RRM
2011 Rustbelt RNA Meeting
RRM
|
|
|
|
|
|
Poster abstracts
Abstract:
Six RNA hairpin sequences containing a single-nucleotide bulge loop with the fluorescent analog 2-aminopurine (2-AP) were optically melted in 1M NaCl and subject to fluorescent spectroscopy. Four of the bulge loops were of the group II variety, where the bulged nucleotide is identical to one of its nearest neighbors, leading to ambiguity in the exact position of the bulge. The structural similarity to adenine and the fluorescent nature and properties of 2-AP were used to analyze the uncertainty in position by inserting the fluorophore into the bulge loop on the 5’ and 3’ sides of the hairpin stem. Of the two remaining hairpins, one contained a group I bulge loop and the other was fully paired. Preliminary results show that the amount of fluorescence increases with temperature in group I bulge loops. Previously, structural probing of group II bulge loops within hairpin motifs (McCann et al. 2011) indicated that the bulged nucleotide is the one positioned farther from the hairpin loop. This study suggests that when 2-AP exists in group II bulge loops as the nucleotide closer to the hairpin loop, it exhibits behavior indicative of an unpaired nucleotide.
References:
Ballin, J.D.; Bharill, S.; Fioalcowitz-White, E.J.; Gryczynski, I.; Gryczynski, Z.; Wilson, G.M.; Site-Specific Variations in RNA Folding Thermodynamics Visualized by 2-Aminopuring Fluorescence. Biochemistry 2007, 46, 13948-13960.
McCann, M.D.; Lim, G.F.S.; Manni, M.L.; Estes, J.; Klapec, K.A.; Frattini, G.D.; Knarr, R.J.; Gratton, J.L.;Serra, M. J. Non-Nearest-Neighbor Dependence of the Stability for RNA Group II Single Nucleotide Bulge Loops. RNA 2007, 17, 108-119.
Keywords: 2-Aminopurine, Thermodynamics, Group II Bulge Loop
