title: Conformational and stacking properties of 3'-5' and 2'-5' linked oligoribonucleotides studied by CD.
abstract: Comparative CD studies have been carried out to characterize the properties of 2'-5' and 3'-5' oligoriboadenylates and oligoribouridylates from dimer to decamer. The CD band of the 3'-5' oligoribonucleotides was larger than that of the 2'-5' oligoribonucleotides and increased with the increase in chain length, while the CD band of the 2'-5' oligoribonucleotides increased little beyond the dimer level. The CD analysis of the chain length dependency revealed that the 3'-5' oligoribonucleotides adopt mainly the base-base stacking interaction, while the base-sugar interaction is predominant in the 2'-5' oligoribonucleotides. The CD intensity of 3'-5' oligoribonucleotides decreased to a larger extent at elevated temperatures or in the presence of ethanol compared to that of the 2'-5' counterparts. Mg2+ or Mn2+ ion enhanced the magnitude of the CD of 3'-5' octariboadenylate, while a small decrease in the CD was observed by the presence of Mg2+ or Mn2+ ion to the 2'-5' octariboadenylate. The 3'-5' oligoribonucleotide is likely conformationally flexible and can form helical ordered structure with strong base-base stacking depending on changes in the environment such as temperature the presence of Mg2+ ion, or hydrophobicity of the solution.
authors.affiliation: Department of Chemistry, Gunma University, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Sawai
authors.forename: K
authors.initials: K
authors.lastname: Kuroda
authors.forename: J
authors.initials: J
authors.lastname: Seki
authors.forename: H
authors.initials: H
authors.lastname: Ozaki
mesh_terms: D002942:Circular Dichroism; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry*
chemical_list: D009843:Oligoribonucleotides