Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base PairingReportar como inadecuado




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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.



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





Autor: Shu-ichi Nakano 1,* and Naoki Sugimoto 1,2

Fuente: http://mdpi.com/



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