title: Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes.
abstract: The pyr*pur.pyr type of nucleic acid triplex has a purine strand that is Hoogsteen-paired with a parallel pyrimidine strand (pyr*pur pair) and that is Watson-Crick-paired with an antiparallel pyrimidine strand (pur.pyr pair). In most cases, the Watson-Crick pair is more stable than the Hoogsteen pair, although stable formation of DNA Hoogsteen-paired duplexes has been reported. Using oligomer triplexes of repeating d(AG)12 and d(CT)12 or r(CU)12 sequences that were 24 nt long, we found that hybrid RNA*DNA as well as DNA*DNA Hoogsteen-paired strands of triplexes can be more stable than the Watson-Crick-paired strands at low pH. The structures and relative stabilities of these duplexes and triplexes were evaluated by circular dichroism (CD) spectroscopy and UV absorption melting studies of triplexes as a function of pH. The CD contributions of Hoogsteen-paired RNA*DNA and DNA*DNA duplexes were found to dominate the CD spectra of the corresponding pyr*pur.pyr triplexes.
authors.affiliation: Department of Molecular and Cell Biology, Mail Stop FO31, The University of Texas at Dallas, Box 830688, Richardson, TX 75083-0688, USA.
authors.forename: G M
authors.initials: GM
authors.lastname: Hashem
authors.forename: J D
authors.initials: JD
authors.lastname: Wen
authors.forename: Q
authors.initials: Q
authors.lastname: Do
authors.forename: D M
authors.initials: DM
authors.lastname: Gray
mesh_terms: D001704:Biopolymers; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D013696:Temperature
chemical_list: D001704:Biopolymers; C051802:triplex DNA; D004247:DNA