UNCG tetraloops in short oligoribonucleotides reveal high thermodynamic stability and unusual structural properties in aqueous phase as confirmed by optical and NMR spectroscopies

Abstract

UNCG tetraloops ( N = U, A, C, G) (the most frequently found tetraloops in 16S rRNAs) studied in very short hairpins formed in octaribonucleotides with only two closing G·C base pairs in their stems reveal high thermodynamic stability ( T M ≈ 50°C) in aqueous solutions. On the basis of the experimental results (UV absorption, vibrational and NMR spectra), the unusual high stability of these hairpins is correlated to the particular structural features of the nucleotides involved in these tetraloops. As a consequence of our analyses, we can now postulate that all the UNCG tetraloops possess common overall structural features which are independent of the stem length and the nature of the base ( N) located in the second position of the loop.