Homotactic enthalpic pairwise interactions of four deoxynucleosides (dU, dC, dG, dT) in dimethylformamide (DMF) + water mixtures at 298.15 K
Highlights
► This work focuses on hXX as the measurement of solute–solute interaction. ► Dilution enthalpies of them in mixed solvent were determined by ITC. ► It is found that the hXX values of them are all large negative. ► The hXX values of them increase gradually in certain concentration range. ► We deduced that the strength of interaction follows the order: dC > dT > dT > dU according to hXX.
Introduction
Nucleotides are the construction units of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), containing a large amount of the genetic codes of each organism. Nucleotides are heterogeneous in composition, not only containing hydrophilic, polar and ionizable groups, but also hydrophobic, apolar and non-ionizable groups. Nucleobase moieties are directly involved in the formation of the well-known double helix structure and others, affecting greatly the thermodynamic stability and diversity of DNA and RNA, due to strong hydrogen bonds, stacking interactions, electrostatic effects and duplex salvation [1]. Among them, the role of hydrophobic interactions in the conformational stability of nucleic acids is still an interesting issue of discussion [2]. A great deal of investigations on thermodynamic properties of aqueous solutions of nucleosides, nucleotides and related derivatives have been reported in the past several decades [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], but less attentions have been paid to their thermodynamic properties in aqueous organic solvents [18], [19].
In our previous work, dilution enthalpies of α-amino acids, chiral aliphatic diols and chiral amino alcohols in DMSO + water and DMF + water mixtures of various mass fractions have been determined using ITC (VP-ITC, MicroCal) [20], [21], [22], [23]. As our on-going interest in enthalpic pairwise interactions of small nonelectrolytes of biological importance in aqueous solutions containing different cosolvents or cosolutes, this work aims at enthalpic discrimination effects in homotatic pairwise interactions of four 2′-deoxynucleosides, the moieties of nucleic acid macromolecule, including 2′-deoxyuridine (dU), 2′-deoxycytidine (dC), 2′-deoxyguanosine (dG) and 2′-deoxythymidine (dT), in various aqueous DMF mixtures rich in water. The four 2′-deoxynucleosides selected contain the same sugar moiety and differ from each other merely in their pyrimidine bases, therefore they can serve as interesting model compounds for the analysis of homotactic pairwise interactions. We hope that this study will be helpful to understand better the origin of genetic codes, chemical evolution and thermodynamic stability of nucleic acids.
Section snippets
Theoretical background
According to Fini and Castagnolo [24], the value of dilution enthalpy per injection in ITC can be expressed as:in which N indicates the number of injections, and nP is the moles of solute in each injection volume (Vinj, μL, i.e. 10−9 m3), which can be calculated as follows:in which, ρsol is the density (kg m−3) of the solution in the syringe, and m0 is defined especially as moles of solute in 1 kg of the solution. Since the solutions used
Experimental
2′-Deoxycytidine (dC) was purchased from TCI, 2′-deoxyuridine (dU), 2′-deoxyguanosine (dG) and 2′-deoxythymidine (dT) were purchased from ACROS, and the purity of each compound is better than 99%. The structures of them are shown in Scheme 1. All of them were used without further purification except necessary drying. DMF (AR grade, mass fraction >99%) were twice distilled under reduced pressure over molecular sieves (0.4 nm), collected finally at 314.15 K, and then dried by molecular sieves for 24
Results and discussion
The accuracy of apparatus and method has been testified previously by us through dilution experiments of glycine, l-alanine and l-serine in pure water at 298.15 K [21], [22], [23]. The possible error sources for the hXX values obtained here are considered to be arising from the systematic errors which relates to the differences in either the principles of calorimetry or the types of microcalorimeters used.
As an example, the typical titration curve of dC in water at 298.15 K is shown in Fig. 1,
Acknowledgements
This work was financially supported by the National Natural Science Foundation of China (No. 21073132), and the Graduate Student Innovation Foundation of Wenzhou University.
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