Universal PBMs containing all possible 10-mers within 60-mer probes are first synthesized as single-stranded oligonucleotide arrays, to which a common primer is annealed and extended in order to biochemically convert the single-stranded array to a double-stranded DNA (dsDNA) array (these steps are not shown in the figure) ( 2).

PBM technology complements other currently available technologies, such as chromatin immunoprecipitation coupled with either microarray readout ( 4–7) or high-throughput sequencing ( 8–10) that identify genomic regions bound in vivo. Universal PBMs provide an efficient and comprehensive method for in vitro interrogation of DNA-binding preferences. The development of universal ( 2) protein binding microarray (PBM) technology ( 3) ( Figure 1) offers a new avenue for the exploration of protein–DNA binding specificity. Despite recent advances in this field, the vast majority of TFs in most major model organisms and pathogens remain either uncharacterized or poorly described ( 1). The study of DNA-binding specificities therefore has profound implications for the analysis and prediction of the regulatory networks that govern intracellular function, responses to external stimuli, differentiation and development in an organism. The characterization of transcription factors’ (TFs’) DNA-binding specificities represents a critical step towards understanding the regulation of gene expression and elucidating the biophysical properties governing protein–DNA interactions. Current web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. In total, the database hosts DNA-binding data for over 175 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse and human. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive PBM data on the preferences of proteins for all possible sequence variants (‘words’) of length k (‘ k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins.

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