Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• RNA oligomers form ordered structures at low temperatures.
• These structures exhibit base-paired stacking arrangements.
• The A-RNA family configuration serves as a reference for RNA structure.

Purpose of the Study:

• To comparatively study the thermally induced helix-coil transition in two specific RNA oligomers: (A-G-C-U)2 and (A-C-G-U)2.
• To evaluate the agreement between experimental data (1H NMR) and predicted A-RNA family structures for these oligomers.
• To investigate changes in glycosidic torsion angles during base pairing and stacking.

Main Methods:

• Comparative analysis of thermally induced helix-coil transitions.
• 1H Nuclear Magnetic Resonance (1H NMR) spectroscopy.
• Analysis of ring-current and atomic diamagnetic anisotropies.

Main Results:

• Both oligomers adopt ordered structures at low temperatures with 3'-endo ribofuranose conformation and A-RNA-like stacking.
• 1H NMR data show better agreement with the A-form structure for (A-G-C-U)2 compared to (A-C-G-U)2.
• Substantial changes (>=20 degrees) in glycosidic torsion angles occur for adenosine and cytidine residues in both oligomers upon base pairing and stacking.

Conclusions:

• The study highlights sequence-dependent structural variations in RNA oligomers.
• NMR spectroscopy is crucial for validating predicted RNA structures.
• Specific nucleotide residues exhibit distinct conformational flexibility during RNA helix formation.