Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing
AbstractThe 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. View Full-Text
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Nakano, S.-I.; Sugimoto, N. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing. Molecules 2014, 19, 11613-11627.
Nakano S-I, Sugimoto N. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing. Molecules. 2014; 19(8):11613-11627.Chicago/Turabian Style
Nakano, Shu-ichi; Sugimoto, Naoki. 2014. "Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing." Molecules 19, no. 8: 11613-11627.