Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

Chromosome Res. 2011 Oct;19(7):901-9. doi: 10.1007/s10577-011-9245-0. Epub 2011 Oct 18.


The ability to visualize specific DNA sequences, on chromosomes and in nuclei, by fluorescence in situ hybridization (FISH) is fundamental to many aspects of genetics, genomics and cell biology. Probe selection is currently limited by the availability of DNA clones or the appropriate pool of DNA sequences for PCR amplification. Here, we show that liquid-phase probe pools from sequence capture technology can be adapted to generate fluorescently labelled pools of oligonucleotides that are very effective as repeat-free FISH probes in mammalian cells. As well as detection of small (15 kb) and larger (100 kb) specific loci in both cultured cells and tissue sections, we show that complex oligonucleotide pools can be used as probes to visualize features of nuclear organization. Using this approach, we dramatically reveal the disposition of exons around the outside of a chromosome territory core and away from the nuclear periphery.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Nucleus / chemistry*
  • Cell Nucleus / genetics
  • Chromosome Painting / methods*
  • Chromosomes / chemistry*
  • Chromosomes / genetics
  • DNA / analysis
  • DNA Probes / biosynthesis*
  • DNA Probes / genetics
  • Exome*
  • Exons
  • Fluoresceins / analysis
  • Fluorescent Dyes / analysis
  • Genetic Loci*
  • In Situ Hybridization, Fluorescence
  • Mice
  • Oligonucleotide Probes / biosynthesis*
  • Oligonucleotide Probes / genetics
  • Polymerase Chain Reaction
  • Repetitive Sequences, Nucleic Acid
  • Xanthenes / analysis


  • DNA Probes
  • Fluoresceins
  • Fluorescent Dyes
  • Oligonucleotide Probes
  • Xanthenes
  • 6-carboxyfluorescein
  • Texas red
  • DNA