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Programmable Aggregation of Self-Assembled DNA Constructs.

Pragati K Prasad1, Akhil Inti1, Shiv Pratap S Yadav2

  • 1Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana, 500007, India.

Small Methods
|August 27, 2024
PubMed
Summary
This summary is machine-generated.

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Researchers developed a novel method for controlled DNA aggregation and reversion using lanthanide salts. This technique enables precise measurement of binding constants and offers a rapid way to form G-quadruplex structures.

Area of Science:

  • Biochemistry
  • Synthetic Biology
  • Materials Science

Background:

  • Biomolecular aggregates are crucial for cellular biochemical processes.
  • Synthetic aggregating systems are vital for mimicking natural dynamic condensates.
  • Understanding DNA aggregation is key to developing novel biomaterials.

Purpose of the Study:

  • To report ratiometric DNA aggregation of self-assembled DNA constructs using lanthanide salts.
  • To demonstrate the reversibility of this aggregation using specific lanthanide-binding ligands.
  • To apply this system for evaluating lanthanide-DNA and lanthanide-ligand binding constants.

Main Methods:

  • Utilized dynamic light scattering, electrophoretic mobility shift assay, and field emission scanning electron microscopy for aggregate confirmation.
Keywords:
DNA nanotechnologyaggregatesfluorescencelanthanidesself‐assembly

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  • Employed Forster resonance energy transfer (FRET) pair dyes for tracking binding states.
  • Investigated G-quadruplex (GQ) formation using FRET, circular dichroism (CD), and enzyme-linked immunosorbent assay (ELISA).

    • Main Results:

    • Achieved programmed DNA aggregation and reversion using lanthanide salts and specific ligands.
    • Successfully evaluated lanthanide-DNA and lanthanide-ligand binding constants.
    • Demonstrated a rapid method for lanthanide-induced G-quadruplex formation and stabilization.
    • Observed DNase I resistance and distinctive binding to Protoporphyrin dyes and Thioflavin T in lanthanide-DNA constructs.

    Conclusions:

    • Developed a versatile DNA aggregation system controlled by lanthanides, offering tunable properties.
    • Established a new platform for quantifying biomolecular binding interactions.
    • Provided a rapid and efficient method for G-quadruplex formation, complementing existing techniques.