G-quadruplex formation in RNA aptamers selected for binding to HIV-1 capsid

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• HIV-1 capsid protein (CA) is crucial for viral replication and host interactions.
• CA's functions depend on its assembly into distinct structures like hexamers.
• Understanding CA structure-function relationships is key for therapeutic development, but CA's genetic fragility poses challenges.

Purpose of the Study:

• To characterize the higher-order structures of aptamers targeting HIV-1 CA.
• To enable the use of aptamers as molecular tools for studying CA structure-function relationships in cellular contexts.
• To identify aptamers with specific binding affinities for CA structures.

Main Methods:

• Utilized quantitative biophysical approaches, including multi-effective spectroscopic methods.
• Performed thermodynamic analyses to characterize aptamer structures.
• Investigated aptamer binding specificity for mature CA hexamer lattices and soluble CA hexamers.

Main Results:

• Identified aptamers with binding specificity for CA hexamer lattices.
• Aptamer L15.20.1 showed strong evidence of stable RNA G-quadruplex (rG4) formation under physiological conditions.
• The rG4 structure is located in a region critical for CA-aptamer interaction.

Conclusions:

• Aptamer L15.20.1, with its rG4 motif, is a promising tool for studying HIV-1 CA structure-function dynamics.
• Non-canonical structures like rG4s offer distinct chemical properties for aptamer applications.
• This aptamer may facilitate research into HIV-1 replication and host interactions under cellular conditions.