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5'-Biotin CE-Phosphoramidite

5'-Biotin CE-Phosphoramidite

CAS No.:135137-87-0

Phosphoramidite for incorporation of Biotin at the 5' end of an oligonucleotide.
  • Incorporates a biotin label at the 5' end of an oligonucleotide
  • Biotin is commonly used in detection systems in conjunction with streptavidin
  • DMT group prevents branching during coupling, and can be used as a purification handle
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Product information

Colourimetric detection is one of the oldest diagnostic techniques. This is based on the interaction of an enzyme e.g. HRP interacting with a substrate. This also requires some form of capture of the target with a hapten labelled probe and the duplex captured using an affinity column or matrix loaded with a suitable protein or antibody. Examples of haptens are biotin, DNP and DIG, the most commonly used being biotin in conjunction with streptavidin or avidin. The enzyme labelled oligo then hybridises to another part of the immobilised target and treatment with the substrate produces a distinctive colour.

The uses of avidin-biotin technology are diverse.(1) Applications include the detection of proteins by nonradioactive immunoassays, cytochemical staining, cell separation, isolation of nucleic acids, detection of specific DNA/RNA sequences by hybridisation, and probing of conformational changes in ion channels.

Many of these applications require the use of oligos containing biotin at one or more positions. The availability of functional biotin, in turn, provides the opportunity for immobilisation on pre-coated solid surfaces.(2)

Several different reagents are available for labelling nucleic acids with biotin. Choosing the right one will depend largely on the position within the oligonucleotide requiring to be labelled. Biotin-CE Phosphoramidite is based on a 1,3-diol structure where one hydroxyl is protected with DMTr and the other is the phosphoramidite, hence it can be used for adding multiple biotins to either the 3’, or 5’ end of an oligonucleotide. It has been suggested that this property could be exploited in the development of diagnostic probes, in applications such as ELISA, in which signal amplification is often beneficial. This has been shown using in situ hybridisation studies where three biotins at either end of the oligo gives the optimal signal.(3)

Biotin-TEG-CE Phosphoramidite can be used in a similar way for adding biotin to the 3'- and 5'- ends of an oligo. This phosphoramidite also has an extended 15 atom mixed polarity spacer arm based on triethylene glycol linker. The benefits of an extended spacer arm separating the biotin function from the rest of the oligo may be seen in applications where possible steric hindrance effects could be reduced as a result, e.g. when dual-labelling with bulky reporter molecules, such as haptens, dyes, or enzymes. Note the 1,2-diol arrangement makes cleavage during deprotection possible therefore it is advisable to keep the 5'-DMTr group on until after deprotection.

The 5'-Biotin phosphoramidite can also be used for adding biotin to an oligo, but only to the 5'-end.(4) The DMTr protection on the N1 of biotin prevents branching during coupling. The DMTr group can, however, be used to assist in reverse-phase cartridge and HPLC purification although biotin is hydrophobic enough to obtain good separation of biotin labelled oligos (DMT OFF) and unlabelled oligos.

The addition of biotin internally within an oligonucleotide sequence is achieved using Biotin- dT phosphoramidite, where any suitable dT position within the sequence can be replaced with biotin-dT. The tert-butylbenzoyl group, used to increase solubility and to protect the biotin, is removed in the ammonium hydroxide deprotection step.

Finally, the direct labelling of the 3'-end of an oligonucleotide sequence with biotin is also possible and is routinely achieved using either the 3'-Biotin-TEG or –C3 spacer CPGs, depending on your application.


  1. 263 See for example: (a) Avidin-Biotin Technology, M. Wilchek and E.A. Bayer (Eds.), in Methods in Enzymology, J.N. Abelson and M.I. Simon (Series Eds.), Volume 184, 671pp, Academic Press, 1990; (b) The biotin-(strept)avidin system: Principles and applications in biotechnology, E.P. Diamandis and T.K. Christopoulos, Clinical Chem., 37, 625-636, 1991.
  2. See for example: Electrochemical detection of non-labelled oligonucleotide DNA using biotin-modified DNA(ss) on a streptavidin-modified gold electrode, J.W. Park, H.-Y. Lee, J.M. Kim, R. Yamasaki, T. Kanno, H. Tanaka, H. Tanaka and T. Kawai, J. Bioscience and Bioengineering, 97, 29-32, 2004.
  3. A comparative study of digoxigenin, 2,4-dinitrophenyl, and alkaline phosphatase as deoxyoligonucleotide labels in non-radioisotopic in situ hybridisation, S.J. Harper, E. Bailey, C.M. McKeen, A.S. Stewart, J.H. Pringle, J. Feeholly and T. Brown, J. Clinical Pathology, 50, 686-690, 1997.
  4. For a diagnostic application see: Detection and differentiation of Plasmodium species by polymerase chain reaction and colorimetric detection in blood sample of patients with suspected malaria, D.M. Whiley, G.M. LeCornec, A. Baddeley, J. Savill, M.W. Syrmis, I.M. Mackay, D.J. Siebert, D. Burns, M. Nissen and T.P. Sloots, Diagnostic Microbiology and Infectious Disease, 49, 25-29, 2004.

Applicable Products

LK2067 Biotin-dT-CE Phosphoramidite
LK2109 5'-Biotin-CE Phosphoramidite
LK2132 Biotin-TEG-CE Phosphoramidite
LK2140 Biotin-CE Phosphoramidite
LK2353 3'-Biotin-TEG CPG

Physical & Dilution Data

Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (LK4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.


Mol. Formula

Mol. Wt.

Unit Wt.




LK2067 C69H89N8O12PS 1285.55 684.70 1.94 3.89 7.78
LK2109 C46H64N5O6PS 846.08 405.45 2.95 5.91 11.82
LK2132 C52H76N5O11PS 1010.24 569.61 2.47 4.95 9.90
LK2140 C47H66N5O7PS 876.10 435.48 2.85 5.71 11.41
LK2353 - - 313.21 - - -


The use of 0.1M oxidiser must be avoided to prevent oxidation of the biotin. However, should this occur, there is no adverse affect on the biotin-avidin coupling.

Coupling, Deprotection & Purification

Biotin-CE Phosphoramidite (LK2140) – A 15min coupling time is recommended. This is stable to most deprotection conditions.

Biotin-TEG-CE Phosphoramidite (LK2132) – A 12-15min coupling time is recommended. Most deprotection conditions are applicable. For optimal yield, oligos are prepared DMT ON, with removal of the DMTr group after cleavage and deprotection. Otherwise, the 1,2-diol configuration allows cleavage of the biotin TEG during deprotection.

3’-Biotin-TEG CPG (LK2353) – Since non-nucleosidic solid supports have a slower detritylation rate than nucleosidic supports, it is recommended than an additional detritylation be carried out. Note in this case an initial capping step must be avoided. Most cleavage and deprotection conditions are applicable.

Biotin-dT-CE Phosphoramidite (LK2067) – An extended coupling time of 15min is recommended. Most cleavage and deprotection are applicable. The t-butylbenzoyl group, used to aid the solubility and to protect the biotin, is removed during deprotection.

5’-Biotin-CE Phosphoramidite (LK2109) – A 5min coupling time is recommended. The trityl group is slow to detritylate, therefore removal on the synthesiser requires an additional deblocking step. If the biotin DMTr group is retained to aid cartridge purification, we recommend that the oligo is left in contact with the TFA solution for 10min.

Storage & Stability

All compounds are stored in a freezer at –10 to –30°C. LK2140 & LK2132 are stable in solution for 2-3 days, LK2109 for 1-2 days, and LK2067 for 3-5 days.

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