title: Structural Aspects of the Antiparallel and Parallel Duplexes Formed by DNA, 2'-O-Methyl RNA and RNA Oligonucleotides.
abstract: This study investigated the influence of the nature of oligonucleotides on the abilities to form antiparallel and parallel duplexes. Base pairing of homopurine DNA, 2'-O-MeRNA and RNA oligonucleotides with respective homopyrimidine DNA, 2'-O-MeRNA and RNA as well as chimeric oligonucleotides containing LNA resulted in the formation of 18 various duplexes. UV melting, circular dichroism and fluorescence studies revealed the influence of nucleotide composition on duplex structure and thermal stability depending on the buffer pH value. Most duplexes simultaneously adopted both orientations. However, at pH 5.0, parallel duplexes were more favorable. Moreover, the presence of LNA nucleotides within a homopyrimidine strand favored the formation of parallel duplexes.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Szabat
authors.affiliation: Department of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61-614 Poznan, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Pedzinski
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Czapik
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
mesh_terms: D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D012313:RNA; D004247:DNA