Synthesis, Thermal Stability, Biophysical Properties, and Molecular Modeling of Oligonucleotides of RNA Containing 2′-O-2-Thiophenylmethyl Groups

Dodecamers of RNA [CUACGGAAUCAU] were functionalized with C2'-O-2-thiophenylmethyl groups to obtain oligonucleotides 10-14 and 17. The modified nucleotides were incorporated into RNA strands via solid-phase synthesis. The biophysical properties of these ONs were used to quantify the effects of this modification on RNA:RNA and RNA:DNA duplexes. A combination of UV-vis and circular dichroism were used to determine thermal stabilities of all strands, which hybridized into A-form. geometries. Destabilization of the double stranded RNA was measured as a function of number of consecutive modifications, reflected in decreased thermal denaturation values (Delta T-m, ca. 2.5-11.5 degrees C). Van't Hoff plots on a duplex containing one modification (10:15) displayed a ca. Delta Delta G degrees of +4 kcal/mol with respect to its canonical analogue. Interestingly, hybridization of two modified strands (13:17, containing a total of eight modifications) resulted in increased stability and a distinct secondary structure, reflected in its CD spectrum. Molecular modeling based on DFT calailations shed light on the nature of this stability, with induced changes in the torsional angle delta (C5' -C4' -C3'-O3) and phosphate-phosphate distances that are in agreement with a compacted structure. The described synthetic methodology and. structural information will be useful in the design of thermodynamically stable structures containing chemically reactive modifications.