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

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, doublestranded 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 proteinDNA interaction studies and show th...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Julian Mintseris, Michael B. Eisen
• Keywords: BMCBI 2006, Gene Regulation, Site Identification, Transcription Factors