The base flipping of A-DNA—a molecular dynamic simulation study
Due to different solvent conditions, double helix DNA exists in various conformations, such as B-DNA, A-DNA, C-DNA, and Z-DNA. Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions...
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| Veröffentlicht in: | Structural chemistry 2024, Vol.35 (5), p.1649-1656 |
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| creator | Wang, Shudong Zheng, Xuan Wu, Jingjie |
| description | Due to different solvent conditions, double helix DNA exists in various conformations, such as B-DNA, A-DNA, C-DNA, and Z-DNA. Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions. In this study, the well-tempered meta-dynamics (WTM-eABF) were used to explore the free energy barriers for base flipping of the four natural bases, adenine, guanine, cytosine, and thymine, in both A-form and B-form DNA duplex. The results show that the free energy barriers for base flipping were lower in A-DNA than that in B-DNA for all of the four natural bases. We analyzed the factors that may affect base flipping, such as π-π stacking, SASA, H-bonding, and conformational changes, and concluded that conformational changes and π-π stacking are the most important factors affecting base flipping. |
| doi_str_mv | 10.1007/s11224-024-02299-0 |
| format | Article |
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Studies have found that A-DNA is present in complexes with proteins and has an important biological role in the context of cellular defense mechanisms under harsh conditions. In this study, the well-tempered meta-dynamics (WTM-eABF) were used to explore the free energy barriers for base flipping of the four natural bases, adenine, guanine, cytosine, and thymine, in both A-form and B-form DNA duplex. The results show that the free energy barriers for base flipping were lower in A-DNA than that in B-DNA for all of the four natural bases. 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| subjects | Adenine Chemistry Chemistry and Materials Science Computer Applications in Chemistry Free energy Molecular dynamics Physical Chemistry Theoretical and Computational Chemistry Thymine |
| title | The base flipping of A-DNA—a molecular dynamic simulation study |
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