Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Minimized Structures of DNA Duplex Containing an X:G Base Pair
2.2. The Destabilization Energies of the Base Pairs on 5'- and 3'-Side of X
2.2.1. The Destabilization Energies of the Base Pairs on 5'- Side of X
A1T1 | G3C3 | A1T1 + G3C3 | |||||||
---|---|---|---|---|---|---|---|---|---|
X a | ΔE1DFT | ΔE1SCRF | ΔE3DFT | ΔE3SCRF | ΔE1 + 3DFT | ΔE1 + 3SCRF | |||
Oz | 1.3 | 1.1 | −0.1 | 0.6 | 1.1 | 1.0 | |||
S-Ia | 1.4 | 1.3 | 2.6 | 1.3 | 4.1 | 4.5 | |||
R-Ia | 0.5 | 0.6 | 4.0 | 3.9 | 4.8 | 4.6 | |||
S-Sp | 2.1 | 2.1 | 2.7 | 2.8 | 4.8 | 5.3 | |||
R-Sp | 12.6 | 12.4 | 5.3 | 4.5 | 18.3 | 18.3 |
2.2.2. The Destabilization Energies of the Base Pairs on the 3'-Side of X
2.2.3. The Destabilization Energy of Each Model Duplex was Calculated by Including both Adjacent Base Pairs and Excluding the Central “G2X2” Base Pair
2.3. The Degree of Distortion from DNA Duplex Containing a G:C Base Pair
2.3.1. The Degree of Distortion at the 5'-Side of X
X a | θ (G2–A1) | θ (G2–T1) | θ (A1–T1) | δ1 |
---|---|---|---|---|
C | 25.2° | 12.5° | 13.3° | 51.0° |
Oz | 19.4° | 18.2° | 18.0° | 55.6° |
S-Ia | 38.3° | 28.2° | 11.3° | 77.8° |
R-Ia | 3.3° | 4.0° | 4.0° | 11.3° |
S-Sp | 56.1° | 29.9° | 26.4° | 112.4° |
R-Sp | 10.9° | 32.4° | 43.2° | 86.5° |
2.3.2. The Degree of Distortion at the 3'-Side of X
X a | θ (G2–G3) | θ (G2–C3) | θ (G3–C3) | δ3 |
---|---|---|---|---|
C | 9.5° | 8.0° | 17.2° | 34.6° |
Oz | 11.1° | 3.1° | 11.9° | 26.1° |
S-Ia | 5.4° | 13.9° | 19.2° | 38.5° |
R-Ia | 17.9° | 42.6° | 49.2° | 109.7° |
S-Sp | 5.5° | 25.7° | 23.2° | 54.4° |
R-Sp | 22.9° | 36.2° | 43.3° | 102.5° |
2.3.3. The Total Degree of Distortion at the 5'-Side and 3'-Side of X
X a | δ1 + δ3 |
---|---|
C | 85.6° |
Oz | 81.7° |
S-Ia | 116.3° |
R-Ia | 121.1° |
S-Sp | 166.8° |
R-Sp | 189.0° |
2.3.4. The Difference Between the Degree of Distortion for Oxidatively Damaged Guanine and that for C
3. Experimental
3.1. Molecular Modeling
3.2. ab Initio Calculations
–E(“A1T1” of G:X complex (X = Oz, S-Ia, R-Ia, S-Sp or R-Sp))
–E(“G3C3” of G:X complex (X = Oz, S-Ia, R-Ia, S-Sp or R-Sp))
–E(“A1T1+G3C3” of G:X complex (X = Oz, S-Ia, R-Ia, S-Sp or R-Sp))
3.3. Calculating the Degree of Distortion
= (xN1– xC5, yN1 – yC5, zN1– zC5) × (xN3– xC5, yN3– yC5, zN3– zC5)
= ((yN1– yC5)•(zN3– zC5)−(zN1– zC5)•(yN3– yC5), (zN1– zC5)•(xN3– xC5) – (xN1–xC5)•(zN3– zC5),
(xN1– xC5)•(yN3– yC5) − (yN1– yC5)•(xN3– xC5))
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Suzuki, M.; Kino, K.; Morikawa, M.; Kobayashi, T.; Miyazawa, H. Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine. Molecules 2014, 19, 11030-11044. https://doi.org/10.3390/molecules190811030
Suzuki M, Kino K, Morikawa M, Kobayashi T, Miyazawa H. Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine. Molecules. 2014; 19(8):11030-11044. https://doi.org/10.3390/molecules190811030
Chicago/Turabian StyleSuzuki, Masayo, Katsuhito Kino, Masayuki Morikawa, Takanobu Kobayashi, and Hiroshi Miyazawa. 2014. "Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine" Molecules 19, no. 8: 11030-11044. https://doi.org/10.3390/molecules190811030