title: Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.
abstract: The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G • C > D • T ≈ I • C > A • T > G • T > I • T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.
authors.affiliation: Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. shuichi@center.konan-u.ac.jp.
authors.forename: Shu-ichi
authors.initials: S
authors.lastname: Nakano
authors.affiliation: Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. sugimoto@konan-u.ac.jp.
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D015075:2-Aminopurine / Q000031:analogs & derivatives / Q000737:chemistry; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011687:Purines / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D011687:Purines; D012997:Solvents; D015075:2-Aminopurine; C007300:2,6-diaminopurine; D004247:DNA; D012964:Sodium; D008274:Magnesium; C030985:purine
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