Structural analysis of ribonucleopeptide aptamer against ATP

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Ribonucleopeptide aptamers are engineered nucleic acid molecules with high specificity for target molecules.
• Adenosine triphosphate (ATP) is a crucial molecule in cellular energy transfer and signaling.

Purpose of the Study:

• To determine the structure of a novel ribonucleopeptide aptamer designed to bind ATP.
• To elucidate the molecular interactions responsible for the selective binding of ATP by the aptamer.

Main Methods:

• In vitro selection was used to obtain the ATP-specific ribonucleopeptide aptamer.
• Nuclear Magnetic Resonance (NMR) spectroscopy was employed for structural analysis.
• Heteronuclear NMR experiments (HNN-COSY) were utilized to confirm base pairing interactions.

Main Results:

• The secondary structure of the RNA component, linked to the Rev-responsive element (RRE) and bound to adenosine (Ado), was determined.
• Non-canonical base pairs (G:A, G:G) and canonical base pairs were observed within the RRE duplex.
• A key finding was the formation of a U:A:U base triple involving two uracil residues in the selected RNA region, which traps Ado.

Conclusions:

• The ribonucleopeptide aptamer selectively binds ATP through specific structural features.
• The U:A:U base triple is critical for the aptamer's ability to bind adenosine, confirming its role in target recognition.