University of Oulu

Ishizuka, Y., Mergiya, T.F., Baldinotti, R. et al. Development and Validation of Arc Nanobodies: New Tools for Probing Arc Dynamics and Function. Neurochem Res 47, 2656–2666 (2022).

Development and validation of Arc nanobodies : new tools for probing Arc dynamics and function

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Author: Ishizuka, Yuta1,2; Mergiya, Tadiwos F.1,3; Baldinotti, Rodolfo1,3;
Organizations: 1Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
2Department of Pathophysiology and Metabolism, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan
3Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway
4Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
5Biocenter Oulu, University of Oulu, Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.1 MB)
Persistent link:
Language: English
Published: Springer Nature, 2022
Publish Date: 2022-10-28


Activity-regulated cytoskeleton-associated (Arc) protein plays key roles in long-term synaptic plasticity, memory, and cognitive flexibility. However, an integral understanding of Arc mechanisms is lacking. Arc is proposed to function as an interaction hub in neuronal dendrites and the nucleus, yet Arc can also form retrovirus-like capsids with proposed roles in intercellular communication. Here, we sought to develop anti-Arc nanobodies (ArcNbs) as new tools for probing Arc dynamics and function. Six ArcNbs representing different clonal lines were selected from immunized alpaca. Immunoblotting with recombinant ArcNbs fused to a small ALFA-epitope tag demonstrated binding to recombinant Arc as well as endogenous Arc from rat cortical tissue. ALFA-tagged ArcNb also provided efficient immunoprecipitation of stimulus-induced Arc after carbachol-treatment of SH-SY5Y neuroblastoma cells and induction of long-term potentiation in the rat dentate gyrus in vivo. Epitope mapping showed that all Nbs recognize the Arc C-terminal region containing the retroviral Gag capsid homology domain, comprised of tandem N- and C-lobes. ArcNbs E5 and H11 selectively bound the N-lobe, which harbors a peptide ligand binding pocket specific to mammals. Four additional ArcNbs bound the region containing the C-lobe and C-terminal tail. For use as genetically encoded fluorescent intrabodies, we show that ArcNbs fused to mScarlet-I are uniformly expressed, without aggregation, in the cytoplasm and nucleus of HEK293FT cells. Finally, mScarlet-I-ArcNb H11 expressed as intrabody selectively bound the N-lobe and enabled co-immunoprecipitation of full-length intracellular Arc. ArcNbs are versatile tools for live-cell labeling and purification of Arc, and interrogation of Arc capsid domain specific functions.

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Series: Neurochemical research
ISSN: 0364-3190
ISSN-E: 1573-6903
ISSN-L: 0364-3190
Volume: 47
Issue: 9
Pages: 2656 - 2666
DOI: 10.1007/s11064-022-03573-5
Type of Publication: A1 Journal article – refereed
Field of Science: 3111 Biomedicine
Funding: This work was supported by a Research Council of Norway Toppforsk grant (249951) to CRB. Open access funding provided by University of Bergen (incl Haukeland University Hospital).
Dataset Reference: The online version contains supplementary material available at
Copyright information: © The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit