NMR spectroscopy and kinetic studies of the quadruplex forming RNA r(UGGAGGU)

Abstract

It is well documented that G-rich DNA or RNA sequences are able to fold into inter- and/or intramolecular G quadruplex structures. The repertoire of the canonical G quadruplex structures comprised entirely of G tetrads has been expanded to include non-G tetrads, mixed purine tetrads, as well as purine hexads. RNA/DNA sequences containing the GGAGG repeat have received special attention as they are widely spread throughout the eukaryotic genome, and it has been proposed that they might be linked to various biological functions, either directly, or through protein-mediated interactions. Nuclear magnetic resonance spectroscopy studies have shown that such sequences form unique G quadruplex structures containing A:(G:G:G:G):A hexads. However, despite the fact that several high resolution structural studies of these unique structures are available, information about their kinetics and thermodynamics is limited to a single DNA sequence. In general, kinetics and energetics data about RNAG quadruplexes is even more scarce, being limited to the sequences r(U_nGGGGU_n) with n = 1, 2. In this study we have analyzed the RNA sequence r(UGGAGGU), which contains a single GGAGG repeat. Our NMR spectroscopy results strongly suggest that this RNA folds into a dimeric structure containing G:G:G:G tetrads and A:(G:G:G:G):A hexads and our UV spectroscopy studies provide for the first time information about the kinetics and energetics of this unique structure.