Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope.

Autor: Szalai AM; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany. alan.szalai@cup.uni-muenchen.de.; Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina. alan.szalai@cup.uni-muenchen.de., Ferrari G; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Richter L; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Hartmann J; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Kesici MZ; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Ji B; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Coshic K; Department of Physics, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Dagleish MRJ; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Jaeger A; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Aksimentiev A; Department of Physics, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Tessmer I; Rudolf Virchow Center, University of Würzburg, Würzburg, Germany., Kamińska I; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany.; Institute of Physical Chemistry of the Polish Academy of Sciences, Warsaw, Poland., Vera AM; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany., Tinnefeld P; Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany. philip.tinnefeld@cup.uni-muenchen.de.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2024 Nov 08. Date of Electronic Publication: 2024 Nov 08.
DOI: 10.1038/s41592-024-02498-x
Abstrakt: The intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription and repair. Dynamic nanoscale observations of DNA structural features are necessary for understanding these interactions. Here we introduce graphene energy transfer with vertical nucleic acids (GETvNA), a method to investigate DNA-protein interactions that exploits the vertical orientation adopted by double-stranded DNA on graphene. This approach enables the dynamic study of DNA conformational changes via energy transfer from a probe dye to graphene, achieving spatial resolution down to the Ångström scale at subsecond temporal resolution. We measured DNA bending induced by adenine tracts, bulges, abasic sites and the binding of endonuclease IV. In addition, we observed the translocation of the O 6 -alkylguanine DNA alkyltransferase on DNA, reaching single base-pair resolution and detecting preferential binding to adenine tracts. This method promises widespread use for dynamical studies of nucleic acids and nucleic acid-protein interactions with resolution so far reserved for traditional structural biology techniques.
Competing Interests: Competing interests: P.T., A.M.S., L.R., G.F. and I.K. are inventors on a US provisional patent application #18/672,616 related to GETvNA. The other authors declare no competing interests.
(© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
Externí odkaz: