Spectroscopic approaches for studies of site-specific DNA base and backbone "breathing" using exciton-coupled dimer-labeled DNA
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arXiv
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| Autores principales: | , , , , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866909153844264960 |
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| author | Marcus, Andrew H. Matsika, Spiridoula Heussman, Dylan Sorour, Mohammed I. Maurer, Jack Albrecht, Claire S. Enkhbaatar, Lulu Herbert, Patrick Kistler, Kurt A. von Hippel, Peter H. |
| author_facet | Marcus, Andrew H. Matsika, Spiridoula Heussman, Dylan Sorour, Mohammed I. Maurer, Jack Albrecht, Claire S. Enkhbaatar, Lulu Herbert, Patrick Kistler, Kurt A. von Hippel, Peter H. |
| contents | DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as "sensors" of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_16251 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Spectroscopic approaches for studies of site-specific DNA base and backbone "breathing" using exciton-coupled dimer-labeled DNA Marcus, Andrew H. Matsika, Spiridoula Heussman, Dylan Sorour, Mohammed I. Maurer, Jack Albrecht, Claire S. Enkhbaatar, Lulu Herbert, Patrick Kistler, Kurt A. von Hippel, Peter H. Biological Physics Biomolecules DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as "sensors" of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites. |
| title | Spectroscopic approaches for studies of site-specific DNA base and backbone "breathing" using exciton-coupled dimer-labeled DNA |
| topic | Biological Physics Biomolecules |
| url | https://arxiv.org/abs/2403.16251 |