Aptamer binding footprints discriminate α-synuclein fibrillar polymorphs from different synucleinopathies
Alix Bouvier-Müller1,2,3, Deborah Fourmy1,2,3, Alexis Fenyi1,2,3
1CEA, DRF, Institut of biology JACOB, Molecular Imaging Research Center (MIRCen), Fontenay aux roses 92335, France.
Nucleic Acids Research
|June 25, 2024
Summary
Researchers developed AptaFOOT-Seq, a novel method using RNA aptamers to detect distinct alpha-synuclein (α-syn) protein structures. This technique can differentiate between polymorphs found in synucleinopathies like Parkinson's disease, improving diagnostic potential.
Area of Science:
- Neuroscience
- Biochemistry
- Molecular Biology
Background:
- Synucleinopathies, such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA), are neurodegenerative disorders characterized by alpha-synuclein (α-syn) aggregation.
- Disease heterogeneity in synucleinopathies may arise from structural variations (polymorphs) in aggregated α-syn.
Purpose of the Study:
- To identify RNA aptamers that can specifically bind to different α-syn fibrillar polymorphs.
- To develop a high-throughput method (AptaFOOT-Seq) for assessing aptamer binding affinities to α-syn polymorphs.
- To evaluate the potential of AptaFOOT-Seq in distinguishing α-syn polymorphs associated with different synucleinopathies.
Main Methods:
- Selection of nuclease-resistant 2'fluoro-pyrimidine RNA aptamers with differential binding capabilities.
- Development and application of AptaFOOT-Seq, utilizing next-generation sequencing to analyze aptamer-polymorph interactions.
- Assessment of aptamer binding behavior in isolation versus in a mixture to capture cooperative and competitive effects.
Main Results:
- Identified RNA aptamers capable of differentially binding to structurally distinct α-syn fibrillar polymorphs.
- Demonstrated that aptamer binding is context-dependent, with competition and cooperation providing richer information.
- Developed specific 'footprints' for different α-syn polymorphs using AptaFOOT-Seq.
- Successfully distinguished α-syn polymorphs derived from patients with PD, DLB, and MSA.
Conclusions:
- AptaFOOT-Seq is a powerful tool for rapidly assessing aptamer-polymorph interactions.
- The distinct 'footprints' generated by AptaFOOT-Seq can differentiate α-syn polymorphs associated with specific synucleinopathies.
- This method holds promise for the improved diagnosis of synucleinopathies by detecting abnormal protein conformations.
