DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins
Abstract Single-stranded DNA-binding proteins (SSBs) protect transiently exposed ssDNA, yet how DNA polymerase (DNAp) displaces them during replication remains unclear. Using single-molecule force spectroscopy, dual-color imaging, and molecular dynamics simulations on bacteriophage T7 DNAp and SSB,...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62531-1 |
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| author | Longfu Xu Shikai Jin Mia Urem Seung-Joo Lee Meindert H. Lamers Xun Chen Peter G. Wolynes Gijs J. L. Wuite |
| author_facet | Longfu Xu Shikai Jin Mia Urem Seung-Joo Lee Meindert H. Lamers Xun Chen Peter G. Wolynes Gijs J. L. Wuite |
| author_sort | Longfu Xu |
| collection | DOAJ |
| description | Abstract Single-stranded DNA-binding proteins (SSBs) protect transiently exposed ssDNA, yet how DNA polymerase (DNAp) displaces them during replication remains unclear. Using single-molecule force spectroscopy, dual-color imaging, and molecular dynamics simulations on bacteriophage T7 DNAp and SSB, we investigated molecular mechanisms underlying SSB displacement. T7 SSB modulates replication in a force-dependent manner: enhancing it at low tension by preventing secondary structures while impeding it at high tension. Dual-color imaging shows SSBs remain stationary as DNAp advances, supporting a sequential displacement model. Molecular dynamics suggests that DNAp actively lowers the SSB dissociation energy barrier through interactions mediated by the SSB C-terminal tail. FRET confirms close protein proximity during encounters. Optimal replication requires SSB saturation of ssDNA, establishing a delicate balance between protection and efficiency. This spatiotemporal coordination between DNAp and SSB is critical for resolving molecular collisions and may represent a general mechanism for resolving molecular collisions, ensuring both processivity and genomic integrity. |
| format | Article |
| id | doaj-art-17bce899d7154fa8b9d98b7a0f1cd840 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-17bce899d7154fa8b9d98b7a0f1cd8402025-08-20T03:43:22ZengNature PortfolioNature Communications2041-17232025-08-0116111610.1038/s41467-025-62531-1DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteinsLongfu Xu0Shikai Jin1Mia Urem2Seung-Joo Lee3Meindert H. Lamers4Xun Chen5Peter G. Wolynes6Gijs J. L. Wuite7Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081Center for Theoretical Biological Physics, Rice UniversityLeiden University Center of Infectious Diseases (LUCID), Leiden University Medical CenterDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolDepartment of Cell and Chemical Biology, Leiden University Medical Center (LUMC)Department of Medicinal Chemistry, National Vaccine Innovation Platform, Nanjing Medical UniversityCenter for Theoretical Biological Physics, Rice UniversityDepartment of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081Abstract Single-stranded DNA-binding proteins (SSBs) protect transiently exposed ssDNA, yet how DNA polymerase (DNAp) displaces them during replication remains unclear. Using single-molecule force spectroscopy, dual-color imaging, and molecular dynamics simulations on bacteriophage T7 DNAp and SSB, we investigated molecular mechanisms underlying SSB displacement. T7 SSB modulates replication in a force-dependent manner: enhancing it at low tension by preventing secondary structures while impeding it at high tension. Dual-color imaging shows SSBs remain stationary as DNAp advances, supporting a sequential displacement model. Molecular dynamics suggests that DNAp actively lowers the SSB dissociation energy barrier through interactions mediated by the SSB C-terminal tail. FRET confirms close protein proximity during encounters. Optimal replication requires SSB saturation of ssDNA, establishing a delicate balance between protection and efficiency. This spatiotemporal coordination between DNAp and SSB is critical for resolving molecular collisions and may represent a general mechanism for resolving molecular collisions, ensuring both processivity and genomic integrity.https://doi.org/10.1038/s41467-025-62531-1 |
| spellingShingle | Longfu Xu Shikai Jin Mia Urem Seung-Joo Lee Meindert H. Lamers Xun Chen Peter G. Wolynes Gijs J. L. Wuite DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins Nature Communications |
| title | DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins |
| title_full | DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins |
| title_fullStr | DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins |
| title_full_unstemmed | DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins |
| title_short | DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins |
| title_sort | dna polymerase actively and sequentially displaces single stranded dna binding proteins |
| url | https://doi.org/10.1038/s41467-025-62531-1 |
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