The NPH-II Helicase Displays Efficient DNA X RNA Helicase Activity and a Pronounced Purine Sequence Bias

J Biol Chem. 2010 Apr 9;285(15):11692-703. doi: 10.1074/jbc.M109.088559. Epub 2010 Jan 28.


The superfamily 2 vaccinia viral helicase nucleoside triphosphate phosphohydrolase-II (NPH-II) exhibits robust RNA helicase activity but typically displays little activity on DNA substrates. NPH-II is thus believed to make primary contacts with backbone residues of an RNA substrate. We report an unusual nucleobase bias, previously unreported in any superfamily 1 or 2 helicase, whereby purines are heavily preferred as components of both RNA and DNA tracking strands. The observed sequence bias allows NPH-II to efficiently unwind a DNA x RNA hybrid containing a purine-rich DNA track derived from the 3'-untranslated region of an early vaccinia gene. These results provide insight into potential biological functions of NPH-II and the role of sequence in targeting NPH-II to appropriate substrates. Furthermore, they demonstrate that in addition to backbone contacts, nucleotide bases play an important role in modulating the behavior of NPH-II. They also establish that processive helicase enzymes can display sequence selectivity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • DNA / chemistry*
  • Genetic Techniques
  • Kinetics
  • Molecular Sequence Data
  • Nucleic Acids / chemistry
  • Nucleoside-Triphosphatase / metabolism*
  • Proteins / chemistry
  • Purines / chemistry*
  • Pyrimidines / chemistry
  • RNA Helicases / metabolism*
  • Substrate Specificity
  • Vaccinia virus / enzymology


  • Nucleic Acids
  • Proteins
  • Purines
  • Pyrimidines
  • DNA
  • Nucleoside-Triphosphatase
  • RNA Helicases
  • purine