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Molecules 2014, 19(8), 11613-11627; https://doi.org/10.3390/molecules190811613

Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

1
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
2
Frontier Institute of Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
*
Author to whom correspondence should be addressed.
Received: 27 June 2014 / Revised: 28 July 2014 / Accepted: 31 July 2014 / Published: 5 August 2014
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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. View Full-Text
Keywords: DNA oligonucleotide; Watson-Crick base pair; hydrogen-bonding amino group; 2'-deoxyriboinosine; 2'-deoxyribo-2,6-diaminopurine; thermodynamic parameters; complementary base recognition; ion binding DNA oligonucleotide; Watson-Crick base pair; hydrogen-bonding amino group; 2'-deoxyriboinosine; 2'-deoxyribo-2,6-diaminopurine; thermodynamic parameters; complementary base recognition; ion binding
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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.

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