De Novo Single-Stranded RNA-Binding Peptides Discovered by Codon-Restricted mRNA Display

Area of Science:

• Molecular Biology
• Biotechnology
• RNA Biology

Background:

• RNA-binding proteins (RBPs) are crucial for cellular processes like DNA repair and cancer progression.
• Developing novel RNA-binding peptides de novo is challenging, especially for flexible, low-complexity single-stranded RNAs.
• Targeting specific RNA sequences offers biotechnological potential.

Purpose of the Study:

• To develop a platform for discovering de novo RNA-binding peptides.
• To identify peptides that bind to single-stranded RNA with high affinity.
• To explore the potential of these peptides in targeting disease-related RNAs.

Main Methods:

• Utilized a codon-restricted mRNA display system.
• Screened a peptide library against poly(C) and poly(A) RNA homopolymers.
• Characterized peptide-RNA binding affinities using dissociation constants (K_Ds).

Main Results:

• Identified multiple de novo peptides binding to poly(C) and poly(A) RNA with micromolar to submicromolar affinities.
• Discovered a peptide that binds to cytosine-rich sequences in oncogenic Cdk6 3'UTR RNA and MYU lncRNA.
• Achieved binding affinity comparable to endogenous proteins for specific RNA targets.

Conclusions:

• Presented a novel platform for discovering de novo single-stranded RNA-binding peptides.
• Demonstrated the ability of identified peptides to bind specific disease-associated RNA sequences.
• Highlighted the potential of these peptides for RNA-based biotechnological applications and therapeutic strategies.