title: Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration.
abstract: Formalin-fixed, paraffin-embedded specimens typically provide molecular biologists with low yields of extractable nucleic acids that exhibit extensive strand cleavage and covalent modification of nucleic acid bases. This study supports the idea that these deleterious effects are promoted by the first step in formalin-fixed tissue processing--i.e., tissue dehydration with a graded series of alcohols. We analyzed the conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate (dAMP) by reverse-phase ion-pair, high-performance liquid chromatography and found that dehydration does not stabilize N-methylol groups in the modified nucleotide. Furthermore, spontaneous demodification in a dry state or in anhydrous ethanol can be as fast as it is in aqueous solutions if the preparation is contaminated with salts of orthophosphoric acid. In ethanol, orthophosphates also catalyze formation of abundant N6-ethoxymethyl-dAMP, as well as cross-linking and depurination of nucleotides present in the mixture. Identification of the products was performed using ultraviolet absorbance spectroscopy and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry. Alternatives to the traditional processing of formalin-fixed tissues are discussed.
authors.affiliation: Department of Biophysics, Armed Forces Institute of Pathology, Rockville, Maryland, USA.
authors.forename: Vladimir K
authors.initials: VK
authors.lastname: Rait
authors.forename: Qingrong
authors.initials: Q
authors.lastname: Zhang
authors.forename: Daniele
authors.initials: D
authors.lastname: Fabris
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Mason
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: O'Leary
mesh_terms: D000080:Acetals / Q000737:chemistry; D000249:Adenosine Monophosphate / Q000031:analogs & derivatives / Q000737:chemistry; D002384:Catalysis; D002851:Chromatography, High Pressure Liquid; D003432:Cross-Linking Reagents / Q000737:chemistry; D003838:Deoxyadenine Nucleotides / Q000737:chemistry*; D000431:Ethanol; D005404:Fixatives / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D005583:Fourier Analysis; D016612:Paraffin Embedding; D010710:Phosphates; D012996:Solutions; D021241:Spectrometry, Mass, Electrospray Ionization; D013056:Spectrophotometry, Ultraviolet; D016707:Tissue Fixation / Q000379:methods*; D014867:Water
chemical_list: D000080:Acetals; D003432:Cross-Linking Reagents; D003838:Deoxyadenine Nucleotides; D005404:Fixatives; C509206:N(6)-ethoxymethyl-2'-deoxyadenosine 5'-monophosphate; D010710:Phosphates; D012996:Solutions; D014867:Water; D005557:Formaldehyde; D000431:Ethanol; D000249:Adenosine Monophosphate; C012873:2'-deoxy-5'-adenosine monophosphate