Thursday, 26 October 2006 - 1:50 PM
OLCC-Oakley (Oakley-Lindsay Center)
141

Nearest neighbor parameters for Inosine-Uridine pairs located within Watson-Crick helices

Daniel J. Wright, Jamie L. Rice, Dawn M. Yanker, and Brent M. Znosko. Saint Louis University, St. Louis, MO

An enzyme family known as adenosine deaminases that act on RNA (ADARs) catalyzes adenosine deamination in RNA. ADARs act on RNA that is largely double-stranded and convert adenosine to inosine, resulting, in many cases, in an I•U pair. Thermodynamic parameters derived from optical melting studies are reported for a series of 14 oligoribonucleotides containing single I•U pairs adjacent to Watson-Crick pairs. Four duplexes containing 3'- terminal I•U pairs and four duplexes containing 5'-terminal I•U pairs have also been thermodynamically characterized. This data was combined with previously published data of seven duplexes containing internal, terminal, or tandem I•U pairs from Strobel et al. (1994) Serra et al. (2004). On average, a duplex with an internal I•U pair is 2.3 kcal/mol less stable than the same duplex with an A-U pair, however, a duplex with a terminal I•U pair is 0.8 kcal/mol more stable than the same duplex with an A-U pair. Although isosteric with a G-U pair, on average, a duplex with an internal I•U pair is 1.9 kcal/mol less stable than the same duplex with a G-U pair, however, a duplex with a terminal I•U pair is 0.9 kcal/mol more stable than the same duplex with a G-U pair. Duplexes with tandem I•U pairs are on average 5.9 and 3.8 kcal/mol less stable than the same duplex with tandem A-U or tandem G-U pairs, respectively. Nearest neighbor parameters for all nearest neighbor combinations of I•U pairs and an additional parameter for terminal I•U pairs have been derived.

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