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Phase Separation of RX Repeat Peptides with Nucleic Acids.

Sumit Shil1, Mitsuki Tsuruta1, Ryosuke Suzuki1

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Glycine residues in proteins are key to biomolecular liquid-liquid phase separation (LLPS) with G-quadruplex DNA. Substituting glycine reveals how peptide properties control LLPS and liquid-solid phase separation (LSPS).

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DNA structureLiquid‐Liquid Phase SeparationLiquid‐Solid Phase separationRX‐repat peptides

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • Biomolecular liquid-liquid phase separation (LLPS) organizes membraneless cellular compartments.
  • Intrinsically disordered proteins, rich in arginine and glycine (RGG/RG), mediate LLPS with nucleic acids, particularly G-quadruplex (G4) DNA.
  • The role of glycine in protein-nucleic acid LLPS is less understood than arginine's.

Purpose of the Study:

  • To systematically investigate the contribution of glycine residues to LLPS and liquid-solid phase separation (LSPS) with DNA.
  • To determine how peptide properties like side-chain size, hydrophobicity, and aromaticity influence phase separation.
  • To guide the rational design of peptides for controlled LLPS with nucleic acids.

Main Methods:

  • Systematic substitution of glycine residues with alanine, proline, valine, and tyrosine in RX repeat peptides.
  • Turbidity and microscopy assays to observe phase separation.
  • Testing interactions with DNA oligonucleotides forming G4, duplex, and random coil structures.

Main Results:

  • RP and RA peptides enhanced LLPS with G4 DNA compared to RG peptides.
  • RY peptide promoted liquid-solid phase separation (LSPS) with G4 DNA but LLPS with random coil and duplex DNA.
  • RV peptide formed aggregates independently of DNA, while alanine and proline substitutions modulated LLPS/LSPS selectivity.

Conclusions:

  • Peptide side-chain characteristics (size, hydrophobicity, aromaticity) are critical for selective LLPS and LSPS with DNA secondary structures.
  • Understanding these factors provides mechanistic insights into protein-nucleic acid interactions.
  • This knowledge aids in designing peptides for specific phase separation behaviors, distinguishing between LLPS and LSPS.