3’ FAM, 3’-FAM CPG
AHP-CH-FAM0103 100 mg
AHP-CH-FAM1003 1000 mg Deprotection: Pretreat with diethylamine or DBU for 30
Name: 3’-FAM CPG
Chemical Name: 1-Dimethoxytrityloxy-3-[O-(N-carboxy-(3’,6’-
dipivaloylfluoresceinyl)-3-aminopropyl)]-propyl-2-O-succinoyl-
long chain alkylamino-CPG
Formula: N/A
Use: 3’-FAM CPG is used to label fluorescein at the 3’ end of
oligonucleotides.
Purity: 95%+
Diluent: N/A, Stability in Solution: N/A
Background:
Dye-labeled oligonucleotides have many important biochemi-
cal, diagnostic, and analytical uses. Depending on the fluores-
cent properties of the dye, singly labeled oligonucleotides can
be used for DNA sequencing and in situ hybridization. Doubly
labeled oligonucleotides can be used as diagnostic probes
for DNA and RNA quantification and to discriminate single
nucleotide variations (i.e., Fluorophore-Quencher, Molecular
Beacon™). In dual labeled oligonucleotides and peptides, one
dye acts as a fluorophore while the other acts as a quencher.
Fluorescein is a fluorophore. When a dual-labeled probe con-
taining fluorescein is inactive, the light emitted by the fluores-
cein is absorbed by a neighboring quencher molecule through
Fluorescent Resonance Energy Transfer (FRET). FRET
efficiency is dependent on various interactions: (1) the close
proximity between the excited state of the donor and accep-
tor dye molecules, (2) spectral overlap of the donor emission
spectrum with the acceptor absorption spectrum, and (3) rela-
tive orientation of the donor and acceptor dipole moments.
Labeling the 3’-end of an oligo with fluorescein can be
achieved using 3’-FAM CPGs. Deprotection
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of the result-
ing oligo can be performed in the usual way with ammonium
hydroxide and will require two hours at room temperature.
Fluorescence occurs when the fluorophore and quencher
separate—through breakage of the H-bonds that keep them
juxtaposed. For Molecular Beacons™, this occurs when the
Molecular Beacon™ probe is hybridized to its target sequence.
Coupling: Proceed in a manner identical to the use of normal
nucleoside support since it contains the DMT group.
minutes at room temperature. Then use ammonium hydroxide
to cleave the oligonucleotide. This requires 2 hours at room
temperature. Use an appropriate protocol (depending on the
nucleobases) to complete the deprotection.
Storage: Freezer storage, -10 to -30°C, dry, dark area
Labeled Oligo Storage: Store labeled oligo in the dark, either
dry or in a neutral aqueous media at -20°C. Do not store crude
fluorescently labeled oligonucleotides using ammonia.
MSDS: www.allelebiotech.com
Reference:
Browne KA. Sequence-specific, self-reporting hairpin inversion probes.
J Am Chem Soc, 127, 1989. (2005)
Kim SJ, Bang EK, Kwon HJ, Shim JS, Kim BH. Modified oligonucleo-
tides containing lithocholic acid in their backbones: their enhanced cel-
lular uptake and their mimicking of hairpin structures. Chembiochem,
5, 1517. (2004)
Dobson N, McDowell DG, French DJ, Brown LJ, Mellor JM, Brown T.
Synthesis ofHyBeacons and dual-labelled probes containing 2’-fluores-
cent groups for use in geneticanalysis. Chem Commun (Camb), 1234.
(2003)
Kutyavin IV, Lokhov SG, Afonina IA, Dempcy R, Gall AA, Gorn VV,
Lukhtanov E, Metcalf M, Mills A, Reed MW, Sanders S, Shishkina I, Ver-
meulen NM. Reduced aggregation and improved specificity of G-rich
oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine
bases. Nucleic Acids Res, 30, 4952. (2002)
Hill KW, Taunton-Rigby J, Carter JD, Kropp E, Vagle K, Pieken W,
McGee DP, Husar GM, Leuck M, Anziano DJ, Sebesta DP. Diels--Alder
bioconjugation of dienemodified oligonucleotides. J Org Chem, 66,
5352. (2001)
Wu H, Skrzypczynski Z, Cornwell MJ, Aboleneen H. Identification of
unexpected modifications of fluorescein-labeled oligodeoxynucleotides
by nuclease P1 digestion and mass spectrometric techniques. Rapid
Commun Mass Spectrom, 14, 26. (2000)
Hakala H, Virta P, Salo H, Lonnberg H. Simultaneous detection of sev-
eral oligonucleotides by time-resolved fluorometry: the use of a mixture
of categorized microparticles in a sandwich type mixed-phase hybridiza-
tion assay. Nucleic Acids Res, 26, 5581. (1998)
Ramirez-Vick JE, Garcia AA, Lee J. Recovery of an oligonucleotide us-
ing silver ions immobilized onto paramagnetic particles. Prep Biochem
Biotechnol, 28, 243. (1998)
Meyer KL, Hanna MM. Synthesis and characterization of a new 5-thiol-
protected deoxyuridine phosphoramidite for site-specific modification of
DNA. Bioconjug Chem, 7, 401. (1996)
Hagmar P, Bailey M, Tong G, Haralambidis J, Sawyer WH, Davidson
BE. Synthesis and characterisation of fluorescent oligonucleotides.
Effect of internal labeling on protein recognition. Biochim Biophys Acta,
1244, 259. (1995)