The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study
Abstract
:1. Introduction
2. Results and Discussion
2.1. Structural Analysis of Isolated, Tandem, and Closured DNA Damage
2.2. The Ionization Potential of Isolated, Tandem, and Closured DNA Damage
3. Materials and Methods
3.1. Computation Methodology of QM/MM Studies [42,43]
3.2. Computation Methodology of Density Functional Theory (DFT) Study
4. Conclusions
Supplementary Materials
Funding
Conflicts of Interest
References
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Sample Availability: Samples of the compounds are not available from the author. |
DNA Damage Type | Oligonucleotide | Oligonucleotide Base Sequence |
---|---|---|
Undamaged Native ds-DNA | N-DNA | d[A1G2A3G4G5A6]*d[T6C5C4A3C2T1] |
Single | 3Goxo-N-DNA | d[A1G2A3oxoG4G5A6]*d[T6C5C4A3C2T1] |
5Goxo-N-DNA | d[A1oxoG2A3G4G5A6]*d[T6C5C4A3C2T1] | |
Tandem | ScA-DNA | d[A1G2(5′S)cA3G4G5A6]*d[T6C5C4A3C2T1] |
Clustered | 3Goxo-ScA-DNA | d[A1G2(5′S)cA3oxoG4G5A6]*d[T6C5C4A3C2T1] |
5Goxo-ScA-DNA | d[A1oxoG2(5′S)cA3G4G5A6]*d[T6C5C4A3C2T1] | |
Tandem | RcA-DNA | d[A1G2(5′R)cA3G4G5A6]*d[T6C5C4A3C2T1] |
Clustered | 3Goxo-RcA-DNA | d[A1G2(5′R)cA3oxoG4G5A6]*d[T6C5C4A3C2T1] |
5Goxo-RcA-DNA | d[A1oxoG2(5′R)cA3G4G5A6]*d[T6C5C4A3C2T1] |
ds-DNA Base Dimer h-rise Parameter [Å] | ||||||||
---|---|---|---|---|---|---|---|---|
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | ||||||
NEUT. | ARC | NEUT. | ARC | NEUT. | ARC | |||
G2A3 | 2.96 | 3.01 | G2A3 | 3.06 | 3.02 | oxoG2A3 | 2.89 | 2.86 |
A3G4 | 3.31 | 2.88 | A3G4oxo | 3.33 | 3.25 | A3G4 | 3.24 | 3.23 |
G4G5 | 3.34 | 3.14 | oxoG4G5 | 3.28 | 3.07 | G4G5 | 3.34 | 3.38 |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | ||||||
G2(5′S)cA3 | 3.36 | 3.29 | G2(5′S)cA3 | 3.36 | 3.39 | oxoG2(5′S)cA3 | 3.26 | 3.11 |
(5′S)cA3G4 | 2.98 | 2.82 | (5′S)cA3G4oxo | 3.05 | 2.87 | (5′S)cA3G4 | 2.94 | 2.97 |
G4G5 | 3.68 | 3.56 | oxoG4G5 | 3.65 | 3.5 | G4G5 | 3.68 | 3.68 |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | ||||||
G2(5′R)cA3 | 3.32 | 3.26 | G2(5′R)c A3 | 3.45 | 3.41 | oxoG2(5′R)c A3 | 3.37 | 3.24 |
(5′R)cA3G4 | 2.8 | 2.7 | (5′R)cA3G4oxo | 3.15 | 3.12 | (5′R)cA3G4 | 2.87 | 3.05 |
G4G5 | 3.6 | 3.49 | oxoG4G5 | 3.68 | 3.55 | G4G5 | 3.63 | 3.67 |
ds-DNA Bases Aromatic Rings Overlap [Å2] | ||||||||
---|---|---|---|---|---|---|---|---|
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | ||||||
NEUT. | ARC | NEUT. | ARC | NEUT. | ARC | |||
G2A3 | 2.14 | 1.3 | G2A3 | 2.95 | 2.9 | G2oxoA3 | 1.95 | 1.62 |
A3G4 | 3.79 | 3.46 | A3G4oxo | 2.56 | 2.93 | A3G4 | 3.31 | 3.66 |
G4G5 | 1.28 | 1.07 | G4oxoG5 | 0.56 | 0.52 | G4G5 | 0.77 | 0.83 |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | ||||||
G2A3 | 2.29 | 2.2 | G2A3 | 2.27 | 2.22 | oxoG2A3 | 1.95 | 2.14 |
(5′S)cA3G4 | 3.10 | 5.59 | (5′S)cA3G4oxo | 6.51 | 6.31 | (5′S)cA3G4 | 5.30 | 5.21 |
oxoG4G5 | 2.97 | 3.22 | oxoG4G5 | 3.44 | 3.12 | oxoG4G5 | 3.40 | 3.42 |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | ||||||
G2A3 | 1.99 | 2.11 | G2A3 | 0.99 | 0.89 | oxoG2A3 | 2.05 | 1.86 |
(5′R)cA3G4 | 2.00 | 5.03 | (5′R)cA3G4oxo | 3.27 | 3.13 | (5′R)cA3G4 | 4.98 | 3.34 |
oxoG4G5 | 2.81 | 2.99 | oxoG4G5 | 1.86 | 1.99 | oxoG4G5 | 2.89 | 0.94 |
ds-DNA Stacking Energy (kcal/mol) | ||||||||
---|---|---|---|---|---|---|---|---|
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | ||||||
NEUT. | VER.N | NEUT. | VER.N | NEUT. | VER.N | |||
G2A3 | −14.56 | −14.55 | G2A3 | −14.23 | −14.91 | G2oxoA3 | −14.43 | −13.75 |
A3G4 | −13.59 | −14.88 | A3G4oxo | −14.69 | −14.63 | A3G4 | −13.38 | −14.55 |
G4G5 | −12.05 | −13.39 | G4oxoG5 | −12.86 | −13.03 | G4G5 | −12.09 | −12.76 |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | ||||||
G2A3 | −12.94 | −13.10 | G2A3 | −12.90 | −13.10 | oxo G2A3 | −12.82 | −12.31 |
(5′S)cA3G4 | −11.25 | −11.20 | (5′S)cA3G4oxo | −11.88 | −11.07 | (5′S)cA3G4 | −11.40 | −11.90 |
oxoG4G5 | −14.15 | −13.27 | oxoG4G5 | −14.68 | −13.86 | oxoG4G5 | −14.16 | −14.25 |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | ||||||
G2A3 | −13.23 | −13.39 | G2A3 | −12.92 | −12.86 | oxoG2A3 | −13.05 | −10.58 |
(5′R)cA3G4 | −13.39 | −12.52 | (5′R)cA3G4oxo | −14.73 | −13.77 | (5′R)cA3G4 | −13.24 | −13.70 |
oxoG4G5 | −13.50 | −12.92 | oxoG4G5 | −14.84 | −14.28 | oxoG4G5 | −13.48 | −14.54 |
ds-DNA Hydrogen Bond Energy | ||||||||
---|---|---|---|---|---|---|---|---|
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | ||||||
NEUT. | VER.N | NEUT. | VER.N | NEUT. | VER.N | |||
G2C2 | −17.23 −17.54 (a) −14.36 (b) | −17.22 −18.10 (a) | G2C2 | −17.32 | −17.36 | oxoG2C2 | −17.69 | −18.16 |
A3T3 | −10.81 −10.95 (a) −8.64 (b) | −10.74 −9.75 (a) | A3T3 | −10.53 | −10.44 | A3T3 | −10.80 | −10.39 |
G4C4 | −17.20 | −17.00 | oxoG4C4 | −17.74 −18.04 (a) −16.83 (c) | −17.97 −18.49 (a) | G4C4 | −17.26 | −17.14 |
G5C5 | −17.21 | −17.73 | G5C5 | −17.23 | −17.32 | G5C5 | −17.23 | −17.31 |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | ||||||
G2C2 | −17.30 | −17.48 | G2C2 | −17.25 | −17.30 | oxoG2C2 | −17.84 | −18.38 |
(5′S)cA3T3 | −10.62 −10.98 (a) −5.89 (b) | −10.81 −9.77 (a) | (5′S)A3T3 | −10.54 | −10.61 | (5′S)A3T3 | −10.66 | −9.99 |
G4C4 | −17.10 | −17.80 | oxoG4C4 | −17.58 | −18.07 | G4C4 | −17.12 | −17.04 |
G5C5 | −17.06 | −17.19 | G5C5 | −17.08 | −17.23 | G5C5 | −17.04 | −17.06 |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | ||||||
G2C2 | −17.19 | −17.15 | G2C2 | −16.94 | −17.03 | oxoG2C2 | −17.81 | −18.01 |
(5′R)cA3T3 | −10.60 −10.98 (a) | −10.49 −9.74 (a) | (5′R)A3T3 | −10.65 | −10.55 | (5′R)A3T3 | −10.65 | −9.88 |
G4C4 | −16.77 | −17.86 | oxoG4C4 | −18.07 | −18.60 | G4C4 | −16.82 | −17.50 |
G5C5 | −16.95 | −17.17 | G5C5 | −16.81 | −16.85 | G5C5 | −16.96 | −16.80 |
AIP | VIP | AIP | VIP | AIP | VIP | ||||
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ds-trimers | |||||||||
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | |||||||
G2A3G4 | 5.72 | 6.10 | G2A3oxoG4 | 5.51 | 5.85 | oxoG2A3G4 | 5.45 | 5.90 | |
A3G4G5 | 5.64 | 6.03 | A3oxoG4G5 | 5.37 | 5.79 | A3G4G5 | 6.01 | 6.02 | |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | |||||||
G2(5′S)cA3G4 | 5.74 | 6.13 | G2(5′S)cA3oxoG4 | 5.51 | 5.91 | oxoG2(5′S)cA3G4 | 5.44 | 5.86 | |
(5′S)cA3G4G5 | 5.69 | 6.08 | (5′S)cA3oxoG4G5 | 5.45 | 5.88 | (5′S)cA3G4G5 | 6.09 | 6.14 | |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | |||||||
G2(5′R)cA3G4 | 5.72 | 6.08 | G2(5′R)cA3oxoG4 | 5.50 | 5.94 | oxoG2(5′R)cA3G4 | 5.43 | 5.87 | |
(5′R)cA3G4G5 | 5.66 | 6.03 | (5′R)cA3oxoG4G5 | 5.47 | 5.91 | (5′R)cA3G4G5 | 6.13 | 6.03 | |
ds-dimers | |||||||||
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | |||||||
G2A3 | 6.13 | 6.15 | G2A3 | 6.13 | 6.12 | oxoG2A3 | 5.50 | 5.91 | |
A3G4 | 5.73 | 6.12 | A3oxoG4 | 5.48 | 5.88 | A3G4 | 6.12 | 6.11 | |
G4G5 | 5.68 | 6.05 | oxoG4G5 | 5.40 | 5.83 | G4G5 | 6.04 | 6.05 | |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | |||||||
G2A3 | 6.12 | 6.10 | G2A3 | 6.13 | 6.10 | oxoG2A3 | 5.47 | 5.87 | |
(5′S)cA3G4 | 5.75 | 6.14 | (5′S)cA3G4 | 5.52 | 5.93 | (5′S)cA3G4 | 6.20 | 6.15 | |
G4G5 | 5.78 | 6.12 | G4G5 | 5.48 | 5.89 | G4G5 | 6.13 | 6.13 | |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | |||||||
G2A3 | 6.12 | 6.10 | G2A3 | 6.14 | 6.12 | oxoG2A3 | 5.53 | 5.89 | |
(5′R)cA3G4 | 5.74 | 6.09 | (5′R)cA3G4 | 5.51 | 5.94 | (5′R)cA3G4 | 6.13 | 6.10 | |
G4G5 | 5.73 | 6.21 | G4G5 | 5.49 | 5.93 | G4G5 | 6.21 | 6.21 | |
Single base pairs | |||||||||
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | |||||||
G2C2 | 6.17 | 6.17 | G2C2 | 6.19 | 6.19 | oxoG2C2 | 5.55 | 5.93 | |
A3T3 | 6.63 | 6.65 | A3T3 | 6.69 | 6.65 | A3T3 | 6.65 | 6.64 | |
G4C4 | 5.86 | 6.13 | oxoG4C4 | 5.55 | 5.91 | G4C4 | 6.14 | 6.13 | |
G5C5 | 6.15 | 6.20 | G5C5 | 6.14 | 6.18 | G5C5 | 6.19 | 6.20 | |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | |||||||
G2C2 | 6.13 | 6.19 | G2C2 | 6.14 | 6.15 | oxoG2C2 | 5.55 | 5.92 | |
(5′S)cA3T3 | 6.65 | 6.68 | (5′S)cA3T3 | 6.67 | 6.68 | (5′S)cA3T3 | 6.83 | 6.69 | |
G4C4 | 5.84 | 6.14 | oxoG4C4 | 5.55 | 5.94 | G4C4 | 6.19 | 6.18 | |
G5C5 | 6.19 | 6.22 | G5C5 | 6.19 | 6.22 | G5C5 | 6.22 | 6.23 | |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | |||||||
G2C2 | 6.12 | 6.23 | G2C2 | 6.16 | 6.18 | oxoG2C2 | 5.58 | 5.93 | |
(5′R)c A3T3 | 6.68 | 6.61 | (5′R)cA3T3 | 6.65 | 6.61 | (5′R)cA3T3 | 6.77 | 6.61 | |
G4C4 | 5.80 | 6.12 | oxoG4C4 | 5.53 | 5.96 | G4C4 | 6.08 | 6.20 | |
G5C5 | 6.18 | 6.22 | G5C5 | 6.15 | 6.19 | G5C5 | 6.19 | 6.22 | |
Ideal Base Pair Model | Isolated from 5ivl.pdb [45] and 21sf.pdb [44] Structure | ||||||||
AIP | VIP | ||||||||
G:::C | 5.58 | 6.13 | VIP | ||||||
Goxo:::C | 5.55 | 5.90 | G:::C** | 6.14 | |||||
ScA::T | 6.35 | 6.62 | Goxo:::C* | 5.82 | |||||
RcA::T | 6.35 | 6.62 | ScA::T** | 6.71 | |||||
A::T | 6.34 | 6.62 | A::T** | 6.66 |
ds-oligo | Backbone | Bases | All Nucleic Acid |
---|---|---|---|
N-DNA | 1.347 | 1.039 | 1.197 |
3Goxo-N-DNA | 0.299 | 0.225 | 0.261 |
5Goxo-N-DNA | 0.359 | 0.319 | 0.337 |
ScA-DNA | 0.699 | 0.193 | 0.516 |
3Goxo-ScA-DNA | 0.203 | 0.176 | 0.190 |
5Goxo-ScA-DNA | 0.247 | 0.214 | 0.231 |
RcA-DNA | 0.695 | 0.298 | 0.537 |
3Goxo-RcA-DNA | 0.119 | 0.082 | 0.103 |
5Goxo-RcA-DNA | 1.032 | 0.817 | 0.931 |
ds-DNA Hirshfeld Charge and Spin Density Population | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | |||||||||||||||
N | VC | C | N | VC | C | N | VC | C | |||||||||
Q | Q | S | Q | S | Q | Q | S | Q | S | Q | Q | S | Q | S | |||
T6 | −0.05 | −0.05 | −0.04 | T6 | −0.05 | −0.05 | −0.04 | T6 | −0.05 | −0.05 | −0.05 | ||||||
C5 | 0.18 | 0.19 | 0.18 | C5 | 0.17 | 0.17 | 0.17 | C5 | 0.18 | 0.18 | 0.17 | ||||||
C4 | 0.19 | 0.22 | 0.32 | C4 | 0.21 | 0.24 | 0.29 | C4 | 0.19 | 0.19 | 0.20 | ||||||
T3 | −0.07 | −0.05 | −0.02 | T3 | −0.07 | −0.05 | −0.05 | T3 | −0.06 | −0.06 | −0.05 | ||||||
C2 | 0.21 | 0.22 | 0.22 | C2 | 0.20 | 0.21 | 0.21 | C2 | 0.21 | 0.25 | 0.31 | ||||||
T1 | −0.08 | −0.07 | −0.07 | T1 | −0.08 | −0.07 | −0.07 | T1 | −0.08 | −0.05 | −0.02 | ||||||
A1 | 0.01 | 0.01 | 0.00 | A1 | 0.01 | 0.01 | 0.01 | A1 | 0.02 | 0.06 | 0.01 | 0.05 | 0.02 | ||||
G2 | −0.14 | −0.13 | −0.14 | G2 | −0.14 | −0.13 | −0.13 | G2oxo | −0.16 | 0.69 | 0.97 | 0.59 | 0.97 | ||||
A3 | 0.03 | 0.06 | 0.02 | 0.05 | 0.03 | A3 | 0.03 | 0.07 | 0.02 | 0.07 | 0.02 | A3 | 0.03 | 0.06 | 0.02 | 0.05 | 0.01 |
G4 | −0.18 | 0.67 | 0.96 | 0.55 | 0.96 | G4oxo | −0.19 | 0.66 | 0.97 | 0.59 | 0.97 | G4 | −0.18 | −0.17 | −0.16 | ||
G5 | −0.14 | −0.10 | 0.02 | −0.09 | 0.02 | G5 | −0.13 | −0.10 | 0.01 | −0.10 | 0.01 | G5 | −0.14 | −0.14 | −0.13 | ||
A6 | 0.03 | 0.04 | 0.03 | A6 | 0.04 | 0.04 | 0.05 | A6 | 0.04 | 0.04 | 0.04 | ||||||
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | |||||||||||||||
T6 | −0.06 | −0.06 | −0.05 | T6 | −0.06 | −0.06 | −0.05 | T6 | −0.06 | −0.06 | −0.06 | ||||||
C5 | 0.21 | 0.22 | 0.22 | C5 | 0.21 | 0.22 | 0.22 | C5 | 0.21 | 0.21 | 0.22 | ||||||
C4 | 0.13 | 0.16 | 0.23 | C4 | 0.13 | 0.16 | 0.23 | C4 | 0.12 | 0.12 | 0.13 | ||||||
T3 | −0.08 | −0.07 | −0.06 | T3 | −0.08 | −0.07 | −0.07 | T3 | −0.08 | −0.07 | −0.07 | ||||||
C2 | 0.22 | 0.22 | 0.23 | C2 | 0.22 | 0.22 | 0.23 | C2 | 0.22 | 0.25 | 0.31 | ||||||
T1 | −0.07 | −0.07 | −0.05 | T1 | −0.06 | −0.06 | −0.06 | T1 | −0.05 | −0.03 | −0.01 | ||||||
A1 | 0.00 | 0.00 | −0.01 | A1 | −0.01 | −0.01 | −0.01 | A1 | 0.06 | 0.11 | 0.02 | 0.10 | |||||
G2 | −0.16 | −0.16 | −0.15 | G2 | −0.16 | −0.16 | −0.14 | G2oxo | −0.24 | 0.63 | 0.97 | 0.53 | 0.97 | ||||
ScA3 | 0.04 | 0.08 | 0.03 | 0.07 | 0.03 | ScA3 | 0.03 | 0.07 | 0.03 | 0.07 | 0.02 | ScA3 | 0.03 | 0.06 | 0.01 | 0.06 | 0.03 |
G4 | −0.15 | 0.72 | 0.96 | 0.62 | 0.96 | G4oxo | −0.16 | 0.71 | 0.96 | 0.61 | 0.97 | G4 | −0.14 | −0.14 | −0.13 | ||
G5 | −0.11 | −0.08 | 0.01 | −0.09 | 0.01 | G5 | −0.11 | −0.08 | 0.01 | −0.08 | 0.01 | G5 | −0.11 | −0.11 | −0.11 | ||
A6 | 0.03 | 0.04 | 0.04 | A6 | 0.03 | 0.04 | 0.04 | A6 | 0.03 | 0.03 | 0.03 | ||||||
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | |||||||||||||||
T6 | 0.05 | −0.05 | −0.05 | T6 | −0.05 | −0.05 | −0.05 | T6 | −0.05 | −0.05 | −0.05 | ||||||
C5 | −0.21 | 0.21 | 0.22 | C5 | 0.21 | 0.22 | 0.23 | C5 | 0.21 | 0.21 | 0.21 | ||||||
C4 | 0.13 | 0.16 | 0.24 | C4 | 0.14 | 0.17 | 0.23 | C4 | 0.13 | 0.13 | 0.14 | ||||||
T3 | −0.06 | −0.04 | −0.04 | T3 | −0.09 | −0.08 | −0.08 | T3 | −0.06 | −0.05 | −0.08 | ||||||
C2 | 0.22 | 0.23 | 0.23 | C2 | 0.21 | 0.21 | 0.21 | C2 | 0.23 | 0.26 | 0.30 | ||||||
T1 | −0.03 | −0.03 | −0.03 | T1 | −0.03 | −0.03 | −0.03 | T1 | −0.04 | −0.02 | 0.00 | ||||||
A1 | −0.02 | −0.02 | −0.02 | A1 | −0.02 | −0.02 | −0.02 | A1 | −0.01 | 0.06 | 0.04 | 0.07 | 0.05 | ||||
G2 | −0.15 | −0.15 | −0.14 | G2 | −0.15 | −0.14 | −0.13 | G2oxo | −0.17 | 0.66 | 0.95 | 0.55 | 0.92 | ||||
RcA3 | 0.02 | 0.10 | 0.07 | 0.06 | 0.03 | RcA3 | 0.06 | 0.10 | 0.02 | 0.08 | 0.02 | RcA3 | 0.03 | 0.06 | 0.01 | 0.06 | 0.03 |
G4 | −0.17 | 0.63 | 0.89 | 0.59 | 0.95 | G4oxo | −0.19 | 0.67 | 0.96 | 0.61 | 0.97 | G4 | −0.16 | −0.16 | −0.13 | ||
G5 | −0.12 | −0.07 | 0.04 | −0.09 | 0.02 | G5 | −0.12 | −0.08 | 0.02 | −0.09 | 0.01 | G5 | −0.12 | −0.12 | −0.12 | ||
A6 | 0.03 | 0.04 | 0.04 | A6 | 0.04 | 0.04 | 0.05 | A6 | 0.03 | 0.03 | 0.04 |
ds-oligo | Mode | Discussed Trimers | |||||
---|---|---|---|---|---|---|---|
G2A3G4 | A3G4 G5 | ||||||
G2→A3 | A3→G4 | G2→G4 | A3→G4 | G4→G5 | A3→G5 | ||
N-DNA | Vertical | 0.49 | −0.49 | −0.03 | −0.49 | 0.73 | −0.04 |
Adiabatic | 0.46 | −0.77 | −0.31 | −0.77 | 0.29 | −0.48 | |
G2A3 | A3←G4 | G2←G4 | A3←G4 | G4←G5 | A3←G5 | ||
Vertical | −0.46 | 1.18 | 0.31 | 1.18 | −0.01 | 0.89 | |
Adiabatic | −0.46 | 0.77 | 0.31 | 0.77 | −0.29 | 0.48 | |
3Goxo-N-DNA | G2→A3 | A3→ oxoG4 | G2→ oxoG4 | A3→ oxoG4 | oxoG4→G5 | A3→G5 | |
Vertical | 0.46 | −0.77 | −0.27 | −0.77 | 0.98 | −0.16 | |
Adiabatic | 0.50 | −1.14 | −0.64 | −1.14 | 0.59 | −0.54 | |
G2←A3 | A3←oxoG4 | G2←oxoG4 | A3←oxoG4 | oxoG4←G5 | A3←G5 | ||
Vertical | −0.49 | 1.44 | 0.64 | 1.44 | −0.23 | 0.85 | |
Adiabatic | −0.50 | 1.14 | 0.64 | 1.14 | −0.59 | 0.54 | |
5Goxo-N-DNA | oxoG2→A3 | A3→G4 | oxoG2→G4 | A3→G4 | G4→G5 | A3→G5 | |
Vertical | 1.45 | −0.50 | 0.61 | −0.50 | 0.06 | −0.45 | |
Adiabatic | 1.10 | −0.51 | 0.59 | −0.51 | 0.05 | −0.46 | |
oxoG2←A3 | A3←G4 | oxoG2←G4 | A3←G4 | G4←G5 | A3←G5 | ||
Vertical | −0.69 | 0.50 | −0.18 | 0.50 | −0.05 | 0.46 | |
Adiabatic | −1.10 | 0.51 | −0.59 | 0.51 | −0.05 | 0.46 | |
ScA-DNA | G2→ScA3 | ScA3→G4 | G2→G4 | ScA3→G4 | G4→G5 | ScA3→G5 | |
Vertical | 0.55 | −0.51 | 0.02 | −0.51 | 0.71 | −0.11 | |
Adiabatic | 0.52 | −0.82 | −0.29 | −0.82 | 0.35 | −0.47 | |
G2←ScA3 | ScA3←G4 | G2←G4 | ScA3←G4 | G4←G5 | ScA3←G5 | ||
Vertical | −0.46 | 1.16 | 0.35 | 1.16 | −0.05 | 0.82 | |
Adiabatic | −0.52 | 0.82 | 0.29 | 0.82 | −0.35 | 0.47 | |
3Goxo-ScA-DNA | G2→ScA3 | ScA3→oxoG4 | G2→oxoG4 | cSA3→oxoG4 | oxoG4→G5 | ScA3→G5 | |
Vertical | 0.55 | −0.73 | −0.20 | −0.73 | 1.01 | −0.11 | |
Adiabatic | 0.53 | −1.12 | −0.59 | −1.12 | 0.64 | −0.48 | |
G2←ScA3 | ScA3←oxoG4 | G2←oxoG4 | ScA3←oxoG4 | oxoG4←G5 | ScA3←G5 | ||
Vertical | −0.53 | 1.47 | 0.60 | 1.47 | −0.25 | 0.83 | |
Adiabatic | −0.53 | 1.12 | 0.59 | 1.12 | −0.64 | 0.48 | |
5Goxo-ScA-DNA | oxoG2→ScA3 | ScA3→G4 | oxoG2→G4 | ScA3→G4 | G4→G5 | ScA3→G5 | |
Vertical | 1.48 | −0.61 | 0.67 | −0.61 | 0.05 | −0.59 | |
Adiabatic | 1.28 | −0.64 | 0.64 | −0.64 | 0.03 | −0.61 | |
oxoG2←ScA3 | ScA3←G4 | oxoG2←G4 | ScA3←G4 | G4←G5 | ScA3←G5 | ||
Vertical | −0.87 | 0.52 | −0.23 | 0.52 | −0.04 | 0.48 | |
Adiabatic | −1.28 | 0.64 | −0.64 | 0.64 | −0.03 | 0.61 | |
RcA-DNA | G2→RcA3 | RcA3→G4 | G2→G4 | cA3→G4 | G4→G5 | cA3→G5 | |
Vertical | 0.49 | −0.52 | 0.02 | −0.52 | 0.69 | −0.18 | |
Adiabatic | 0.55 | −0.88 | −0.33 | −0.88 | 0.38 | −0.50 | |
G2←RcA3 | RcA3←G4 | G2←G4 | RcA3←G4 | G4←G5 | RcA3←G5 | ||
Vertical | −0.42 | 1.08 | 0.46 | 1.08 | −0.06 | 0.70 | |
Adiabatic | −0.55 | 0.88 | 0.33 | 0.88 | −0.38 | 0.50 | |
3Goxo-RcA-DNA | G2→RcA3 | cA3→oxoG4 | G2→G4 | RcA3→oxoG4 | oxoG4→G5 | RcA3→G5 | |
Vertical | 0.45 | −0.69 | −0.19 | −0.69 | 0.96 | −0.16 | |
Adiabatic | 0.50 | −1.12 | −0.63 | −1.12 | 0.62 | −0.50 | |
G2←RcA3 | RcA3←oxoG4 | G2←oxoG4 | RcA3←G4 | oxoG4←G5 | RcA3←G5 | ||
Vertical | −0.47 | 1.39 | 0.66 | 1.39 | −0.20 | 0.76 | |
Adiabatic | −0.50 | 1.12 | 0.63 | 1.12 | −0.62 | 0.50 | |
5Goxo-RcA-DNA | oxoG2→RcA3 | RcA3→G4 | oxoG2→G4 | RcA3→G4 | G4→G5 | RcA3→G5 | |
Vertical | 1.36 | −0.53 | 0.67 | −0.53 | 0.08 | −0.61 | |
Adiabatic | 1.19 | −0.69 | −0.50 | −0.69 | 0.11 | −0.58 | |
oxoG2←RcA3 | RcA3←G4 | oxoG2←G4 | RcA3←G4 | G4←G5 | RcA3←G5 | ||
Vertical | −0.80 | 0.47 | −0.11 | 0.47 | 0.01 | 0.36 | |
Adiabatic | −1.19 | 0.69 | −0.50 | 0.69 | −0.11 | 0.58 |
System | ds-DNA Hole Transfer between Stacked Base Pairs | ||||||||||||||||
λ | ΔG | Ea | V12 | KHT | λ | ΔG | Ea | V12 | KHT | λ | ΔG | Ea | V12 | kHT | |||
N-DNA | 3Goxo-N-DNA | 5Goxo-N-DNA | |||||||||||||||
G2←A3 | 0.00 | −0.46 | 18.60 | 0.221 | 0.00 | G2←A3 | 0.01 | −0.50 | 10.09 | 0.220 | 0.00 | oxoG2←A3 | 0.41 | −1.10 | 0.29 | 0.320 | 3.2 × 1010 |
A3→G4 | 0.28 | −0.77 | 0.22 | 0.246 | 3.8 × 1011 | A3→oxoG4 | 0.37 | −1.14 | 0.41 | 0.363 | 5.2 × 108 | A3→G4 | 0.01 | −0.51 | 4.31 | 0.246 | 0.00 |
G4←G5 | 0.44 | −0.29 | 0.01 | 0.051 | 4.0 × 1013 | oxoG4←G5 | 0.38 | −0.59 | 0.03 | 0.113 | 1.1 × 1014 | G4←G5 | 0.02 | −0.05 | 0.01 | 0.048 | 1.7 × 1014 |
ScA-DNA | 3Goxo-ScA-DNA | 5Goxo-ScA-DNA | |||||||||||||||
G2←ScA3 | 0.06 | −0.52 | 0.86 | 0.263 | 14.58 | G2←cSA3 | 0.02 | −0.53 | 4.30 | 0.271 | 0.00 | oxoG2←ScA3 | 0.41 | −1.28 | 0.45 | 0.367 | 7.3 × 107 |
ScA3→G4 | 0.31 | −0.82 | 0.21 | 0.264 | 6.4 × 1011 | ScA3→oxoG4 | 0.39 | −1.12 | 0.35 | 0.378 | 5.5 × 109 | ScA3→G4 | 0.04 | −0.64 | 2.62 | 0.271 | 0.00 |
G4←G5 | 0.36 | −0.35 | 0.00 | 0.035 | 3.4 × 1013 | oxoG4←G5 | 0.37 | −0.64 | 0.05 | 0.157 | 1.0 × 1014 | G4←G5 | 0.01 | −0.03 | 0.01 | 0.038 | 1.5 × 1014 |
RcA-DNA | 3Goxo-RcA-DNA | 5Goxo-RcA-DNA | |||||||||||||||
G2←RcA3 | 0.13 | −0.55 | 0.33 | 0.260 | 9.1 × 109 | G2←RcA3 | 0.03 | −0.50 | 1.91 | 0.268 | 0.00 | oxoG2←RcA3 | 0.39 | −1.19 | 0.41 | 0.352 | 3.28 × 108 |
RcA3→G4 | 0.35 | −0.88 | 0.19 | 0.297 | 1.3 × 1012 | RcA3→oxoG4 | 0.43 | −1.12 | 0.27 | 0.349 | 7.8 × 1010 | RcA3→G4 | 0.16 | −0.69 | 0.43 | 0.291 | 1.75 × 108 |
G4←G5 | 0.31 | −0.38 | 0.00 | 0.086 | 1.9 × 1014 | oxoG4←G5 | 0.34 | −0.62 | 0.06 | 0.131 | 5.3 × 1013 | G4←G5 | 0.12 | −0.11 | 0.00 | 0.085 | 3.5 × 1014 |
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Karwowski, B.T. The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study. Molecules 2020, 25, 3126. https://doi.org/10.3390/molecules25143126
Karwowski BT. The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study. Molecules. 2020; 25(14):3126. https://doi.org/10.3390/molecules25143126
Chicago/Turabian StyleKarwowski, Bolesław T. 2020. "The Influence of Single, Tandem, and Clustered DNA Damage on the Electronic Properties of the Double Helix: A Theoretical Study" Molecules 25, no. 14: 3126. https://doi.org/10.3390/molecules25143126