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BMC Bioinformatics. 2006 Oct 3;7:429.

Design of a combinatorial DNA microarray for protein-DNA interaction studies.

Author information

  • 1Boston University, Bioinformatics Program, Boston, MA, USA. julianm@bu.edu

Abstract

BACKGROUND:

Discovery of precise specificity of transcription factors is an important step on the way to understanding the complex mechanisms of gene regulation in eukaryotes. Recently, double-stranded protein-binding microarrays were developed as a potentially scalable approach to tackle transcription factor binding site identification.

RESULTS:

Here we present an algorithmic approach to experimental design of a microarray that allows for testing full specificity of a transcription factor binding to all possible DNA binding sites of a given length, with optimally efficient use of the array. This design is universal, works for any factor that binds a sequence motif and is not species-specific. Furthermore, simulation results show that data produced with the designed arrays is easier to analyze and would result in more precise identification of binding sites.

CONCLUSION:

In this study, we present a design of a double stranded DNA microarray for protein-DNA interaction studies and show that our algorithm allows optimally efficient use of the arrays for this purpose. We believe such a design will prove useful for transcription factor binding site identification and other biological problems.

PMID:
17018151
PMCID:
PMC1635571
DOI:
10.1186/1471-2105-7-429
[PubMed - indexed for MEDLINE]
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