The Effects of Flexibility on dsDNA–dsDNA Interactions
A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-05-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/5/699 |
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| author | Chuanying Chen B. Montgomery Pettitt |
| author_facet | Chuanying Chen B. Montgomery Pettitt |
| author_sort | Chuanying Chen |
| collection | DOAJ |
| description | A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is elucidated by studying the energetic properties of Na<sup>+</sup> ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na<sup>+</sup> ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches. |
| first_indexed | 2024-03-10T03:34:15Z |
| format | Article |
| id | doaj.art-e5873088ef504259a0a759e5c1b850d4 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:34:15Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-e5873088ef504259a0a759e5c1b850d42023-11-23T11:50:09ZengMDPI AGLife2075-17292022-05-0112569910.3390/life12050699The Effects of Flexibility on dsDNA–dsDNA InteractionsChuanying Chen0B. Montgomery Pettitt1Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USADepartment of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USAA detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is elucidated by studying the energetic properties of Na<sup>+</sup> ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na<sup>+</sup> ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches.https://www.mdpi.com/2075-1729/12/5/699molecular dynamics simulation (MD)potential of mean force (PMF)dsDNA–dsDNA interactionsflexibility |
| spellingShingle | Chuanying Chen B. Montgomery Pettitt The Effects of Flexibility on dsDNA–dsDNA Interactions Life molecular dynamics simulation (MD) potential of mean force (PMF) dsDNA–dsDNA interactions flexibility |
| title | The Effects of Flexibility on dsDNA–dsDNA Interactions |
| title_full | The Effects of Flexibility on dsDNA–dsDNA Interactions |
| title_fullStr | The Effects of Flexibility on dsDNA–dsDNA Interactions |
| title_full_unstemmed | The Effects of Flexibility on dsDNA–dsDNA Interactions |
| title_short | The Effects of Flexibility on dsDNA–dsDNA Interactions |
| title_sort | effects of flexibility on dsdna dsdna interactions |
| topic | molecular dynamics simulation (MD) potential of mean force (PMF) dsDNA–dsDNA interactions flexibility |
| url | https://www.mdpi.com/2075-1729/12/5/699 |
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