Fast and non-toxic in situ hybridization without blocking of repetitive sequences

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Matthiesen, Steen H ^a   Hansen, Charles M ^b  

^a Research and Development   (Denmark)

^b Charles M Hansen Consulting   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

2 PIPERIDONE; 2 PYRROLIDINONE; BUTYROLACTONE; DNA; ETHYLENE CARBONATE; FORMAMIDE; PEPTIDE NUCLEIC ACID; PROPYLENE CARBONATE; SOLVENT; SULFOLANE; UNCLASSIFIED DRUG;

ARTICLE; CANCER DIAGNOSIS; DNA BINDING; DNA DENATURATION; DNA PROBE; DNA STRAND; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN; HUMAN TISSUE; NUCLEOTIDE REPEAT;

BUFFERS; DNA PROBES; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; NEOPLASMS; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84864251915     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040675     Document Type: Article

References (33)

1. McConaughy BL, Laird CD, McCarthy BJ, (1969) Nucleic acid reassociation in formamide. Biochemistry 8: 3289-3295.
2. Bauman JG, Wiegant J, Borst P, van Duijn P, (1980) A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. Exp Cell Res 128: 485-490.
3. Gerhard DS, Kawasaki ES, Bancroft FC, Szabo P, (1981) Localization of a unique gene by direct hybridization in situ. Proc Natl Acad Sci U S A 78: 3755-3759.
4. Harper ME, Saunders GF, (1981) Localization of single copy DNA sequences of G-banded human chromosomes by in situ hybridization. Chromosoma 83: 431-439.
5. Blake RD, Delcourt SG, (1996) Thermodynamic effects of formamide on DNA stability. Nucleic Acids Res 24: 2095-2103.
6. Summersgill B, Clark J, Shipley J, (2008) Fluorescence and chromogenic in situ hybridization to detect genetic aberrations in formalin-fixed paraffin embedded material, including tissue microarrays. Nat Protocols 3: 220-234.
7. (2008) NTP Toxicology and Carcinogenesis Studies of Formamide (CAS No. 75-12-7) in F344/N Rats and B6C3F1 Mice (Gavage Studies). Natl Toxicol Program Tech Rep Ser pp. 1-192.
8. Kallioniemi OP, Kallioniemi A, Kurisu W, Thor A, Chen LC, et al. (1992) ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc Natl Acad Sci U S A 89: 5321-5325.
9. Bang YJ, Van Cutsem E, Feyereislova A, Chung HC, Shen L, et al. (2010) Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial. Lancet 376: 687-697.
10. Copie-Bergman C, Gaulard P, Leroy K, Briere J, Baia M, et al. (2009) Immuno-fluorescence in situ hybridization index predicts survival in patients with diffuse large B-cell lymphoma treated with R-CHOP: a GELA study. J Clin Oncol 27: 5573-5579.
11. Tapia C, Glatz K, Novotny H, Lugli A, Horcic M, et al. (2007) Close association between HER-2 amplification and overexpression in human tumors of non-breast origin. Mod Pathol 20: 192-198.
12. Hattab EM, Martin SE, Al-Khatib SM, Kupsky WJ, Vance GH, et al. (2009) Most primary central nervous system diffuse large B-cell lymphomas occurring in immunocompetent individuals belong to the nongerminal center subtype: a retrospective analysis of 31 cases. Mod Pathol 23: 235-243.
13. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818-821.
14. Landegent JE, Jansen in de Wal N, Dirks RW, Baao F, van der Ploeg M, (1987) Use of whole cosmid cloned genomic sequences for chromosomal localization by non-radioactive in situ hybridization. Hum Genet 77: 366-370.
15. Nielsen KV, Möller S, Agerholm IE, Poulsen TS, Matthiesen SH, et al. (2006) PNA Suppression Method Combined with Fluorescence In Situ Hybridisation (FISH) Technique. In: Pellestor F, editors. pp. 143-168 editor. PRINS and PNA technologies in chromosomal investigations New York: Nova Biomedical Books.
16. van Rijk A, Mason D, Jones M, Cabecadas J, Crespo M, et al. (2008) Translocation detection in lymphoma diagnosis by split-signal FISH: a standardised approach. J Hematop 1: 119-126.
17. Lionnet T, Czaplinski K, Darzacq X, Shav-Tal Y, Wells AL, et al. (2011) A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods 8: 165-170.
18. Hansen CM, (2007) Hansen solubility parameters: a user's handbook. Boca Raton, Fla.: CRC; London: Taylor & Francis [distributor]. 519 p.
19. Lawrence JB, Singer RH, (1986) Intracellular localization of messenger RNAs for cytoskeletal proteins. Cell 45: 407-415.
20. Pinkel D, Straume T, Gray JW, (1986) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci U S A 83: 2934-2938.
21. Dadsetan M, Christenson EM, Unger F, Ausborn M, Kissel T, et al. (2003) In vivo biocompatibility and biodegradation of poly(ethylene carbonate). J Control Release 93: 259-270.
22. Hanley TR Jr, Schumann AM, Langvardt PW, Rusek TF, Watanabe PG, (1989) Metabolism and disposition of ethylene carbonate in male Fischer 344 rats. Toxicol Appl Pharmacol 100: 24-31.
23. Stoll GH, Nimmerfall F, Acemoglu M, Bodmer D, Bantle S, et al. (2001) Poly(ethylene carbonate)s, part II: degradation mechanisms and parenteral delivery of bioactive agents. J Control Release 76: 209-225.
24. Bilous M, Dowsett M, Hanna W, Isola J, Lebeau A, et al. (2003) Current perspectives on HER2 testing: a review of national testing guidelines. Mod Pathol 16: 173-182.
25. Rose DJ, (1993) Characterization of antisense binding properties of peptide nucleic acids by capillary gel electrophoresis. Anal Chem 65: 3545-3549.
26. Hutton JR, (1977) Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea. Nucleic Acids Res 4: 3537-3555.
27. Wetmur JG, (1975) Acceleration of DNA renaturation rates. Biopolymers 14: 2517-2524.
28. Wahl GM, Stern M, Stark GR, (1979) Efficient transfer of large DNA fragments from agarose gels to diazobenzyloxymethyl-paper and rapid hybridization by using dextran sulfate. Proc Natl Acad Sci U S A 76: 3683-3687.
29. Ts'O PO, Helmkamp GK, Sander C, (1962) Interaction of nucleosides and related compounds with nucleic acids as indicated by the change of helix-coil transition temperature. Proc Natl Acad Sci U S A 48: 686-698.
30. Yakovchuk P, Protozanova E, Frank-Kamenetskii MD, (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34: 564-574.
31. Britten RJ, Kohne DE, (1968) Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 161: 529-540.
32. Brosius J, (1991) Retroposons-seeds of evolution. Science 251: 753.
33. Novick GE, Batzer MA, Deininger PL, Herrera RJ, (1996) The mobile genetic element Alu in the human genome. Bioscience 46: 32-41.