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Helmerich, Dominic A. ; Budiarta, Made ; Eiring, Patrick ; Sauer, Markus ; Doose, Sören ; Beliu, Gerti

Impact of Docking Strand Design on Spatial Resolution in DNA‐Points Accumulation for Imaging in Nanoscale Topography

Helmerich, Dominic A., Budiarta, Made, Eiring, Patrick, Sauer, Markus, Doose, Sören and Beliu, Gerti (2026) Impact of Docking Strand Design on Spatial Resolution in DNA‐Points Accumulation for Imaging in Nanoscale Topography. ChemPhysChem 27 (5), e202500803.

Date of publication of this fulltext: 12 Mar 2026 07:10
Article
DOI to cite this document: 10.5283/epub.78936


Abstract

DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) has become a widely adopted single-molecule localization microscopy (SMLM) technique owing to its high spatial resolution, versatile labeling strategies, and theoretically unlimited multiplexing capability. Recent developments in repetitive docking strand designs have enabled faster image acquisition by increasing the number ...

DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) has become a widely adopted single-molecule localization microscopy (SMLM) technique owing to its high spatial resolution, versatile labeling strategies, and theoretically unlimited multiplexing capability. Recent developments in repetitive docking strand designs have enabled faster image acquisition by increasing the number of potential binding motifs per target. However, the effect of such architectural modifications on effective spatial resolution remains largely unexplored. Here, we systematically quantify how repetitive docking strands influence localization distributions and effective resolution using the well-defined geometry of the trimeric proliferating cell nuclear antigen (PCNA) as a model system. Whereas classical single-motif docking strands resolve the expected ∼6 nm spacing between PCNA subunits with high precision, repetitive docking motifs produce broadened localization distributions, despite comparable localization precision. Our results suggest that spatial blurring arises from a combination of variable binding site geometry, rotational flexibility of elongated multivalent DNA docking sequences, as well as the dynamic behavior of imager strands. This study provides a quantitative framework for understanding how docking strand architecture determines resolution limits in DNA-PAINT and underscores the need to balance multiplexing and imaging speed with structural fidelity. Our results thus offer guidance for the rational design of docking strands for high-precision DNA-PAINT imaging of protein complexes.



Involved Institutions


Details

Item typeArticle
Journal or Publication TitleChemPhysChem
Publisher:Wiley
Volume:27
Number of Issue or Book Chapter:5
Page Range:e202500803
Date3 March 2026
InstitutionsRegensburg Center for UltrafastNanoscopy (RUN)
Identification Number
ValueType
10.1002/cphc.202500803DOI
Related URLs
URLURL Type
https://doi.org/10.1002/cphc.70351Supplementary Material
KeywordsDNA points accumulation for imaging in nanoscale topography | docking strand design | localization precision | nanoscopic resolution | super-resolution microscopy
Dewey Decimal Classification500 Science > 500 Natural sciences & mathematics
500 Science > 540 Chemistry & allied sciences
500 Science > 570 Life sciences
StatusPublished
RefereedYes, this version has been refereed
Created at the University of RegensburgPartially
URN of the UB Regensburgurn:nbn:de:bvb:355-epub-789367
Item ID78936

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