Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DN...
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| Veröffentlicht in: | The journal of physical chemistry. B 2015-09, Vol.119 (35), p.11459-11465 |
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| container_title | The journal of physical chemistry. B |
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| creator | Markegard, Cade B Mazaheripour, Amir Jocson, Jonah-Micah Burke, Anthony M Dickson, Mary N Gorodetsky, Alon A Nguyen, Hung D |
| description | Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks. |
| doi_str_mv | 10.1021/acs.jpcb.5b03874 |
| format | Article |
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| source | MEDLINE; American Chemical Society Journals |
| subjects | Assembly Constants Deoxyribonucleic acid Dimerization DNA - chemistry Dynamical systems Dynamics Imides - chemistry Kinetics Molecular dynamics Molecular Dynamics Simulation Molecular structure Perylene - analogs & derivatives Perylene - chemistry Simulation Spectrum Analysis Temperature |
| title | Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates |
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