Thermodynamic and structural properties of RNA oligomers containing purine rich internal loops and DNA:RNA hybrids with C5-propynyl substitutions

Understanding thermodynamic and structural features of RNA duplexes containing internal loops and modified nucleotides can contribute to a better understanding of RNA secondary and tertiary structure, function, dynamics, and molecular recognition. The three-dimensional structure of the 5'(rGGC AAGCCU)2 duplex was modeled with NMR-derived restraints. Although the 5'(rCAAG)2 loop is thermodynamically destabilizing by 1.1 kcal/mol, the tandem A·A pairs adopt a predominant sheared conformation. Thus, thermodynamically destabilizing internal loops can be preorganized.;The contribution of amino groups to the thermodynamics, structure, and dynamics of tandem A·A mismatches is investigated by substitution of purine for adenine within 5'(rGGCAAGCCU) 2. In comparison to 5'(rGGCAAGCCU) 2, replacing the amino group of A4, A5, and both A4 and A5 with hydrogen results in a stabilization of 1.3, destabilization of 0.6, and destabilization of 0.8 kcal/mol, respectively. The P·A pairs of the 5' (rGGCPAGCCU)2 duplex, the A·P pairs of the 5'(rGGCAPGCCU) 2 duplex, and the P·P pairs of the 5'(rGGC PPGCCU)2 duplex have a sheared, face-to-face, and undefined conformation, respectively. The results illustrate that amino groups play important roles in determining the characteristics of purine rich internal loops.;NMR results with a mimic of the Candida albicans and Candida dubliniensis J4/5 loop, GAAGGUAAUU , suggest that the adenosines form tandem sheared A·A pairs, but only the G·U pair not adjacent to an A·A pair forms a static wobble G·U pair. The results contribute to an understanding of the structure and dynamics of purine rich internal loops and potential G·U pairs adjacent to internal loops.;The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37°C by over 1 kcal/mol of substitution [Barnes, T. W., III, & Turner, D. H. (2001) J. Am. Chem. Soc. 123, 4107--4118]. To provide information on the structural consequences of propynylation, 2D NMR spectroscopy was used to study the structures of several oligonucleotides. NMR structures of the fully propynylated, partially propynylated, and unmodified. 5'(dCCUCCUU)3':3 '(rGAGGAGGAAAU)5 ' duplexes indicate that their global structures are almost identical. The results suggest that the increased stability of the propynylated duplexes is caused by preorganization of the propynylated single strand and different interactions in the double strand.