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Conformational and stacking properties of 3′–5′ and 2′–5′ linked oligoribonucleotides studied by CD
Author(s) -
Sawai H.,
Kuroda K.,
Seki J.,
Ozaki H.
Publication year - 1996
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(199608)39:2<173::aid-bip5>3.0.co;2-m
Subject(s) - chemistry , stacking , dimer , base pair , base (topology) , crystallography , stereochemistry , dna , biochemistry , organic chemistry , mathematical analysis , mathematics
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. Mg 2+ or Mn 2+ ion enhanced the magnitude of the CD of 3′–5′ octariboadenylate, while a small decrease in the CD was observed by the presence of Mg 2+ or Mn 2+ 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 Mg 2+ ion, or hydrophobicity of the solution. © 1996 John Wiley & Sons, Inc.