The effect of formaldehyde fixation on RNA: Optimization of formaldehyde adduct removal

Journal of Molecular Diagnostics

Volumn 13, Issue 3, 2011, Pages 282-288

  David L Evers, ^a   Fowler, Carol B ^a   Cunningham, Brady R ^b   Mason, Jeffrey T ^c   O'Leary, Timothy J ^a  

^a VETERANS AFFAIRS MEDICAL CENTER   (United States)

^b DEPARTMENT OF VETERANS AFFAIRS   (United States)

^c ARMED FORCES INSTITUTE OF PATHOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE; OLIGONUCLEOTIDE; PHOSPHATE BUFFERED SALINE; RNA;

ARTICLE; CONTROLLED STUDY; ELECTROPHORESIS; GENE EXPRESSION; HUMAN; HUMAN TISSUE; HYPERTHERMIC THERAPY; PH; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RETROSPECTIVE STUDY; RNA EXTRACTION; RNA HYBRIDIZATION; TEMPERATURE; TIME; TISSUE PRESERVATION;

EID: 79954603515     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2011.01.010     Document Type: Article

References (25)

1. Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P: Unlocking the archive-gene expression in paraffin-embedded tissue. J Pathol 2001, 195:66-71 (Pubitemid 32899046)
2. Hewitt SM, Lewis FA, Cao Y, Richard C, Conrad RC, Cronin M, Danenberg KD, Goralski TJ, Langmore JP, Raja RG, Williams PM, Palma JF, Warrington JA: Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue. Arch Pathol Lab Med 2008, 132:1929-1935
3. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M: Determinants of RNA quality from FFPE samples. PLoS One 2007, doi: 10.1371/journal.pone.0001261 (Pubitemid 351663850)
4. Krafft AE, Duncan BW, Bijwaard KE, Taubenberger JK, Lichy JH: Optimization of the isolation and amplification of RNA from formalin-fixed, paraffin-embedded tissue: the Armed Forces Institute of Pathology experience and literature review. Mol Diagn 1997, 2:217-230 (Pubitemid 127734948)
5. Madabusi LV, Latham GJ, Andruss BF: RNA extraction for arrays. Methods Enz 2006, 411:1-14
6. Chung JY, Braunschweig T, Hewitt SM: Optimization of recovery of RNA from formalin-fixed, paraffin-embedded tissue. Diagn Mol Pathol 2006, 15:229-236 (Pubitemid 44813662)
7. Scicchitano MS, Dalmas DA, Bertiaux MA, Anderson SM, Turner LR, Thomas RA, Mirable R, Boyce RW: Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J Histochem Cytochem 2006, 54:1229-1237 (Pubitemid 44623343)
8. Xi Y, Nakajima G, Gavin E, Morris CG, Kudo K, Hayashi K, Ju J: Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. RNA 2007, 13:1668-1674 (Pubitemid 47481675)
9. Feldman MY: Reactions of nucleic acids and nucleoproteins with formaldehyde. Prog Nucleic Acid Res Mol Biol 1973, 13:1-49
10. McGhee JD, von Hippel PH: Formaldehyde as a probe of DNA structure, II: reaction with endocyclic imino groups of DNA bases. Biochemistry 1975, 14:1297-1303
11. Rait VK, Zhang Q, Fabris D, Mason JT, O'Leary TJ: Conversions of formaldehyde-modified 2=-deoxyadenosine 5=-monophosphate in conditions modeling formalin-fixed tissue dehydration. J Histochem Cytochem 2006, 54:301-310 (Pubitemid 43291274)
12. Masuda N, Ohnishi T, Kawamoto S, Monden M, Obuko K: Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 1999, 27:4436-4443 (Pubitemid 29533185)
13. Shi SR, Cote RJ, Taylor CR: Antigen retrieval techniques: current perspectives. J Histochem Cytochem 2001, 49:931-937 (Pubitemid 32675000)
14. Hamatani K, Eguchi H, Takahashi K, Koyama K, Mukai M, Ito R, Taga M, Yasui W, Nakachi K: Improved RT-PCR amplification for molecular analyses with long-term preserved formalin-fixed, paraffin-embedded tissue specimens. J Histochem Cytochem 2006, 54:773-780 (Pubitemid 43946244)
15. Li J, Smyth P, Cahill S, Denning K, Flavin R, Aherne S, Pirotta M, Guenther SM, O'Leary JJ, Sheils O: Improved RNA quality and TaqMan Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials. BMC Biotechnol 2008, 8:10
16. Chen J, Byrne GE Jr, Lossos IS: Optimization of RNA extraction from formalin-fixed paraffin-embedded lymphoid tissues. Diagn Mol Pathol 2007, 16:61-72 (Pubitemid 47164737)
17. Penniston JT, Doty P: Reaction of formaldehyde with soluble ribonucleic acid. Biopolymers 1963, 1:145-164
18. Maniatis T, Fritsch EF, Sambrook J: Molecular Cloning: A Laboratory Manual. New York, Cold Spring Harbor Laboratory, 1982
19. Mason JT, Xu L, Sheng ZM, O'Leary TJ: A liposome-PCR assay for the ultrasensitive detection of biological toxins. Nature Biotech 2006, 24:555-557
20. Mason JT, Xu L, Sheng ZM, He J, O'Leary TJ: Liposome polymerase chain reaction assay for the sub-attomolar detection of cholera toxin and botulinum neurotoxin type A. Nature Protoc 2006, 1:2003-2011 (Pubitemid 46773324)
21. Gottschalk M, Nilsson H, Roos H, Halle B: Protein self-association in solution: the bovine beta-lactoglobulin dimer and octamer. Protein Sci 2003, 12:2404-2411 (Pubitemid 37310782)
22. Vagedes P, Saenger W, Knapp EW: Driving forces of protein association: the dimer-octamer equilibrium in arylsulfatase A. Biophys J 2002, 83:3066-3078 (Pubitemid 36041929)
23. Ebeling W, Hennrich N, Klockow M, Metz H, Orth HD, Lang H: Proteinase K from Tritirachium album Limber. Eur J Biochem 1974, 47:91-97
24. Durst RA, Staples BR: Tris-tris-HCl: a standard buffer for use in the physiologic pH range. Clin Chem 1972, 18:206-208
25. Emilsson GM, Nakamura S, Roth A, Breaker RR: Ribozyme speed limits. RNA 2003, 9:907-918 (Pubitemid 36899233)