Poster abstracts

Poster number 71 submitted by Charlotte Kunkler

Stability of RNA•DNA-DNA triple helices depends on base triple composition and length of the RNA strand

Charlotte N. Kunkler (Department of Chemistry and Biochemistry, University of Notre Dame), Jacob P. Hulewicz (Department of Chemistry and Biochemistry, University of Notre Dame), Sarah C. Hickman (Department of Chemistry and Biochemistry, University of Notre Dame), Matthew C. Wang (Department of Chemistry and Biochemistry, University of Notre Dame), Jessica A. Brown (Department of Chemistry and Biochemistry, University of Notre Dame)

Abstract:
Recent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA-DNA triple helix that regulates gene expression. However, base triple composition of pyrimidine motif RNA•DNA-DNA triple helices is not well understood beyond the canonical U•A-T and C•G-C base triples. Using native gel-shift assays, the relative stability of 16 different base triples (Z•X-Y, where Z = C, U, A, G and X-Y = A-T, G-C, T-A, C-G) at a single position in an RNA•DNA-DNA triple helix was determined. The canonical U•A-T and C•G-C base triples were the most stable, while three non-canonical base triples completely disrupted triple-helix formation. We further show that our RNA•DNA-DNA triple helix can tolerate up to two consecutive non-canonical A•G-C base triples. Additionally, the RNA third strand must be at least 19 nucleotides to form an RNA•DNA-DNA triple helix but increasing the length to 27 nucleotides does not increase stability. The relative stability of 16 different base triples in DNA•DNA-DNA and RNA•RNA-RNA triple helices was distinctly different from those in RNA•DNA-DNA triple helices, showing that base triple stability depends on strand composition being DNA and/or RNA. Multiple factors influence the stability of triple helices, emphasizing the importance of experimentally validating formation of computationally predicted triple helices.

Keywords: triple helix, triplex, base triple