The role of G-quadruplex structures of LIGS-generated aptamers R1.2 and R1.3 in IgM specific recognition.

Area of Science:

• Biochemistry
• Molecular Biology
• Biophysics

Background:

• Membrane-bound IgM (mIgM) is a key B-cell marker.
• Aptamers are short nucleic acid sequences with therapeutic and diagnostic potential.
• Ligand-Guided Selection (LI-GS) is a SELEX variant for aptamer discovery.

Purpose of the Study:

• To analyze the conformational behavior of novel aptamers R1.2 and R1.3.
• To investigate the functional secondary structures of these aptamers in various cellular environments.
• To understand the role of aptamer folding in binding to membrane-bound IgM (mIgM).

Main Methods:

• Ligand-Guided Selection (LI-GS) for aptamer identification.
• Multiple biophysical methods to study aptamer conformation.
• Experiments in pseudo-physiological buffers with varying ion concentrations (K+, Na+, Mg2+).

Main Results:

• Aptamers R1.2 and R1.3 are G-rich and specific for mIgM.
• Aptamers exhibit polymorphism, forming G-quadruplex structures in K+-rich buffers and duplex structures in Na+/Mg2+ buffers.
• Effective binding to mIgM on B-cell lymphoma cells occurred exclusively in the presence of potassium ions.

Conclusions:

• G-quadruplex folding is essential for the molecular recognition and binding of aptamers R1.2 and R1.3 to mIgM.
• These findings provide a basis for designing aptamer-based biosensors for cancer biomarkers.
• The study highlights the importance of ionic conditions for aptamer functionality in cellular environments.