STRUCTURAL FEATURES OF THE UCCG AND UGCG TETRALOOPS IN VERY SHORT HAIRPINS AS EVIDENCED BY OPTICAL SPECTROSCOPY

Structures of the UCCG and UGCG tetraloops formed in octamer ribonucle otidic hairpin sequences, i.e., 5'-r[GC(UCCG)GC]-3' and 5'-r[GC(UGCG)G C]-3', have been studied in aqueous solution by methods of optical spe ctroscopy. UV absorption melting profiles of these short hairpins, con taining only two closing GC base pairs in the stem, are consistent wit h a monophasic, completely reversible order-to-disorder transition and clearly confirm their unusual structural stability (with T-m congruen t to 50 degrees C). To establish structural characteristics of these t etraloops, Raman and FTIR spectroscopies have been used and vibrationa l conformation markers arising from the phosphate backbone and various nucleosides have been analyzed. They have been assigned on the basis of known unambiguous vibrational markers established for DNA and RNA c hains. Surprisingly, they are easily transferable to short oligonucleo tidic sequences. Intensities and wavenumbers of these conformation mar kers have been monitored in the 0-70 degrees C temperature range, i.e. , in going from an ordered to a disordered structure. The main structu ral features of the UCCG and UGCG tetraloops are similar to those prev iously found in the UUCG and UACG tetraloops by means of NMR and vibra tional spectroscopies, except those of the second nucleosides of the t etraloops (rC and rG, respectively) which adopt a 3'-endo/anti rather than a 2'-endo/anti conformation.