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- W2020692008 abstract "A key question in the function of DNA-processing enzymes is their mechanism for rapid location and binding of target sites in DNA. DNA polymerase I (Pol) is involved in high-fidelity DNA replication and repair, and must recognize gapped and flapped DNA substrates. Due to their transient and dynamic nature, the structures of these complexes and the recognition mechanism by which they are formed are largely unknown.Combining single-molecule Forster Resonance Energy Transfer (smFRET) with dye-position modelling, we can obtain absolute distance measurements with angstrom precision. We have used 120 such distances in a rigid-body docking approach to determine the structure of the single-nucleotide-gapped DNA-Pol binary complex, and that of the gapped-DNA substrate alone.In the complex structure, the DNA substrate exhibits a 120-degree bend. The upstream DNA is channeled into the Pol active site, and its position is in excellent agreement (RMSD < 3 A) with the position of short DNA fragments seen in crystal structures of Pol. The downstream DNA is partially melted and held in close proximity to F771, a residue important for strand displacement.The structure of the gapped-DNA substrate alone adopts a 20-degree bend and a twist. Our coarse-grained simulations show short excursions of the substrate to partially kinked conformations not accessible to duplex DNA. Together, these data are consistent with a two-step model whereby Pol recognizes and binds a partially kinked conformation of gapped DNA, which then further rearranges to the fully bent state seen in the complex structure.Finally, using our method of internalization by electroporation, we have observed single-molecule FRET signals corresponding to unbound and Pol-bound gapped DNA in live bacteria, confirming the physiological relevance of the proposed substrate and complex structures and the recognition mechanism." @default.
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- W2020692008 date "2015-01-01" @default.
- W2020692008 modified "2023-09-28" @default.
- W2020692008 title "Single-Molecule FRET for Dynamic Structural Biology: DNA Polymerase i Structure and Mechanism with Angstrom Precision" @default.
- W2020692008 doi "https://doi.org/10.1016/j.bpj.2014.11.103" @default.
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