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

The NPH-II helicase displays efficient DNA x RNA helicase activity and a pronounced purine sequence bias.

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Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.


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.

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