期刊
MOLECULES
卷 19, 期 8, 页码 11613-11627出版社
MDPI
DOI: 10.3390/molecules190811613
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
资金
- JSPS (Japan Society for the Promotion of Science) [24550200]
- MEXT (Ministry of Education, Culture, Sports, Science and Technology in Japan)
- Grants-in-Aid for Scientific Research [24550200] Funding Source: KAKEN
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 center dot C > D center dot T approximate to I center dot C > A center dot T > G center dot T > I center dot 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.
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