Probing TDP-43 condensation using an in silico designed aptamer.

Abstract

Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.

• Authors: Elsa Zacco, Owen Kantelberg, Edoardo Milanetti, Alexandros Armaos, Francesco Paolo Panei, Jenna Gregory, Kiani Jeacock, David J Clarke, Siddharthan Chandran, Giancarlo Ruocco, Stefano Gustincich, Mathew H Horrocks, Annalisa Pastore, Gian Gaetano Tartaglia
• Journal: Nature communications (Nat Commun) Vol. 13 Issue 1 Pg. 3306 (06 23 2022) ISSN: 2041-1723 [Electronic] England
• PMID: 35739092 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © 2022. The Author(s).

Chemical References

• DNA-Binding Proteins
• Oligonucleotides

Topics

• Amyotrophic Lateral Sclerosis (metabolism)
• DNA-Binding Proteins (metabolism)
• Humans
• Inclusion Bodies (metabolism)
• Oligonucleotides
• Phase Transition