Skip Navigation

Nucleic Acids Research 2005 33(8):e79; doi:10.1093/nar/gni079
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (304K) Freely available
Right arrow Screen PDF (305K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Egener, T.
Right arrow Articles by Mermod, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Egener, T.
Right arrow Articles by Mermod, N.
Related Collections
Right arrow Microarray
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 12 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts

Tanja Egener, Emmanuelle Roulet, Marc Zehnder, Philipp Bucher1 and Nicolas Mermod*

Institute of Biotechnology, University of Lausanne 1015 Lausanne, Switzerland 1Swiss Institute of Bioinformatics and Swiss Institute for Experimental Cancer Research 1066 Epalinges, Switzerland

*To whom correspondence should be addressed at Laboratory of Molecular Biotechnology, Station 6, FSB-ISP-ISIC, EPFL, 1015 Lausanne, Switzerland. Tel: +41 21 693 61 51; Fax: +41 21 693 76 10; Email: Nicolas.Mermod{at}unil.ch

Received February 4, 2005. Revised April 12, 2005. Accepted April 27, 2005.

The function of DNA-binding proteins is controlled not just by their abundance, but mainly at the level of their activity in terms of their interactions with DNA and protein targets. Moreover, the affinity of such transcription factors to their target sequences is often controlled by co-factors and/or modifications that are not easily assessed from biological samples. Here, we describe a scalable method for monitoring protein–DNA interactions on a microarray surface. This approach was designed to determine the DNA-binding activity of proteins in crude cell extracts, complementing conventional expression profiling arrays. Enzymatic labeling of DNA enables direct normalization of the protein binding to the microarray, allowing the estimation of relative binding affinities. Using DNA sequences covering a range of affinities, we show that the new microarray-based method yields binding strength estimates similar to low-throughput gel mobility-shift assays. The microarray is also of high sensitivity, as it allows the detection of a rare DNA-binding protein from breast cancer cells, the human tumor suppressor AP-2. This approach thus mediates precise and robust assessment of the activity of DNA-binding proteins and takes present DNA-binding assays to a high throughput level.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
G. Mittler, F. Butter, and M. Mann
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements
Genome Res., February 1, 2009; 19(2): 284 - 293.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
P. Hou, Z. Chen, M. Ji, N. He, and Z. Lu
Real-time PCR Assay for Ultrasensitive Quantification of DNA-Binding Proteins
Clin. Chem., April 1, 2007; 53(4): 581 - 586.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. Zhang, S. Kasif, and a. C. R. Cantor
Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy
PNAS, February 27, 2007; 104(9): 3061 - 3066.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.