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.
Highlights
IntroductionDNA is a molecule with the ability to assemble base pairs through the formation of hydrogen bonds
DNA is a molecule with the ability to assemble base pairs through the formation of hydrogen bonds.The GC base pair forms three hydrogen bonds, and the AT base pair forms two hydrogen bonds, leading to a greater thermodynamic stability of GC than AT base pairs [1]
In an effort to determine the electrostatic component of the 2-amino group of DNA purine bases, the present study compared the thermodynamic parameters of DNA duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I)
Summary
DNA is a molecule with the ability to assemble base pairs through the formation of hydrogen bonds. DNA duplex stability is strongly dependent on the salt concentration and solvent conditions. In an effort to determine the electrostatic component of the 2-amino group of DNA purine bases, the present study compared the thermodynamic parameters of DNA duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I). This study was designed to investigate the role of the 2-amino group of purine bases in determining the stability of DNA duplexes and the salt effects, which have not been well addressed. Sequence-dependent salt effects on the thermodynamic stability of DNA duplexes are presented, and the role of the 2-amino group in affecting ion binding as well as in creating base-pair hydrogen bonding is proposed. The results of this study provide insight into the design of non-natural nucleotides and suggest suitable experimental conditions for practical applications of DNA oligonucleotides
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