Specialty Proteomics Microarrays - Customer Publications

Our genomics products and services include the use of custom synthesized microarrays based on the µParaflo^® on-chip synthesis technology which enables the total customization of content on each individual microarray to suit your needs. In addition, the flexibility of µParaflo^® enables the incorporation of modifications within the probes, which significantly expands the range of applications for these microarrays.  Listed below are publications illustrating the application of custom microarrays containing non-standard probes.

Protein-Oligonucleotide Binding (Transcription Factor) Microarrays

Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain.

Proc Natl Acad Sci U S A. 2006 Nov 14;103(46):17225-30.

Author: Anbanandam A, Albarado DC, Nguyen CT, Halder G, Gao X, Veeraraghavan S.

Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, TX 77030.

Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. Our results provide a model for understanding the regulation of genome-wide gene expression during development by TEA/ATTS family of transcription factors.

Phosphopeptide Microarrays

PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

Author: Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T.

Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, Atactic Technologies and LC Sciences, Houston, TX 77054, USA.

Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions. Our motivation is to provide the research community with a rich information source emphasizing the reported, experimentally validated data for specific PPBD-PPEP interactions. This information is not only useful for designing, comparing and validating the relevant experiments, but it also serves as a knowledge-base for computationally constructing systems signaling pathways and networks. PepCyber:P approximately PEP is accessible through the URL, http://www.pepcyber.org/PPEP/. The current release of the database contains 7044 PPBD-mediated interactions involving 337 PPBD-containing proteins and 1123 substrate proteins.

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