Relative stability of guanosine-cytidine diribonucleotide cores: a 1H NMR assessment

Proton NMR was used to study the secondary structure and melting behavior of six self-complementary oligoribonucleotide tetramers, each containing two guanosine and two cytidine residues (GGCC, CCGG, GCCG, CGGC, GCGC, and CGCG). GGCC and CCGG formed perfect duplexes containing four G.C base pairs with Tms of 54 and 47.8 degrees C, respectively; GCCG and CGGC formed staggered duplexes with two G.C base pairs and four 3' double-dangling bases, with Tms of 35.5 and 29.2 degrees C, respectively; GCGC formed a perfect duplex with a Tm of 49.9 degrees C, while CGCG formed a staggered duplex with a Tm of 36.9 degrees C. From these results, an order of stability of the cores containing two G.C base pairs was proposed: GC:GC is more stable than GG:CC which is more stable than CG:CG. The RY model for secondary structure stability prediction was applied to the above tetramers with reasonable success. Suggestions for refinements are discussed.