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Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.

Rob Abdur1, Oksana O Gerlits1, Jianhua Gan1

  • 1Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA.

Acta Crystallographica. Section D, Biological Crystallography
|February 18, 2014
PubMed
Summary

Researchers developed a new method using selenium-labeled nucleic acids to determine protein-nucleic acid complex structures. This technique enhances understanding of RNA cleavage mechanisms by RNase H.

Keywords:
DNA and modificationRNase H and RNA cleavageprotein–nucleic acid complexesselenium derivatization and phasing

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • Protein-nucleic acid complex structures are crucial for understanding biological processes.
  • Current methods like Multiple Isomorphous Replacement (MIR) or Single-wavelength Anomalous Dispersion (SAD) phasing often rely on selenium-derivatized proteins.

Purpose of the Study:

  • To introduce and validate a novel method for determining protein-nucleic acid complex structures using selenium-derivatized nucleic acids.
  • To investigate the structural and catalytic effects of selenium incorporation into nucleic acid substrates.
  • To elucidate the mechanism of guide-dependent RNA cleavage by RNase H.

Main Methods:

  • Crystallography
  • Selenium derivatization of nucleic acids
  • Multi-wavelength Anomalous Dispersion (MAD) or Single-wavelength Anomalous Dispersion (SAD) phasing
  • Enzymatic activity assays

Main Results:

  • Successfully determined the high-resolution crystal structure of a protein-nucleic acid complex using selenium-derivatized nucleic acids.
  • Observed that selenium substitution causes subtle unwinding of the RNA/DNA duplex, positioning the scissile phosphate closer to the enzymatic transition state.
  • Identified a hydrogen bond between the scissile phosphate and the water nucleophile, aiding in substrate positioning.
  • Demonstrated that substituting oxygen with selenium in guide DNA significantly accelerates RNase H catalysis.

Conclusions:

  • Selenium-derivatized nucleic acids provide a viable alternative for phasing protein-nucleic acid complex structures.
  • Selenium incorporation influences substrate conformation and catalytic efficiency in RNase H-mediated RNA cleavage.
  • These findings offer new insights into the mechanism of guide-dependent RNA cleavage.