Int. J. Mol. Sci. 2010, 11(10), 4094-4105; doi:10.3390/ijms11104094
Article

COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci

1 Kirchhoff-Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany 2 German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
* Author to whom correspondence should be addressed.
Received: 15 September 2010; in revised form: 16 October 2010 / Accepted: 18 October 2010 / Published: 21 October 2010
(This article belongs to the Special Issue Biomarkers)
PDF Full-text Download PDF Full-Text [592 KB, uploaded 21 October 2010 14:31 CEST]
Abstract: With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization) technique called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs)—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488Ò showed reversible photobleaching (blinking between dark and bright state) a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy) a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome.
Keywords: COMBO-FISH; combinatorial oligo fluorescence in situ hybridization, computer based probe selection; PNA; SPDM; spectral precision distance/position determination microscopy; localization microscopy; nanostructure analysis of the genome

Article Statistics

Load and display the download statistics.

Citations to this Article

Cite This Article

MDPI and ACS Style

Müller, P.; Schmitt, E.; Jacob, A.; Hoheisel, J.; Kaufmann, R.; Cremer, C.; Hausmann, M. COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci. Int. J. Mol. Sci. 2010, 11, 4094-4105.

AMA Style

Müller P, Schmitt E, Jacob A, Hoheisel J, Kaufmann R, Cremer C, Hausmann M. COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci. International Journal of Molecular Sciences. 2010; 11(10):4094-4105.

Chicago/Turabian Style

Müller, Patrick; Schmitt, Eberhard; Jacob, Anette; Hoheisel, Jörg; Kaufmann, Rainer; Cremer, Christoph; Hausmann, Michael. 2010. "COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci." Int. J. Mol. Sci. 11, no. 10: 4094-4105.

Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert