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Our group has recently developed a compact, universal protein binding microarray (PBM) that can be used to determine the binding preferences of transcription factors (TFs) [1]. This design represents all possible sequence variants of a given length k (i.e., all k-mers) on a single array, allowing a complete characterization of the binding specificities of a given TF. Here, we present the mathematical foundations of this design based on de Bruijn sequences generated by linear feedback shift registers. We show that these sequences represent the maximum number of variants for any given set of array dimensions (i.e., number of spots and spot lengths), while also exhibiting desirable pseudo-randomness properties. Moreover, de Bruijn sequences can be selected that represent gapped sequence patterns, further increasing the coverage of the array. This design yields a powerful experimental platform that allows the binding preferences of TFs to be determined with unprecedented resolution. [ABSTRACT FROM AUTHOR]

DNA binding proteins play a number of key roles in cells,in processes including transcriptional regulation,recombination,genome rearrangements,and DNA replication, repair,and modification.Of particular interest are the interactions between transcription factors and their DNA binding sites,as they are an integral part of the transcriptional regulatory networks that control gene expression.Despite their importance,the DNA binding specificities of most DNA binding proteins remain unknown,as earlier technologies aimed at characterizing DNA-protein interactions have been time consuming and not highly scalable.We have developed a new DNA microarray-based technology,termed protein binding microarrays (PBMs),that allows rapid,high-throughput characterization of the in vitro DNA binding site sequence specificities of transcription factors in a single day. The resulting DNA binding site data can be used in a number of ways,including for the prediction of the genes regulated by a given transcription factor,annotation of transcription factor function,and functional annotation of the predicted target genes. [ABSTRACT FROM AUTHOR]