Sequential super-resolution imaging using DNA strand displacement

PloS One
Sandeep PallikkuthKeith A Lidke

Abstract

Sequential labeling and imaging in fluorescence microscopy allows the imaging of multiple structures in the same cell using a single fluorophore species. In super-resolution applications, the optimal dye suited to the method can be chosen, the optical setup can be simpler and there are no chromatic aberrations between images of different structures. We describe a method based on DNA strand displacement that can be used to quickly and easily perform the labeling and removal of the fluorophores during each sequence. Site-specific tags are conjugated with unique and orthogonal single stranded DNA. Labeling for a particular structure is achieved by hybridization of antibody-bound DNA with a complimentary dye-labeled strand. After imaging, the dye is removed using toehold-mediated strand displacement, in which an invader strand competes off the dye-labeled strand than can be subsequently washed away. Labeling and removal of each DNA-species requires only a few minutes. We demonstrate the concept using sequential dSTORM super-resolution for multiplex imaging of subcellular structures.

References

Aug 19, 2000·Nature·B YurkeJ L Neumann
Aug 10, 2006·Nature Methods·Michael J RustXiaowei Zhuang
Jul 23, 2008·Angewandte Chemie·Mike HeilemannMarkus Sauer
Apr 7, 2010·Nature Methods·Carlas S SmithKeith A Lidke
Jul 21, 2010·Journal of Computational Chemistry·Joseph N ZadehNiles A Pierce
Jan 25, 2011·Nature Chemistry·David Yu Zhang, Georg Seelig
May 12, 2011·Biomedical Optics Express·Fang HuangKeith A Lidke
Oct 1, 2013·Nature Nanotechnology·Yuan-Jyue ChenGeorg Seelig
Jul 8, 2014·PloS One·Johnny TamMelike Lakadamyali
Oct 21, 2014·ACS Synthetic Biology·Brian R Wolfe, Niles A Pierce
Apr 11, 2015·PloS One·Christopher C ValleyKeith A Lidke
Dec 23, 2015·Nature Nanotechnology·Benjamin GrovesGeorg Seelig
Nov 5, 2016·Molecular Biology of the Cell·Jason YiLawrence E Samelson
Feb 14, 2017·Journal of the American Chemical Society·Brian R WolfeNiles A Pierce
Mar 4, 2017·Angewandte Chemie·Florian SchuederRalf Jungmann
Apr 26, 2018·Biophysical Journal·Danying LinJoshua C Vaughan

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Citations

Jan 24, 2020·Nature Protocols·Andrés M Cardozo GizziMarcelo Nollmann
Dec 10, 2019·Developmental Cell·Jingyue JiaVojo Deretic
Jul 15, 2021·Nature Cell Biology·Aurore Claude-TaupinVojo Deretic

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Methods Mentioned

BETA
fluorescence microscopy
fluorescence imaging
chemical treatments
Fluorescence

Software Mentioned

MATLAB
NUPACK
DipImage
STORM
dSTORM

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