aptamers with unique quinine-responsive behaviors.
• These findings open avenues for developing novel aptasensors and molecular probes.