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Structural and functional characterization of complexes between heme and dimeric parallel G-quadruplex DNAs.

China Okamoto1, Atsuya Momotake1, Yasuhiko Yamamoto2

  • 1Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan.

Journal of Inorganic Biochemistry
|January 16, 2021
PubMed
Summary

Heme binds selectively to parallel G-quadruplex DNA structures, not antiparallel ones. This selective binding enhances peroxidase-like activity by optimizing substrate access and adenine base orientation.

Keywords:
DeoxyribozymeG-quadruplexHemeMolecular recognitionPeroxidase activityπ-π stacking interaction

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Catalysis

Background:

  • Heme is a crucial prosthetic group in enzymes, and heme-bound nucleic acids exhibit peroxidase-like activity.
  • Understanding the molecular recognition of G-quadruplex DNA by heme is key to developing novel catalysts.

Purpose of the Study:

  • To characterize the interaction between heme and dimeric G-quadruplexes.
  • To elucidate the structural requirements for heme binding to G-quadruplex DNA.
  • To investigate how DNA sequence modifications influence the catalytic activity of heme-G-quadruplex complexes.

Main Methods:

  • Synthesis of dimeric G-quadruplexes from d(TAGGGTTAGGGT) and d(TAGGGTTAGGGA).
  • Spectroscopic characterization of heme binding to parallel and antiparallel G-quadruplexes.
  • Assay of peroxidase-like activity of heme-G-quadruplex complexes with varying DNA sequences.

Main Results:

  • Heme selectively binds to the 3'-terminal G-quartet of parallel G-quadruplexes (d(TAGGGTTAGGGT)).
  • Heme does not bind to antiparallel G-quadruplexes (d(TAGGGTTAGGGA)), indicating the importance of guanine deoxyribose ring arrangement.
  • Catalytic activity increased with adenine bases adjacent to heme, improving substrate accessibility and optimizing base orientation.

Conclusions:

  • The orderly arrangement of guanine deoxyribose rings in parallel G-quadruplexes is critical for heme binding.
  • DNA sequence engineering around the heme-binding site can modulate the peroxidase-like activity of these complexes.
  • These findings advance the design of DNA-based catalysts with tailored functionalities.