Issue 7, 2023

A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy

Abstract

The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA–protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP–DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA–protein interactions.

Graphical abstract: A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy

Supplementary files

Article information

Article type
Paper
Submitted
28 sep 2022
Accepted
16 jan 2023
First published
17 jan 2023
This article is Open Access
Creative Commons BY license

Nanoscale, 2023,15, 3212-3218

A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy

A. K. Natarajan, J. Ryssy and A. Kuzyk, Nanoscale, 2023, 15, 3212 DOI: 10.1039/D2NR05366G

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