title: Structural polymorphism exhibited by a homopurine.homopyrimidine sequence found at the right end of human c-jun protooncogene.
abstract: 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 Mg2+ 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 Mg2+, 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.
authors.affiliation: Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India.
authors.forename: Sarika
authors.initials: S
authors.lastname: Saxena
authors.forename: Aparna
authors.initials: A
authors.lastname: Bansal
authors.forename: Shrikant
authors.initials: S
authors.lastname: Kukreti
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002412:Cations / Q000737:chemistry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D016758:Genes, jun; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008274:Magnesium / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011188:Potassium / Q000737:chemistry; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D011685:Purine Nucleotides / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature
chemical_list: D002412:Cations; D011518:Proto-Oncogene Proteins; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D004247:DNA; D012964:Sodium; D008274:Magnesium; D011188:Potassium