2005 Student Research Conference:
18th Annual Student Research Conference

Science

Effects of 3’ Dangling Nucleotides on the Stability of Small Interfering RNA
Jennifer L. McGinnis
Dr. Maria Nagan, Faculty Mentor

Shortened RNA duplexes (19 base pairs) with two nucleotide 3’ overhangs have been found to be a key component in RNA interference (RNAi), a posttranscriptional gene silencing mechanism. These small interfering RNAs (siRNAs) and mRNA that should not be translated are recruited to the RNA induced silencing complex (RISC) where the mRNA is degraded. In the RISC center, the siRNAs are unwound and one strand of the siRNA is annealed to complementary mRNA. Thus, the stability of these siRNAs are of importance. Experimental data obtained from Dr. Martin Serra shows that the identity of the two 3’ overhanging nucleotides (purine versus pyrimidine) affects the stability of the siRNAs. To aid in the interpretation of this data, we are modeling 8 of Dr. Serra’s 16 model siRNAs with molecular dynamics simulations. This experimental data will be examined by comparing structural changes in the RNAs with respect to 3’ overhang nucleotide identity.

Keywords: siRNA, molecular dynamics, posttranscriptional, 3' overhang, RNAi

Topic(s):Chemistry

Presentation Type: Oral Paper

Session: 10-5
Location: VH 1432
Time: 9:15

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