Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Tight turn DNA: A Novel Structure in Triplex

A DNA oligonucleotide with the sequence of 5?-T1C2T3C4T5C6C7T8C9T10C11T12A13G14A15G16A17G18 was found to be able to form a paper-clip triplex. The structure showed the C6C7/G18 apex base triad (in which C6C7 forms a tight turn structure, or, a folding structure without loop) is required for the intramolecular triplex formation (Biochemistry, 39, 12457-12464 (2000) and Biophys. J., 82, 3170 (2002)). The C6C7/G18 apex base triad was also found in an intermolecular triplex formed by mixing of 5?-T1C2T3C4T5C6C7T8C9T10C11T12-3? and 5?- A13G14A15G16A17G18 -3? (Biophys. J., 91, 2552-2563). In other words, a triplex with C6C7 tight turn, similar to that of paperclip triplex, was formed. These two studies established the existence of tight turn structure. It is a new finding in DNA structure. Furthermore, a T6T7/A18 base triad (i.e., T6T7 forms a tight turn) has also been found in intermolecular triplex composed by 5?-C1T2C3T4C5T6T7C8T9C10T11C12-3? and 5?- G13A14G15A16G17A18 -3? (Biophys. Rev. Lett., 1, 215-227 (2006)). Therefore, the key element of the formation of tight turn structure may be a pymidine-pyrimidine (either CC or TT) motif in the sequence in order to form CC/G or TT/A apex base triads.

The data of gel electrophoresis, UV, CD, fluorescence spectroscopy, NMR, and molecular simulation will be presented in the poster. (Supported by National Science Council and Academia Sinica)

Lou-sing Kan

Institute of Chemistry,
Academia Sinica
Taipei, Taiwan 11529

Email: lskan@chem.sinica.edu.tw