Bent Helix Formation Between RNA Hairpins with Complementary Loops

Abstract

The initial interaction between the ColE1 plasmid specific transcripts RNA I and RNA II, which function as antisense regulators of plasmid replication, comprises a transient complex between complementary loops found within the RNA secondary structures. Multidimensional heteronuclear magnetic resonance spectroscopy was used to characterize complexes formed between model RNA hairpins having seven nucleotide complementary loops. Seven base pairs are formed in the loop-loop helix, with continuous helical stacking of the loop residues on the 3' side of their helical stems. A sharp bend in the loop-loop helix, documented by gel electrophoresis, narrows the major groove and allows bridging of the phosphodiester backbones across the major groove in order to close the hairpin loops at their 5'-ends. The bend is further enhanced by the binding of Rom, a ColE1 encoded protein that regulates replication.

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

“…2b). Similar bending has been documented for a kissing complex formed between ColEl plasmid specific RNA I and RNA II transcripts, comprising seven intermolecular base pairs and no unpaired nucleotides (23,35).…”

“…Similar studies have been performed on the RNAI-RNAII kissing complex involved in the control of the colE1 plasmid replication. This kissing complex has been shown to possess no linking residues between the 7-nt loop-loop helix and the intramolecular helices (23,35). Again, a mutation of the GC closing base pair to a GA base pair leads to a stabilization of the complex (16).…”

“…First, the number of paired loop residues can vary from two up to seven (22,23,35). In addition, some of the kissing complexes possess nonpaired bases (22,24,25,(47)(48)(49).…”

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

“…Once formed, such an initiation complex, a ''kissing hairpin''-like structure (60)(61)(62)(63)(64), is expected to ''zip up'' to form the fully paired duplex, even at low temperatures, as cartooned in Scheme 1. Indeed, we observe such duplex formation from two hairpins with complementary looped regions when we mix X[TTT] 6 X with X[AAA] 6 X (unpublished results).…”

“…In addition, we infer one or more intermediate states in the transition between the isolated hairpins and the duplex. In this scheme, we propose as a working model that the initiation complex for duplex formation is a ''kissing hairpin'' (60,62). More direct structural and kinetic studies will be required to evaluate this proposed state, as well as to define in detail the nature of the surprisingly stable singlestranded triplet repeat looped structure.…”