Poster abstracts

Poster number 108 submitted by Kayla Orr

The effect of 5-Methyl Cytosine on Duplex Stability

Kayla Orr (Biochemistry, Allegheny College ), Abby Dishler (Biochemistry, Allegheny College ), Martin Serra (Biochemistry, Allegheny College )

Abstract:
Thermodynamic parameters for 5-Methylcytosine-guanosine (5MeC-G) pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for RNA duplexes with 5MeC-G pairs to improve nearest neighbor parameters for predicting stabilities of helixes. Duplexes where a 5Me-C-G is substituted for a C-G base pair are on average slightly less stable, by 0.5 kcal/mol on average. Nearest neighbor parameters for 5MeC-G base pairs derived from the data display a wider range of values (0.25-4.0 kcal/mol) than are observed for C-G base pairs (2.11-3.26 kcal/mol). On average, the nearest neighbor values for 5MeC-G base pairs 5’ of a Watson –Crick base pair are 1.7 kcal/mol less stable; while a 3’ 5MeC-G Watson-Crick nearest neighbor pair is 1.4 kcal/mole more stable than the corresponding C-G Watson-Crick nearest neighbor pair. A 5’MeC-G terminal base pair destabilizes a helix by 2.2 kcal/mol while a 3’MeC-G terminal base pair stabilizes a helix by 2.3 kcal/mol. These results should improve predictions of secondary structure for RNAs with modified base pairs.

Keywords: RNA thermodynamic stability, 5-Methyl Cytosine