Conformational States of 2′‑C‑Methylpyrimidine Nucleosides in Single and Double Nucleic Acid Stranded Structures

• Published in: The journal of physical chemistry. B 2013-01, Vol.117 (1), p.57-69
• Main Authors: Robaldo, Laura, Pontiggia, Rodrigo, Di Lella, Santiago, Estrin, Darío A, Engels, Joachim W, Iribarren, Adolfo M, Montserrat, Javier M
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Biological and medical sciences; Circular Dichroism; Dichroism; Disorders; Disturbances; Fundamental and applied biological sciences. Psychology; Gain; General aspects, investigation methods; Molecular dynamics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleic acids; Nucleic Acids - chemistry; Nucleosides; Physical chemistry; Pyrimidine Nucleosides - chemistry; Simulation; Ultraviolet Rays
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp3081645

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 ΔT m 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.