Conformational states of 2’-C-methylpyrimidine nucleosides in single and double nucleic acid 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: 2012 vol. 117 p. 57 - 69

1520-6106

The hybridization performance of a set of 12-merRNA:RNA duplexes containing 2′-C-methyluridine, 5-bromo-2′-Cmethyluridine,or (2′S)-2′-deoxy-2′-C-methyluridine was analyzed.Melting point temperatures of the modified duplexes showed animportant ΔTm decrease (−8.9 to −12.5 °C), while circular dichroismexperiments indicated that the helix was still A-type, suggesting alocalized 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.