2006 Student Research Conference:
19th Annual Student Research Conference


Effects of 3' Dangling Nucleotides on the Stability of siRNA-like Models
Jennifer L. McGinnis
Dr. Maria Nagan, Faculty Mentor

RNA interference (RNAi) has become an extremely important tool for studying gene function. RNAi depends upon small duplexes with two 3’ overhanging dangling bases on either end of the RNA duplex (Hannon, G. Nature, 2002, 418, 244). Recently thermodynamic data has been collected that suggests that these 3’ overhanging nucleotides significantly affect the stability of siRNA-like molecules (O’Toole et al., RNA, 2005, 11, 512). It seems that if the first dangling base is a purine it increases stability of the duplex. If the second dangling base is a pyrimidine the calculated free energy of the duplex is greater than if it were a purine. These interesting results have not been able to be rationalized. Molecular dynamic simulations of ten models with varying bases were performed. The data generated has been analyzed using root mean square distances, 2D base stacking plots, helical parameters, and also mm/pbsa. It is believed that the second base may add more to the free energy through the entropic component.

Keywords: siRNA, molecular dynamics, RNA interference, 3' overhanging base, free energy


Presentation Type: Oral Paper

Session: 9-4
Location: VH 1432
Time: 9:00

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