title: New reagents and methods for the synthesis of internal and 3'-labeled DNA.
abstract: The syntheses of two new nucleoside phosphoramidites containing a hydroxyl functionality masked by a levulinate protecting group are presented; N(4)-(2-(ethylene glycol-2-levulinate)ethyl)-5-methyl-5'-(4,4'-dimethoxytrityl)-3'-O-(2-cyanoethyldiisopropylphosphoramidite)-2'-deoxycytidine 1 and 5-(N-(6-O-levulinoyl-1-aminohexyl)-3(E)-acrylamido)-5'-(4,4'-dimethoxytrityl)-3'-(2-cyanoethyldiisopropylphosphoramidite)-2'-deoxyuridine 3. Optimization of solid-phase-supported synthetic parameters for incorporation of these into DNA, removal of the levulinate group by exposure to dilute hydrazine, and subsequent attachment of dye labels is described. Synthesis of the known compound 5-(N-(6-trifluoroacetylaminohexyl)-3(E)-acrylamido)-5'-(4,4'-dimethoxytrityl)-3'-(2-cyanoethyldiisopropylphosphoramidite)-2'-deoxyuridine 2 (1), containing a masked amine at the end of an alkyl chain attached at the 5 position, was also revisited using new techniques developed for 3.
authors.affiliation: Biosearch Technologies, Inc., 81 Digital Drive, Novato, California 94949, USA. matt@biosearchtech.com
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Lyttle
authors.forename: Troy A
authors.initials: TA
authors.lastname: Walton
authors.forename: Daren J
authors.initials: DJ
authors.lastname: Dick
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Carter
authors.forename: Jacob H
authors.initials: JH
authors.lastname: Beckman
authors.forename: Ronald M
authors.initials: RM
authors.lastname: Cook
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D007202:Indicators and Reagents; D008722:Methods; D015335:Molecular Probes / Q000138:chemical synthesis*; D009711:Nucleotides / Q000138:chemical synthesis; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D009943:Organophosphorus Compounds / Q000138:chemical synthesis; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D007202:Indicators and Reagents; D015335:Molecular Probes; D009711:Nucleotides; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA