Thiouracils adenine-thiouracil base pairing

Adenine-Uracil and Adenine-Thiouracil Base Pairing... 

Table 8 collects the information on the interaction features of the Watson-Crick A-U and A-thiouracils base pairs. As follows from its last column, the total energies of the A-U and A-2TU base pairs after ZPVE correction are nearly identical and differ from each other by 0.4 kcal/mol. In this Table we separate the deformation energies of adenine and uracil or thiouracil under the corresponding base pairing. We find then that both uracil and thioracils experience more substantial deformations compared to adenine. These deformations are also indicated in Figures 6 and 7. 

The centrosymmetrical AA42 base pair is mostly observed in complexes 9-ethyl-8-bromo-adenine with 9-ethyl-8-bromo-hypoxanthine [EBAEBH1 9-methyl-adenine with l-methyl-4-thiouracil [SURMAD101 and with 2-thiohydantoin [BIFYOE] 9-ethyladenine with parabanic acid [EADPBA] 3-(adenin-9-yl)pro-piontryptamide [ADPRTR]. 

Table 4 presents the proton affinities PA and deprotonation enthalpies DPE of thiouracils calculated at the B3LYP/6-31+G(d,p) computational level. Inspecting this Table, we find that first, the thio substitution of uracil systematically increases its PAs by 3-6 kcal/mol and second, it decreases the DPEs of uracil by 6-13 kcal/mol. As far as the base pair A thioU is considered, it particularly implies a lowering, on the one hand, of the potential well at the Sio atom of thiouracil corresponding to the proton transfer from the N8 atom of adenine to the Sio of thiouracil and, on the other one, a raising of the potential well at the N3 atom of thiouracil involved in the proton transfer from the N3-H bond to the Ni atom of adenine. Therefore, summarizing, the thio substitution of uracil is in a favor to the double proton transfer mechanism of the occurrence of the spontaneous point mutations proposed by Lowdin [19]. Table 4 also includes the PAs of the T2 tautomer of uracil and thiouracils. A comparison with the corresponding PAs of the parental normal nucleobases shows that their tautomerization to the T2 form is accompanied by an increase of the proton affinity by 20-23 kcal/mol. 

Table 7. Geometrical parameters and hydrogen bond lengths of the adenine-uracil and adenine-thiouracil Watson-Crick base pairs. Distances in A, angles in degrees. In the distance notations, the former base belongs to adenine while the latter one to uracil or thiouracils.

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