Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs |
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Authors: | Mauricio Alcolea Palafox |
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Institution: | Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain |
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Abstract: | The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2′ hydroxyl atom: A-type appears with the ribose ring in 3E-envelope C3′-endo, and B-type in 2E-envelope C2′-endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested. |
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Keywords: | 2 4-dithiouracil 2-thiouracil 4-thiouracil DNA:RNA microhelix uridine 2-thiouridine |
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