REMARKABLE MORPHOLOGICAL VARIABILITY OF A COMMON RNA FOLDING MOTIF - THE GNRA TETRALOOP-RECEPTOR INTERACTION

One of the most common RNA tertiary interactions involves the docking of GNRA hairpin loops into stem-loop structures on other regions of RN A. Domain 5 of the group II intron interacts with Domain 1 through suc h an interaction, which has been characterized thermodynamically and k inetically for the ai5g intron. Using this system, it was possible to test the morphological tolerances of the GNRA tetraloop involved in te rtiary interactions. The data presented herein show that a GNRA tetral oop can still participate in tertiary interaction after being physical ly cut at any phosphodiester linkage within the loop. The ''nicked tet raloop'' can be expanded by many nucleotides in either direction and t he covalently continuous loop can also be expanded without loss of int eraction energy. In the context of the nicked tetraloop, the second nu cleotide of the tetraloop sequence can be completely deleted without l oss of function. By examining radical alterations in tetraloop structu re, this study helps define the minimal sequence and structural requir ements of a GNRA motif involved in long-range tertiary interaction. It shows that ''tetraloop''-like structures capable of forming tertiary interactions can be imbedded in unexpected contexts, such as internal loops and apparently open structure within RNA. It demonstrates that p entaloops and hexaloops can form the same type of interaction, with al most equal affinity, as a tetraloop. Taken together, these data sugges t a more generic term for the GNRA tetraloop-receptor interaction: It is proposed herein that the term ''GNRA tetraloop'' be replaced by ''G N(n)/RA'', where n represents a variable number of nucleotides and / i ndicates that the loop can be divided and interrupted by other sequenc es. (C) 1997 Academic Press Limited.