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Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

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Research in Computational Molecular Biology (RECOMB 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4453))

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Abstract

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.

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Authors and Affiliations

  1. Division of Genetics, Department of Medicine and,  

    Anthony A. Philippakis, Aaron M. Qureshi, Michael F. Berger & Martha L. Bulyk

  2. Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115,  

    Martha L. Bulyk

  3. Harvard/MIT Division of Health Sciences and Technology (HST), Cambridge, MA 02138,  

    Anthony A. Philippakis & Martha L. Bulyk

  4. Harvard University Graduate Biophysics Program, Cambridge, MA 02138,  

    Anthony A. Philippakis, Michael F. Berger & Martha L. Bulyk

  5. Department of Mathematics, University of Maryland, College Park, MD 20742,  

    Aaron M. Qureshi

Authors
  1. Anthony A. Philippakis
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  2. Aaron M. Qureshi
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  3. Michael F. Berger
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  4. Martha L. Bulyk
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Terry Speed Haiyan Huang

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© 2007 Springer Berlin Heidelberg

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Philippakis, A.A., Qureshi, A.M., Berger, M.F., Bulyk, M.L. (2007). Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. In: Speed, T., Huang, H. (eds) Research in Computational Molecular Biology. RECOMB 2007. Lecture Notes in Computer Science(), vol 4453. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71681-5_30

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  • DOI: https://doi.org/10.1007/978-3-540-71681-5_30

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71680-8

  • Online ISBN: 978-3-540-71681-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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