Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix

Abstract

IN large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5′-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent¹. In group I introns there is a covaria-tion in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems²: GNAA loops correlate with successive 5'-C-C · G-G base pairs in stems, whereas GNGA loops correlate with 5′-C-U · G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary inter-actions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahy-mena thermophilc³ and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops⁵ and models have been proposed for the inter-action of GNRA tetraloops with base pairs in the minor groove of A-form RNA^2,4. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.