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Inhibitory Effect on RT-PCR and Restriction Enzyme Activity by Ommochrome and Its Mechanism

Hiroshi Sawada1, Keisuke Mase2, Rimi Koyama2

  • 1Department of Biosciences, College of Humanities and Sciences, Nihon University, Setagaya-ku, Tokyo 156-8550, Japan, sawada.hiroshi@nihon-u.ac.jp.

Zoological Science
|December 8, 2023
PubMed

Insights

Ommochrome, a natural pigment, was found to inhibit RT-PCR and restriction enzymes by binding to DNA. Computational studies suggest ommochrome intercalates into DNA similarly to actinomycin D.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Pharmacology

Background:

  • Ommochrome is a natural organic pigment found widely in Protostomia.
  • Its physiological role and pharmacological effects are not well understood.

Purpose of the Study:

  • To investigate the influence of ommochrome on RT-PCR and restriction enzyme activities.
  • To elucidate the mechanism of ommochrome's inhibitory effects.

Main Methods:

  • Purification of ommin from *Bombyx mori* diapause eggs.
  • Biochemical assays to test inhibition of RT-PCR and restriction enzymes.
  • Computational approaches including molecular docking, molecular dynamics simulation, and free energy calculation to study ommin/DNA interaction.

Main Results:

  • Ommin inhibited both RT-PCR and restriction enzyme activities.
  • The inhibitory mechanism is proposed to be direct binding to DNA, not enzyme inhibition.
  • Computational analyses indicated ommin binds to DNA with strength comparable to actinomycin D, intercalating into the DNA structure.

Conclusions:

  • Ommochrome exhibits pharmacological effects, specifically inhibiting DNA-related processes.
  • The phenoxazine ring in ommochrome facilitates DNA intercalation, similar to actinomycin D.
  • This study provides the first biochemical and computational evidence for ommochrome's pharmacological effects and DNA-binding mechanism.
Keywords:
DNA intercalationenzyme inhibitoromminommochromephenoxazine ring

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