A new synthetic protocol for labeled oligonucleotides, using a chemically cleavable universal linker.
A two-step general method for labeling of synthetic oligonucleotides is described. The protocol employs a cleavable universal linker, 5'-O-(4,4'-dimethoxytrityl)-3'-O-benzoyl-2'-O-(2-cyanoethyl-N,N-diisopropyl)-uridine phosphoramidite, to effect coupling to polymer-bound oligonucleotide chains. Sequentially, coupling with commercially available phosphoramidite reagent of an appropriate label (Biotin, HEX etc.) in an automated DNA synthesizer is carried out. The labeled oligomers, obtained after cleavage and deprotection reactions, are analyzed on RP-HPLC. A distinctive feature of this protocol is the recovery of free oligomers from their labeled analogs under mild conditions. The oligomers obtained are comparable to the corresponding standard oligonucleotides (HPLC).
Mahajan
Shweta
S
Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India.
Patnaik
S
S
Kumar
P
P
Gandhi
R P
RP
Gupta
K C
KC
D001710:Biotin / Q000737:chemistry; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D018398:Homeodomain Proteins / Q000737:chemistry; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry / Q000302:isolation & purification; D009943:Organophosphorus Compounds / Q000737:chemistry; D012680:Sensitivity and Specificity; D013329:Structure-Activity Relationship; D013997:Time Factors; D014157:Transcription Factors / Q000737:chemistry; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry
C512242:5'-O-(4,4'-dimethoxytrityl)-3'-O-benzoyl-2'-O-(2-cyanoethyl-N,N-diisopropyl)uridine phosphoramidite; D018398:Homeodomain Proteins; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D014157:Transcription Factors; C434331:phosphoramidite; D001710:Biotin; D014529:Uridine