Bubble Relaxation Dynamics in Homopolymer DNA Sequences
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to st...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/28/3/1041 |
| _version_ | 1797623757906378752 |
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| author | Malcolm Hillebrand George Kalosakas Alan R. Bishop Charalampos Skokos |
| author_facet | Malcolm Hillebrand George Kalosakas Alan R. Bishop Charalampos Skokos |
| author_sort | Malcolm Hillebrand |
| collection | DOAJ |
| description | Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule. |
| first_indexed | 2024-03-11T09:33:18Z |
| format | Article |
| id | doaj.art-55b8db5dbdf54c4aa93d451d82f2affe |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T09:33:18Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-55b8db5dbdf54c4aa93d451d82f2affe2023-11-16T17:26:49ZengMDPI AGMolecules1420-30492023-01-01283104110.3390/molecules28031041Bubble Relaxation Dynamics in Homopolymer DNA SequencesMalcolm Hillebrand0George Kalosakas1Alan R. Bishop2Charalampos Skokos3Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South AfricaDepartment of Materials Science, University of Patras, GR-26504 Rio, GreeceLos Alamos National Laboratory, Los Alamos, NM 87545, USANonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South AfricaUnderstanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard–Bishop–Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine–thymine (AT) and guanine–cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule’s dynamics, for times between 0.5–500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.https://www.mdpi.com/1420-3049/28/3/1041DNAbase pair stretchingbubblesrelaxationmolecular dynamics |
| spellingShingle | Malcolm Hillebrand George Kalosakas Alan R. Bishop Charalampos Skokos Bubble Relaxation Dynamics in Homopolymer DNA Sequences Molecules DNA base pair stretching bubbles relaxation molecular dynamics |
| title | Bubble Relaxation Dynamics in Homopolymer DNA Sequences |
| title_full | Bubble Relaxation Dynamics in Homopolymer DNA Sequences |
| title_fullStr | Bubble Relaxation Dynamics in Homopolymer DNA Sequences |
| title_full_unstemmed | Bubble Relaxation Dynamics in Homopolymer DNA Sequences |
| title_short | Bubble Relaxation Dynamics in Homopolymer DNA Sequences |
| title_sort | bubble relaxation dynamics in homopolymer dna sequences |
| topic | DNA base pair stretching bubbles relaxation molecular dynamics |
| url | https://www.mdpi.com/1420-3049/28/3/1041 |
| work_keys_str_mv | AT malcolmhillebrand bubblerelaxationdynamicsinhomopolymerdnasequences AT georgekalosakas bubblerelaxationdynamicsinhomopolymerdnasequences AT alanrbishop bubblerelaxationdynamicsinhomopolymerdnasequences AT charalamposskokos bubblerelaxationdynamicsinhomopolymerdnasequences |