Programmable Chromosome Painting with Oligopaints

Methods Mol Biol. 2019;2038:167-180. doi: 10.1007/978-1-4939-9674-2_11.


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.

Keywords: Chromosome painting; FISH; Oligonucleotide; Oligopaint.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 3T3 Cells
  • Animals
  • Chromosome Painting / methods*
  • Chromosomes, Human
  • Chromosomes, Insect*
  • Chromosomes, Mammalian*
  • Drosophila melanogaster / genetics*
  • Fluorescent Dyes / metabolism*
  • HCT116 Cells
  • Humans
  • Mice
  • Microscopy, Fluorescence*
  • Oligonucleotides / genetics
  • Oligonucleotides / metabolism*


  • Fluorescent Dyes
  • Oligonucleotides