Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations
Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior an...
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| Format: | Article |
| Language: | English |
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MDPI AG
2025-04-01
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| Series: | Biosensors |
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| Online Access: | https://www.mdpi.com/2079-6374/15/5/272 |
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| author | Kaitlin Bullard Deborah Okyere Shelbi J. Foster Asmaa A. Sadoon Jiali Li Jingyi Chen Yong Wang |
| author_facet | Kaitlin Bullard Deborah Okyere Shelbi J. Foster Asmaa A. Sadoon Jiali Li Jingyi Chen Yong Wang |
| author_sort | Kaitlin Bullard |
| collection | DOAJ |
| description | Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg<sup>2+</sup> ions at different concentrations. The simulations show that Mg<sup>2+</sup> ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules. |
| format | Article |
| id | doaj-art-da0dce3981ec44a9a7412db3d83a690d |
| institution | DOAJ |
| issn | 2079-6374 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biosensors |
| spelling | doaj-art-da0dce3981ec44a9a7412db3d83a690d2025-08-20T03:14:32ZengMDPI AGBiosensors2079-63742025-04-0115527210.3390/bios15050272Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics SimulationsKaitlin Bullard0Deborah Okyere1Shelbi J. Foster2Asmaa A. Sadoon3Jiali Li4Jingyi Chen5Yong Wang6Department of Physics, University of Arkansas, Fayetteville, AR 72701, USAMaterials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USADepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USADepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USADepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USAMaterials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USADepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USABent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg<sup>2+</sup> ions at different concentrations. The simulations show that Mg<sup>2+</sup> ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules.https://www.mdpi.com/2079-6374/15/5/272DNA bowsmelting curveFRETNAMDVMD |
| spellingShingle | Kaitlin Bullard Deborah Okyere Shelbi J. Foster Asmaa A. Sadoon Jiali Li Jingyi Chen Yong Wang Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations Biosensors DNA bows melting curve FRET NAMD VMD |
| title | Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations |
| title_full | Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations |
| title_fullStr | Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations |
| title_full_unstemmed | Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations |
| title_short | Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations |
| title_sort | understanding the mechanism of bent dna amplifying sensors using all atom molecular dynamics simulations |
| topic | DNA bows melting curve FRET NAMD VMD |
| url | https://www.mdpi.com/2079-6374/15/5/272 |
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