MODEL FOR AN RNA TERTIARY INTERACTION FRONT THE STRUCTURE OF AN INTERMOLECULAR COMPLEX BETWEEN A GAAA TETRALOOP AND AN RNA HELIX

IN large structured RNAs, RNA hairpins in which the strands of the dup lex stem are connected by a tetraloop of the consensus sequence 5'-GNR A (where N is any nucleotide, and R is either G or A) are unusually fr equent(1). In group I introns there is a covariation in sequence betwe en nucleotides in the third and fourth positions of the loop with spec ific distant base pairs in putative RNA duplex stems(2): GNAA loops co rrelate with successive 5'-C-C.G-G base pairs in stems, whereas GNGA l oops correlate with 5'-C-U.G-A. This has led to the suggestion that GN RA tetraloops may be involved in specific long-range tertiary interact ions, 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 Tetrahymena thermophila(3) and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (re f. 4). NMR has revealed the overall structure of the tetraloop for 12- nucleotide hairpins with GCAA and GAAA loops(5) and models have been p roposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA(2,4). Here we describe the crystal structur e of an intermolecular complex between a GAAA tetraloop and an RNA hel ix. The interactions we observe correlate with tbe specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this c omplex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.