Single-molecule Dynamic Structural Biology with Vertically Arranged DNA on a Fluorescence Microscope

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2024 Nov 8

PMID 39516563

Authors

Alan M Szalai

Giovanni Ferrari

Lars Richter

Jakob Hartmann

Merve-Zeynep Kesici

Bosong Ji

Kush Coshic

Martin R J Dagleish

Annika Jaeger

Aleksei Aksimentiev

Ingrid Tessmer

Izabela Kaminska

Andres M Vera

Philip Tinnefeld

Affiliations

Soon will be listed here.

Abstract

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-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.

Citing Articles

Single-molecule DNA dynamics with graphene energy transfer.

Kosuri P Nat Methods. 2024; 22(1):16-17.

PMID: 39658594 DOI: 10.1038/s41592-024-02560-8.

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