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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • Thrombin aptamers (TBAs) are crucial in various applications.
  • Long ssDNA chains with multiple TBA repeats exhibit unique structures and properties distinct from monomers.
  • Traditional methods struggle to elucidate the structure of complex, long-chain ssDNA.

Purpose of the Study:

  • To investigate the structure and properties of repeated ssDNA sequences.
  • To develop a method for synthesizing and analyzing long-chain ssDNA with multiple TBA repeats.
  • To identify novel DNA structures formed by repeat sequences.

Main Methods:

  • Development of a polymerase chain-rolling circle amplification (PC-RCA) method for ssDNA synthesis.
  • Preparation of two-end modified repeated ssDNA.
  • Utilized single-molecule magnetic tweezers and Atomic Force Microscopy (AFM) imaging for structural analysis.

Main Results:

  • First identification of novel rod-like G4 structures formed by intramolecular stacking of TBA repeat sequences.
  • These structures differ from previously known higher-order quadruplex structures.
  • Increasing TBA copy number unifies diverse TBA conformations into an optimal binding structure for thrombin.

Conclusions:

  • The study reveals a novel G4 DNA structure in long ssDNA repeats.
  • The developed methodology is applicable to studying other genomic repeat sequences, including telomeric DNA.
  • Provides insights into ssDNA-binding molecule interactions.