New reagents and methods for the synthesis of internal and 3'-labeled DNA.
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.
Lyttle
Matthew H
MH
Biosearch Technologies, Inc., 81 Digital Drive, Novato, California 94949, USA. matt@biosearchtech.com
Walton
Troy A
TA
Dick
Daren J
DJ
Carter
Timothy G
TG
Beckman
Jacob H
JH
Cook
Ronald M
RM
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
D007202:Indicators and Reagents; D015335:Molecular Probes; D009711:Nucleotides; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA