PMID- 20809312
OWN - NLM
STAT- MEDLINE
DCOM- 20101214
LR  - 20131121
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 659
DP  - 2010
TI  - COMBinatorial Oligo FISH: directed labeling of specific genome domains in 
      differentially fixed cell material and live cells.
PG  - 185-202
LID - 10.1007/978-1-60761-789-1_13 [doi]
AB  - With the improvement and completeness of genome databases, it has become possible 
      to develop a novel fluorescence in situ hybridization (FISH) technique called 
      COMBinatorial Oligo FISH (COMBO-FISH). In contrast to other (standard) FISH 
      applications, COMBO-FISH makes use of a bioinformatic approach for probe set 
      design. By means of computer genome database search, oligonucleotide stretches of 
      typical lengths of 15-30 nucleotides are selected in such a way that they all 
      colocalize within a given genome (gene) target. Typically, probe sets of about 
      20-40 stretches are designed within 50-250 kb, which is enough to get an 
      increased fluorescence signal specifically highlighting the target from the 
      background. Although "specific colocalization" is the only necessary condition 
      for probe selection, i.e. the probes of different lengths can be composed of 
      purines and pyrimidines, we additionally refined the design strategy restricting 
      the probe sets to homopurine or homopyrimidine oligonucleotides so that depending 
      on the probe orientation either double (requiring denaturation of the target 
      double strand) or triple (omitting denaturation of the target strand) strand 
      bonding of the probes is possible. The probes used for the protocols described 
      below are DNA or PNA oligonucleotides, which can be synthesized by established 
      automatized techniques. We describe different protocols that were successfully 
      applied to label gene targets via double- or triple-strand bonding in fixed 
      lymphocyte cell cultures, bone marrow smears, and formalin-fixed, paraffin-wax 
      embedded tissue sections. In addition, we present a procedure of probe 
      microinjection in living cells resulting in specific labeling when 
      microscopically detected after fixation.
FAU - Schmitt, Eberhard
AU  - Schmitt E
AD  - Kirchhoff-Institute of Physics, University of Heidelberg, Heidelberg, Germany.
FAU - Schwarz-Finsterle, Jutta
AU  - Schwarz-Finsterle J
FAU - Stein, Stefan
AU  - Stein S
FAU - Boxler, Carmen
AU  - Boxler C
FAU - Muller, Patrick
AU  - Muller P
FAU - Mokhir, Andriy
AU  - Mokhir A
FAU - Kramer, Roland
AU  - Kramer R
FAU - Cremer, Christoph
AU  - Cremer C
FAU - Hausmann, Michael
AU  - Hausmann M
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 1HG84L3525 (Formaldehyde)
SB  - IM
MH  - Base Sequence
MH  - Bone Marrow Cells/cytology
MH  - Cell Line
MH  - Cell Survival
MH  - Databases, Nucleic Acid
MH  - Formaldehyde/metabolism
MH  - Genome/*genetics
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Paraffin Embedding
MH  - Specimen Handling
MH  - Tissue Fixation
EDAT- 2010/09/03 06:00
MHDA- 2010/12/16 06:00
CRDT- 2010/09/03 06:00
PHST- 2010/09/03 06:00 [entrez]
PHST- 2010/09/03 06:00 [pubmed]
PHST- 2010/12/16 06:00 [medline]
AID - 10.1007/978-1-60761-789-1_13 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2010;659:185-202. doi: 10.1007/978-1-60761-789-1_13.