Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy

CUUG loop is one of the most frequently occurring tetraloops in bacterial 1 6S rRNA. This tetraloop has a high thermodynamic stability as proved by pre vious UV absorption and NMR experiments. Here, we present our results conce rning the thermodynamic and structural features of the 10mer 5 ' -r(GCG-CUU G-CGC)-3 ', forming a highly stable CUUG tetraloop hairpin in aqueous solut ion, by means of several optical techniques (UV and IFT-IR absorption, Rama n scattering). UV melting profile of this decamer provides a high melting t emperature (60.7 degreesC). A set of Raman spectra recorded at different te mperatures allowed us to analyze the order-to-disorder (hairpin-to-random c oil) transition. Assignment of vibrational markers led us to confirm the pa rticular nucleoside conformation, and to get information on the base stacki ng and base pairing in the hairpin structure. Moreover, comparison of the d ata obtained from two highly stable CUUG and UUCG tetraloops containing the same nucleotides but in a different order permitted an overall discussion of their structural features on the basis of Raman marker evidences.