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Fluorescent base analogues are of great importance as sensitive probes to detect the dynamic structures of DNA. In this research, the structural and photophysical properties of 13-mer oligonucleotides containing 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) (4AP0, 4AP') were characterized using both molecular dynamics simulations and quantum mechanics methods. The results indicate that the 4AP:DAP pair is well adapted to the overall B-DNA structure with higher stability and π-stacking abilities. The structural overlap of 4AP' and 4AP0 with the neighboring adenines only lies in the 5'-direction which results in the structure distortion from native B-DNA. Furthermore, the photophysical properties of the fluorescent base monomers and the B-DNA duplex were explored in detail. A very important result is that the hydrogen bond interaction does not have more effect on the fluorescence band apart from the slight red-shifts. In particular, the identity of the neighboring bases stacked with 4AP has an important effect on the fluorescence band. How the local environment can alter the photophysical features of the nucleobases when they are incorporated into the DNA duplex is elucidated.

The detailed formation mechanisms of C-ribonucleoside and N-ribonucleoside via the reaction of 2,4,6-triaminopyrimidine (TAP) with (d)-ribose in aqueous solution were explored using density functional theory (DFT). The calculations indicate that five isomers (α,β-furanose, α,β-pyranose and open-chain aldehyde) of (d)-ribose can exist in equilibrium in aqueous solution. In contrast to cyclic isomers, an open-chain aldehyde is most feasible to react with TAP. In general, the formation pathways of C-nucleoside and N-nucleoside proceed in three steps including nucleophilic addition, dehydration and cyclization. The calculated apparent activation energies are 28.8 kcal mol -1 and 29.2 kcal mol -1 , respectively. It suggests that both C- and N-nucleoside can be formed in aqueous solution, which is in good agreement with the experimental results. The water molecule plays an important "H-bridge" role by the hydrogen atom relay. Finally, a model structure of nucleobase, which will be beneficial for the C-C glycosidic bond formation, is proposed.

Density functional theory is utilized to elucidate the detailed mechanisms of the reactions between 2-aminooxazole O2 /2-aminothiazole S2 and glyceraldehyde 2 . According to our calculations, in O2 / 2 system, aminooxazoline O3 is formed via two steps including C C formation and cyclization. C C formation determines the reaction diastereoselectivity and ribo-aminooxazoline is the most favorable product. Although oxazole-hemiaminal O6 is not detected in the experiment, it is deduced can be formed theoretically. In S2 / 2 system, aminothiazoline S3 is hard to be generated because of the less nucleophilic ability of S2 . The formation of thiazole-hemiaminal S6 is more favorable than S3 formation in kinetics but somewhat unfavorable in thermodynamics. However, the transformation from S6 to thiazole-aminal S7 is favorable both in kinetics and thermodynamics, which provides a driving force for the formation and transformation of S6 . Additionally, our calculations indicate that phosphate is very important in assisting proton transfer in all of the transformations. [ABSTRACT FROM AUTHOR]