Alkyne Phosphoramidite, 5'-terminal

Cat. # Quantity Price Lead time
22260 250 mg $90.00 in stock
42260 1 g $190.00 in stock
62260 5 g $690.00 in stock
82260 10 g $1190.00 in stock

Phosphoramidite for the synthesis of oligonucleotides with 5'-terminal alkyne for Click Chemistry.

This alkyne amidite has several advantages over 5’-hexynyl phosphoramidite, 5'-butynyl-CEP, and other 5'-terminal alkyne phosphoramidites. First, it is solid compound which is easier to handle and dispense. And due to its structure, it is also more stable in solution, and has longer shelf life

Diluent for this phosphoramidite is acetonitrile, 5 min coupling time is recommended. Because this amidite does not contain 5'-terminal DMT group, no 5'-deprotection needed. Oligonucleotides should be deblocked under standard conditions, and purified by PAGE, or ion exchange HPLC.

Oligonucleotides with this modification are ideal for the use in Click Chemistry (see our recommended protocol).

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General properties

Appearance: colorless solid
Molecular weight: 409.50
Molecular formula: C21H36N3O3P
IUPAC name: trans-4-(5-Hexynoylamino)cyclohexyloxy-N,N-diisopropylamino-2-cyanoethyloxyphosphine
Solubility: good in acetonitrile and dichloromethane
Quality control: NMR 1H (95%) and 31P, HPLC-MS
Storage conditions: Storage: 24 months after receival at -20°C. Transportation: at room temperature for up to 3 weeks. Desiccate.
MSDS: Download
Product specifications

Oligo synthesis details

Coupling conditions: Standard coupling, identical to normal nucleobases
Cleavage conditions: standard deprotection
Deprotection conditions: No deprotection required. Compatible with standard deprotection reagents.

Product citations

  1. Farzan, V.M.; Kvach, M.V.; Aparin, I.O.; Kireev, D.E.; Prikazchikova, T.A.; Ustinov, A.V.; Shmanai, V.V.; Shipulin, G.A.; Korshun, V.A.; Zatsepin, T.S. Novel homo Yin-Yang probes improve sensitivity in RT-qPCR detection of low copy HIV RNA. Talanta, 2019, 194, 226–232. doi: 10.1016/j.talanta.2018.10.043
  2. Taskova, M.; Uhd, J.; Miotke, L.; Kubit, M.; Bell, J.; Ji, H.P.; Astakhova, K. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. Analytical Chemistry, 2017, 89(8), 4363–4366. doi: 10.1021/acs.analchem.7b00646
  3. Aparin, I.O.; Farzan, V.M.; Veselova, O.A.; Chistov, A.A.; Podkolzin, A.T.; Ustinov, A.V.; Shipulin, G.A.; Formanovsky, A.A.; Korshun, V.A.; Zatsepin, T.S. 1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. Analyst, 2016, 141, 1331–1338. doi: 10.1039/c5an01767j
  4. Astakhova, I.K.; Santhosh Kumar, T.; Campbell, M.A.; Ustinov, A.V.; Korshun, V.A.; Wengel, J. Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene-perylene 2'-alpha-L-amino-LNA FRET pairs. Chemical Communications, 2013, 49(5), 511-511. doi: 10.1039/c2cc37547h
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