Conformational states of 2′-C-methylpyrimidine nucleosides in single and double nucleic acid stranded structures
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 dichr...
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| Autores principales: | , , , , , , |
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| Formato: | JOUR |
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_15206106_v117_n1_p57_Robaldo |
| Aporte de: |
| Sumario: | 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. © 2012 American Chemical Society. |
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