Structural polymorphism exhibited by a homopurine·homopyrimidine sequence found at the right end of human c-jun protooncogene

• Published in: Archives of biochemistry and biophysics 2008-03, Vol.471 (2), p.95-108
• Main Authors: Saxena, Sarika, Bansal, Aparna, Kukreti, Shrikant
• Format: Article
• Language: English
• Subjects: Circular dichroism; G-quadruplex; Homopurine·homopyrimidine tracts; Human c-jun protooncogene; i-Motif; Structural polymorphism of DNA; Structural transitions in DNA
• ISSN: 0003-9861; 1096-0384
• DOI: 10.1016/j.abb.2008.01.015

Homopurine·homopyrimidine (Pu·Py) tracts are likely to play important biological role in eukaryotes. Using circular dichroism, UV-thermal denaturation and gel electrophoresis, we have analyzed the structural polymorphism of a 21-bp Pu·Py DNA segment within human c-jun protooncogene 3′-region, a potential target for triplex formation. Results show that below physiological pH and in the presence of Na +/K + with Mg 2+ the duplex is destabilized/disproportionated, resulting in strand mediated structural transitions to the self-associated structures of G- and C-rich strands separately, identified as G-quadruplex and i-motif species. A significant differential behavior of the monovalent cations was observed, accordingly the presence of Na + in acidic as well as neutral pH facilitated the duplex formation, while K + favored the formation of self-associated structures. In Na + and Mg 2+, under acidic and neutral pH conditions, the duplex displayed triphasic and biphasic melting profiles, respectively. This self-association property of oligonucleotides might limit their use as duplex targets in triplex formation. Study is also relevant for understanding structural and biological properties of DNA sequence containing homopurine tracts.