Database of RNA Base-pair Structures
BPS is a database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures. The structures are taken from the Nucleic Acid Database (NDB), and the base pairs are identified and characterized with the 3DNA software package. The interactions are classified in terms of residue identities, base-pair positioning, and hydrogen-bonding patterns and related to the structural context in which they occur. A user can browse the atlas of base-pair patterns and carry out searches for patterns of specific types or from specific structures.
Version 1.0 of the BPS (Base-Pair Structure) database is now released. The data, derived from 321 high-resolution RNA crystal structures (≤ 3.0 Å) and 105 lower-resolution structures (> 3.0 Å), include 91265 base pairs, 12209 higher-order base interactions, and 17 clusters of isoteric base pairs.
Higher-order base interactions refer to a hydrogen-bonding network made up of more than two nucleotides. In BPS, we have found higher-order interactions with five or more nucleotides. The figure shows three examples of five-nucleotide interactions (quintuplets) in RNA structures.