Probing TDP-43 condensation using an in silico designed aptamer

Zacco, Elsa; Kantelberg, Owen; Milanetti, Edoardo; Armaos, Alexandros, 1989-; Panei, Francesco Paolo; Gregory, Jenna; Jeacock, Kiani; Clarke, David J.; Chandran, Siddharthan; Ruocco, Giancarlo; Gustincich, Stefano; Horrocks, Mathew H.; Pastore, Annalisa; Tartaglia, Gian Gaetano

doi:http://dx.doi.org/10.1038/s41467-022-30944-x

Probing TDP-43 condensation using an in silico designed aptamer

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Zacco E, Kantelberg O, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer. Nat Commun. 2022 Jun 23;13(1):3306. DOI: 10.1038/s41467-022-30944-x

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.