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

Molecules

Shu-ichi Nakano¹ 

[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

关键词: DNA oligonucleotide;    Watson-Crick base pair;    hydrogen-bonding amino group;    2'-deoxyriboinosine;    2'-deoxyribo-2;    6-diaminopurine;    thermodynamic parameters;    complementary base recognition;    ion binding;   

DOI  :  10.3390/molecules190811613

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.