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The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases

Nature Structural & Molecular Biology volume 13, pages 981986 (2006) | Download Citation

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Abstract

Helicases unwind RNA or DNA duplexes and displace proteins from nucleic acids in an ATP-dependent fashion. To unwind duplexes, helicases typically load onto one of the two nucleic acid strands, usually at a single-stranded region, and then translocate on this strand in a unidirectional fashion, thereby displacing the complementary DNA or RNA. Here we show that the DEAD-box RNA helicase Ded1 unwinds duplexes in a different manner. Ded1 uses the single-stranded region to gain access to the duplex. Strand separation is directly initiated from the duplex region and no covalent connection between the single strand and the duplex region is required. This new type of helicase activity explains observations with other DEAD-box proteins and may be the prototype for duplex-unwinding reactions in RNA metabolism.

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Acknowledgements

We thank M. Fairman for purification of NPH-II and A. Pyle, T. Nilsen, W. Merrick, J. Coller, M. Caprara and N. Kaye for comments on the manuscript. This work was supported by a grant from the US National Institutes of Health to E.J. E.J. is a Scholar of the Damon Runyon Cancer Research Foundation.

Author information

Affiliations

  1. Department of Biochemistry and Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, USA.

    • Quansheng Yang
    •  & Eckhard Jankowsky

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Contributions

Q.Y. conducted experiments. Q.Y. and E.J. conceived and planned experiments, analyzed and interpreted data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eckhard Jankowsky.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Unwinding of MPS III components without streptavidin.

  2. 2.

    Supplementary Fig. 2

    Unwinding reactions under single-turnover conditions.

  3. 3.

    Supplementary Fig. 3

    Representative time courses for duplex unwinding.

  4. 4.

    Supplementary Fig. 4

    Sequences of substrates used in Figures 1, 2, 3.

  5. 5.

    Supplementary Fig. 5

    Unwinding of the 16-bp blunt-end RNA duplex requires ATP hydrolysis.

  6. 6.

    Supplementary Fig. 6

    Sequences and functional characterization of substrates used in Figure 4.

  7. 7.

    Supplementary Fig. 7

    Sequences of multipiece substrates used in Figures 5, 6, 7.

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DOI

https://doi.org/10.1038/nsmb1165

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