Programmable Chromosome Painting with Oligopaints

  • Son C. Nguyen
  • Eric F. JoyceEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2038)


Current methods for chromosome painting via fluorescence in situ hybridization (FISH) are costly, time-consuming, and limited in complexity. In contrast to conventional sources of probe, Oligopaints are computationally designed, synthesized on microarrays, and amplified by PCR. This approach allows for precise control over the sequences they target, which can range from a few kilobases to entire chromosomes with the same basic protocol. We have utilized the flexibility and scalability of Oligopaints to generate low-cost and renewable chromosome paints for Drosophila, mouse, and human chromosomes. These Oligopaint libraries can be customized to label any genomic feature(s) in a chromosome-wide manner. Additionally, this method is compatible with sequential FISH to label entire genomes with a single denaturation step. Here, we outline a protocol and considerations to scale the Oligopaint technology for fluorescent labeling of whole chromosomes.

Key words

FISH Oligopaint Chromosome painting Oligonucleotide 



The authors would like to thank members of the Joyce laboratory for extensive conversations and experience. This work was supported by an NIH grant to E.J. (R35GM128903).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Genetics, Penn Epigenetics Institute, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA

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