Andrea SaltosAmir 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 has a magnitude of 1.6006 Debye and points in the direction of Thymine 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.

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Andrea SaltosAmir Mofrad

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.

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Andrea SaltosAmir Mofrad

Scheme 1. AT Base Pair

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Andrea SaltosAmir Mofrad

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 SaltosAmir 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 SaltosAmir 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 SaltosAmir Mofrad

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Andrea SaltosAmir 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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