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This article is part of the supplement: Epigenetics and Chromatin: Interactions and processes

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Oligopaints: highly efficient, bioinformatically designed probes for fluorescence in situ hybridization

Brian J Beliveau1*, Eric F Joyce1, Nicholas Apostolopoulosa1, Feyza Yilmaza12, Chamith Y Fonseka1, Ruth B McCole1, Yiming Chang13, Jin Billy Li14, Tharanga Niroshini Senaratne1, Benjamin R Williams15, Jean-Marie Rouillard67 and Chao-ting Wu1

  • * Corresponding author: Brian J Beliveau

Author Affiliations

1 Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA

2 Department of Biology, Boston University, Boston, MA, 02215, USA

3 Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA

4 Department of Genetics, Stanford University, Stanford, CA, 94305, USA

5 Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

6 MYcroarray Ann Arbor, Ml, 41805, USA

7 Department of Chemical Engineering, University of Michigan, Ann Arbor, Ml, 48109, USA

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Epigenetics & Chromatin 2013, 6(Suppl 1):P5  doi:10.1186/1756-8935-6-S1-P5

The electronic version of this article is the complete one and can be found online at:

Published:18 March 2013

© 2013 Beliveau et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Poster presentation

Fluorescence in situ hybridization (FISH) is a powerful tool to study chromosome structure, positioning, and gene expression on a cell-by-cell basis. We have developed Oligopaints [1], a PCR-based method for generating highly efficient FISH probes from complex DNA libraries. Our method can visualize genomic regions ranging in size from tens of kilobases to megabases with the same basic protocol and gives researchers precise control over the location and patterning of each probe set. We have mined the reference genomes of C. elegans, D. melanogaster, A. thaliana, M. musculus, and humans for genomically unique 32-base sequences with thermodynamically desirable hybridization properties, and have made these sequences available on the Oligopaints website [] along with a suite of scripts and documentation that will assist researchers with probe set design and allow our technology to be extended to any organism whose genome has been sequenced. Oligopaints robustly label chromosomes both in tissue culture cells and whole-mount tissue preparations and can be generated using standard molecular biology techniques and equipment at a price well below the cost of commercial FISH probes. The flexibility offered by our bioinformatic design platform has allowed us to perform complicated hybridizations, such as the simultaneous targeting of RNA and the genomic DNA flanking its site of transcription. Thus, we anticipate that Oligopaints will be a valuable tool for the study of nuclear architecture and the relationship between chromosome positioning and gene expression.


  1. Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT: Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.

    Proc Nat Acad Sci 2012.

    Epub 2012 Dec 11