Conformational States of 2?-C-Methylpyrimidine Nucleosides in Single and Double Double Stranded Structures

LAURA ROBALDO; RODRIGO PONTIGGIA; SANTIAGO DI LELLA; DARÍO A. ESTRÍN; JOACHIM W. ENGELS; ADOLFO M. IRIBARREN; JAVIER M. MONTSERRAT

JOURNAL OF PHYSICAL CHEMISTRY B - (Print)

AMER CHEMICAL SOC

Lugar: Washington; Año: 2013 vol. 117 p. 57 - 69

1520-6106

The hybridization performance of a set of 12-mer RNA:RNA duplexes containing 2′-C-methyluridine, 5-bromo-2′-C-methyluridine, or (2′S)-2′-deoxy-2′-C-methyluridine was analyzed. Melting point temperatures of the modified duplexes showed an important ΔTm decrease (−8.9 to −12.5 °C), while circular dichroism experiments indicated that the helix was still A-type, suggesting a localized disturbance disorder. Molecular dynamics simulations using AMBER were carried out in order to gain structural knowledge about the effect of the 2′-C-methyl modification in double stranded environments. On the other hand, in an attempt to explain the behavior of the 2′-deoxy-2′-C-methyl nucleosides in single stranded environments, like the 10?23 DNAzyme core, molecular dynamic simulations were performed, incorporating the modified analogues into single stranded reported stem-loop structures, studding the sugar conformations along the MD trajectories. It was observed that, despite their preferential conformational states, the 2′-C-methyl analogues are flexible enough to adopt a different puckering in single stranded environments.