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Identifying protein interactions with metal-modified DNA using microarray technology

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Abstract

Protein microarrays have been used extensively to identify protein–protein interactions; however, this technology has not been widely applied to protein–DNA interactions. In particular, this work demonstrates the utility of this technique for rapidly identifying interactions of proteins with metal-modified DNA. Protein macroarray experiments were carried out with high mobility group protein 1 (HMG-1) and cisplatin- and chromium-modified 50-mer oligonucleotides to demonstrate “proof of principle.” Commercially available protein microarrays containing many different classes of human proteins were then employed to search for additional interactions with cisplatin-modified DNA. The results of the microarray experiments confirmed some known interactions and, more importantly, identified many novel protein interactions, demonstrating the utility of this method as a rapid, high-throughput technique to discover proteins that interact with metal-modified DNA.

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Abbreviations

BCCP:

Biotin carboxyl carrier protein

CoA:

Coenzyme A

GST:

Glutathione S-transferase

HEPES:

N-(2-Hydroxyethyl)piperazine-N′-ethanesulfonic acid

HMG-1:

High mobility group protein 1

PBS:

Phosphate-buffered saline

TAMRA:

Carboxytetramethylrhodamine

XPA:

Xeroderma pigmentosum A complementing protein

ZNF143:

Zinc finger factor 143

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Acknowledgments

Mass-spectral data were obtained by Steve Eyles at the University of Massachusetts Mass Spectrometry Facility, which is supported, in part, by the National Science Foundation. The authors thank Adam Hall (Smith College), Scott Edmands (Smith College), Charles Amass (Smith College), and the Smith College Center for Molecular Biology for access to and assistance with instrumentation; Nicholas Horton (Smith College), Gregory Michaud (Invitrogen), Peter Kraus (Invitrogen), and Jonathan Dordick (RPI) for helpful discussions; and Kim Bure (Invitrogen) and Tamara McLeod (Invitrogen) for assistance in obtaining ProtoArray™ slides. Funding for this work was provided by Smith College.

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Authors and Affiliations

  1. Department of Chemistry, Biochemistry Program, Smith College, Northampton, MA, 01063, USA

    Hope E. Stansfield, Bethany P. Kulczewski, Kyle E. Lybrand & Elizabeth R. Jamieson

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  1. Hope E. Stansfield
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  2. Bethany P. Kulczewski
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  3. Kyle E. Lybrand
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  4. Elizabeth R. Jamieson
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Correspondence to Elizabeth R. Jamieson.

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Stansfield, H.E., Kulczewski, B.P., Lybrand, K.E. et al. Identifying protein interactions with metal-modified DNA using microarray technology. J Biol Inorg Chem 14, 193–199 (2009). https://doi.org/10.1007/s00775-008-0437-9

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  • DOI: https://doi.org/10.1007/s00775-008-0437-9

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