Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis

Area of Science:

• Structural Biology
• RNA Biology
• Bioinformatics

Background:

• Non-canonical base pairs and base triples are essential for RNA structural diversity and stability.
• Understanding these interactions is key to comprehending RNA's complex three-dimensional folded structures.

Purpose of the Study:

• To develop and utilize a program, BPFIND, for analyzing canonical and non-canonical base pairs and base triples in RNA.
• To quantify the prevalence and types of non-canonical interactions in functional RNA structures.
• To assess the role of these interactions in tertiary structure formation and conformational diversity.

Main Methods:

• Development of the BPFIND program to detect and analyze base pairs and triples.
• Analysis of RNA crystal structures to identify and classify base pairing and triplex interactions.
• Quantitative estimation of base pair conformational deformation compared to ideal structures.

Main Results:

• BPFIND identified 87 out of 104 possible base pair types in RNA crystal structures.
• Approximately 32.7% of base pairs in functional RNAs are non-canonical, including GA and GU Wobble pairs.
• Over 10.4% of these non-canonical base pairs participate in triplet formations, vital for tertiary contacts.

Conclusions:

• Non-canonical base pairs and triples are prevalent and play significant roles in RNA structural and functional diversity.
• BPFIND provides valuable insights into the structural variations and functional importance of RNA base interactions.
• The program aids in understanding the contribution of specific base interactions to RNA's complex 3D architecture.