Poster abstracts

Poster number 171 submitted by Oliver Munyaradzi

Helical bPNA targeting U-rich RNA

Oliver Munyaradzi (Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH), Dennis Bong (Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH)

Abstract:
This project seeks to design RNA sequence-specific binders that take advantage of defined secondary structure. Previous work produced bifacial peptide nucleic acid (bPNA) in which melamine displayed on a modified lysine side-chain formed T-M-T/U-M-U base triples with thymine or uracil. We hypothesized that pre-organization of the bPNA peptide backbone into a helical structure would enable biomimetic peptide recognition of a U-rich major groove of A-form RNA. We hypothesize that the combination of helical peptide display with UU targeting by the melamine base, will enable a general method for targeting U-rich A-form RNA. We have designed and synthesized peptides that incorporate lysine derivatives doubly functionalized with melamine (K2M)onto one face of a putative helical fold, using an i,i+4 pattern on an alanine-rich sequence, every third position of a PPII helix, a and d positions of a heptad repeat. Secondary structure was probed by CD spectroscopy which indicated helical propensity in all three peptides. DNA and RNA binding properties were elucidated using Tm measurements, EMSA, ITC and CD studies. For ssDNA (dT6C4T6) peptide complexes , similar thermal stability was observed for all peptides, including prior bPNA designs, though a modest increase in affinity (3-4 fold) was observed using EMSA. In contrast, the helical peptides helped unstructured U6C4U6 ssRNA to fold, yielding complexes with an 8-10 oC higher Tm and with sufficient stability for EMSA and ITC studies compared to those formed by prior bPNA with display of bases at alternate residues. Thus, early results indicate support for the notion that defining backbone secondary structure can impact bPNA recognition of nucleic acids.

Keywords: Sequence-specific, RNA binding, PNA