DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging

Pauline J. Kolbeck; Mihir Dass; Irina V. Martynenko; Relinde J.A. Van Dijk-Moes; Kelly J.H. Brouwer; Alfons Van Blaaderen; Willem Vanderlinden; Tim Liedl; Jan Lipfert

doi:10.1021/acs.nanolett.2c04299

DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging

Pauline J. Kolbeck, Mihir Dass, Irina V. Martynenko^*, Relinde J.A. Van Dijk-Moes, Kelly J.H. Brouwer, Alfons Van Blaaderen, Willem Vanderlinden, Tim Liedl, Jan Lipfert^*

^*Corresponding author for this work

Ludwig Maximilian University of Munich

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

Original language	English
Pages (from-to)	1236-1243
Number of pages	8
Journal	Nano Letters
Volume	23
Issue number	4
DOIs	https://doi.org/10.1021/acs.nanolett.2c04299
Publication status	Published - 22 Feb 2023

Bibliographical note

Funding Information:
This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through SFB 863, Project 111166240 A11, by Utrecht University, by the Federal Ministry of Education and Research (BMBF) and the Free State of Bavaria under the Excellence Strategy of the Federal Government and the Länder through the ONE MUNICH Project Munich Multiscale Biofabrication, and by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant No. 765703.

Publisher Copyright:
© 2023 The Authors. Published by American Chemical Society.

Funding

This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through SFB 863, Project 111166240 A11, by Utrecht University, by the Federal Ministry of Education and Research (BMBF) and the Free State of Bavaria under the Excellence Strategy of the Federal Government and the Länder through the ONE MUNICH Project Munich Multiscale Biofabrication, and by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant No. 765703.

Keywords

AFM
atomic force microscopy
DNA origami
image correction
tip reconstruction

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acs.nanolett.2c04299Final published version, 6.07 MBLicence: CC BY-NC-ND

Cite this

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title = "DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging",

abstract = "Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.",

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author = "Kolbeck, {Pauline J.} and Mihir Dass and Martynenko, {Irina V.} and {Van Dijk-Moes}, {Relinde J.A.} and Brouwer, {Kelly J.H.} and {Van Blaaderen}, Alfons and Willem Vanderlinden and Tim Liedl and Jan Lipfert",

note = "Funding Information: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through SFB 863, Project 111166240 A11, by Utrecht University, by the Federal Ministry of Education and Research (BMBF) and the Free State of Bavaria under the Excellence Strategy of the Federal Government and the L{\"a}nder through the ONE MUNICH Project Munich Multiscale Biofabrication, and by the European Union{\textquoteright}s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant No. 765703. Publisher Copyright: {\textcopyright} 2023 The Authors. Published by American Chemical Society.",

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AU - Van Blaaderen, Alfons

AU - Vanderlinden, Willem

AU - Liedl, Tim

AU - Lipfert, Jan

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N2 - Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

AB - Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

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DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging

Abstract

Bibliographical note

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Keywords

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