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Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing

Nature volume 430, pages 377–380 (2004)Cite this article

Abstract

Almost all DNA polymerases show a strong preference for incorporating the nucleotide that forms the correct Watson–Crick base pair with the template base. In addition, the catalytic efficiencies with which any given polymerase forms the four possible correct base pairs are roughly the same. Human DNA polymerase-ι (hPolι), a member of the Y family of DNA polymerases, is an exception to these rules. hPolι incorporates the correct nucleotide opposite a template adenine with a several hundred to several thousand fold greater efficiency than it incorporates the correct nucleotide opposite a template thymine, whereas its efficiency for correct nucleotide incorporation opposite a template guanine or cytosine is intermediate between these two extremes1,2,3,4,5. Here we present the crystal structure of hPolι bound to a template primer and an incoming nucleotide. The structure reveals a polymerase that is ‘specialized’ for Hoogsteen base-pairing, whereby the templating base is driven to the syn conformation. Hoogsteen base-pairing offers a basis for the varied efficiencies and fidelities of hPolι opposite different template bases, and it provides an elegant mechanism for promoting replication through minor-groove purine adducts that interfere with replication.

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Figure 1: Structure of the hPolι–DNA–dTTP ternary complex.
Figure 2: Comparison between hPolι and Dpo4.
Figure 3: Contacts between DNA and hPolι.

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Acknowledgements

We thank staff at the APS for facilitating data collection; and T. Edwards and C. Escalante for help with structure determination. This work was supported by grants from the NIH (to A.K.A and L.P.).

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Authors and Affiliations

  1. Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York, 10029, USA

    Deepak T. Nair & Aneel K. Aggarwal

  2. Sealy Center for Molecular Science, University of Texas Medical Branch, 6.014 Medical Research Building, 11th and Mechanic Streets, Galveston, Texas, 77755, USA

    Robert E. Johnson, Satya Prakash & Louise Prakash

Authors
  1. Deepak T. Nair
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  3. Satya Prakash
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Corresponding author

Correspondence to Aneel K. Aggarwal.

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Supplementary information

Supplementary Table 1

Table listing data collection, phasing, and refinement statistics. (DOC 38 kb)

Supplementary Figure 1

A figure comparing Pol iota with Dpo4. (JPG 53 kb)

Supplementary Figure 1 Legend

A legend for Supplementary Figure 1. (DOC 19 kb)

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Nair, D., Johnson, R., Prakash, S. et al. Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing. Nature 430, 377–380 (2004). https://doi.org/10.1038/nature02692

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