Andrea Saltos

Amir Mofrad

Characterization of the Bonding of an Adenine-Thymine Base Pair Inside of a Specific Double-Stranded DNA Structure

Discussion

The characterization of the bonding of an Adenine-Thymine base pair inside of a specific double-stranded DNA (ds-DNA) structure was studied by using Semi-Empirical Methods (SEM) and Layer Methods (LM).This was done by first optimizing the free Adenine Thymine (AT) base pair (shown in Scheme 1) at B3LYP/6-311G** level of theory. The overall dipole moment and Mulliken charges were also found, as can be seen in Figure 1. Additional calculations were done by optimizing a 3-base pair AAT sequence at AM1 semi-empirical theory. These calculations included overall optimization of the structure, optimization of the model with frozen backbones, and optimization of the hydrogen positions (see Figure 2). The output file of the former calculations was used to perform an ONIOM (B3LYP/6-311G**:AM1) calculation with the central AT in high layer.

The results obtained for the free AT base pair calculations are shown in Figure 1 and Table 1 (please refer to Scheme 1 for atom numbering). The total energy obtained is -921.727958 a.u. The dipole hasa magnitude of 1.6006 Debye and points in the direction ofThymine structure. Mulliken charges colored according to their electronegativity are also shown in Figure 1. which shows how the hydrogen bonding between these two structures is built. However, the electronic structure presented in Figure 1 and Table 1, should be different when considering that this molecule is placed in a polar and persisted environment, i.e. it is necessary to consider how it interacts within the DNA helix.

The optimized structures corresponding to the 3-base pair ds-DNA models obtained with the AM1 method and with the different constraints specified above, are found in Figure 1. As seen, the complete optimization of the model resulted in a structure that has little resemblance to the actual DNA structure. However, after freezing the C, O, and P atoms of every sugar, the model starts to look similar to actual crystal. A better structure is obtained by determining only the best position of the hydrogen atoms.

Figure 3 shows the optimized 3-base pair ds-DNA model obtained by the ONIOM (B3LYP/6-311G**: AM1). As can be seen, the structure attained is in perfect agreement with the actual DNA structure. This confirms how the combination of ab initio and semi-empirical methods applied to different parts of the molecule, can generate a reliable geometry and electronic structure at a reduced computational time. This conclusion can be confirmed by looking at the Mulliken charges for the free AT base and the 3-base pair model. Placing the AT base within the DNA chain, decreases the negative charges of the fragments, which indicates that the hydrogens are pulling the electron density away from the fragment atoms to form bonds. As a result, A-T pairs maximize the number of hydrogen bonds across the shared helical axis, playing an important role in the stacking of bases in nucleic acids.

Scheme 1. AT Base Pair


Figure 1. B3LYP/6-311G** optimized structure of the free AT base pair . Top figure shows the electric dipole moment vector with a magnitude of 1.6006 Debye, and a total energy of -921.727958 a.u. Bottom figure shows the base pair with atoms color-coded according to their Mulliken charges with red being the most electronegative. N1-H bond length: 1.822 A˚. Charges: 0.304 for H, – 0.513 for N. H-O(on C4) bond length: 1.928 A˚ charges: 0.260 for H. -0.41 for O.

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Andrea Saltos

Amir Mofrad

Table 1. Mulliken Charges in the AT Base Pair at B3LYP/6-311G** Level of Theory

Fragment / free base pair / 3-base pair
Adenine
N1 / -0.516 / -0.336
C2 / 0.162 / 0.058
H(C2) / 0.128 / 0.212
N3 / -0.337 / -0.200
C4 / 0.358 / 0.080
C5 / -0.104 / -0.242
N (C6) / -0.476 / -0.347
H1 on N(C6) / 0.260 / 0.265
H2 on N(C6) / 0.237 / 0.244
N7 / -0.335 / 0.108
C8 / 0.170 / -0.043
H(C8) / 0.115 / 0.197
N9 / -0.390 / -0.183
Thymine
N1 / -0.418 / -0.283
O2 / -0.364 / -0.337
N3 / -0.457 / -0.405
O4 / -0.410 / -0.375
C6 / 0.220 / 0.047
H(C6) / 0.118 / 0.160
C (C5) / -0.225 / -0.144
H(N3) / 0.304 / 0.311

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Andrea Saltos

Amir Mofrad

Figure 2. Structure of 3-base pair ds-DNA. Top: optimized structure model at AM1. Center: partially optimized structure at AM1 with frozen backbones. Bottom: partially optimization of hydrogen positions at AM1.

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Andrea Saltos

Amir Mofrad

Figure 3. Partially optimized structure of 3-base pair ds-DNA model with central AT in high layer at B3LYP/6-311G**:AM1 (ONIOM)

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