Poster abstracts
Poster number 80 submitted by Levan Lomidze
Stability factors of monomolecular DNA and RNA quadruplexes
Levan Lomidze (Center for RNA Biology, The Ohio State University, Columbus, OH 43210; Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia), Elaina Boyle (Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210), Karin Musier-Forsyth (Center for RNA Biology, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210), Besik Kankia (Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia)
Abstract:
One of the most stable quadruplexes is formed by the G3T sequence (GGGTGGGTGGGTGGG) that folds into a parallel quadruplex with three G-tetrads and chain-reversal T-loops containing anti glycosidic conformations of all guanines. In 1 mM K+, G3T unfolds at 75 °C whereas under physiological conditions, it unfolds above 100 °C. The RNA analog, ggguggguggguggg (g3u), which has the same folding topology, demonstrates even higher thermal stability. To understand the higher stability of RNA quadruplexes, we previously performed a comparative thermodynamic study of G3T and g3u quadruplexes, as well as chimeric constructs containing both DNA and RNA nucleotides. The all-RNA sequence was ~13 °C more stable than its DNA analog and the majority of G-g (DNA-for-RNA) substitutions destabilized the quadruplex. Only three G-g substitutions in the top (3'-end) tetrad and loop T-u substitutions increased the stability of the structure. The g3u quadruplex was also characterized by additional stabilizing interactions that are absent in the DNA analog. Taken together, this previous work revealed that stacking interactions are more favorable in DNA quadruplexes, while the chain-reversal loops play an important role in the higher stability of RNA quadruplexes. Here, we characterize the stabilizing factors of another monomolecular quadruplex, the thrombin-binding aptamer (TBA) GGTTGGTGTGGTTGG. In contrast to G3T, the TBA quadruplex adopts an antiparallel topology that requires half of the guanines to be in the syn conformation (two per G-tetrad). Our study reveals that DNA to RNA G-g substitutions in positions with an anti conformation stabilize the TBA quadruplex, while the same substitutions for Gs in the syn conformation inhibit quadruplex formation. The results of this study have implications for the rational design of RNA and DNA quadruplexes for biotechnological applications and for therapeutics targeting quadruplex structures.
Keywords: Quadruplexes, RNA, DNA