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Oligo Modifications List | Oligo Modifications Reference Category
Modification : Alkyne PC NHS
Reference Catalog Number 26-6753
Category Click Chemistry
Modification Code Alkyne PC N
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 302.11
Technical Info (pdf) PS26-6753.pdf
Catalog NoScalePrice
26-6753-0550 nmol$285.00
26-6753-02200 nmol$285.00
26-6753-011 umol$365.00
26-6753-032 umol$475.00
26-6753-1010 umol$1,248.00
26-6753-1515 umol$1,560.00

This modification is a post synthesis NHS conjugation to a primary amino group thus an additional modification with an amino group is required. A C6 or C12 amino group can be placed at the 5' or for the 3' end a C3 or C7 amino and for internal positions an amino modified base is used, e.g Amino dT C6.

Click here for a complete list of Click Chemistry Oligo Modifications


Alkyne NHS ester can be used to incorporate an active alkyne onto the 5’- or 3’-end of an oligonucleotide, as well as at an internal position. Incorporation of this modification to the oligo is done via conjugation to an active primary amine (such as Amino Linker C6). As a result, the alkyne group is separated from the oligo by a spacer arm of varying length, which serves to reduce steric interaction between the reactive group and the oligo. The presence of the alkyne allows the user to use “Click Chemistry” (a [3+2] cycloaddition reaction between alkynes and azides, using copper (I) iodide as a catalyst) to conjugate it to a variety of azide-containing labels/tags (e.g., fluorescent dyes, biotin, or oligos, with extremely high regioselectivity and efficiency (1,2). When conjugation to an azide-oligo is desired, preparation of the azide-oligo can be achieved using either an Azidobutyrate NHS Ester or the 5’-Bromohexyl modifier (see their respective tech sheets for details). Click chemistry can be used to form short, cyclic oligos that can be used as research tools in various biophysical and biological studies (3). In particular, they have considerable potential for in vivo work, as cyclic oligos are known to be very stable in serum for up to several days.

Photo Cleavage Protocol

Cleavage occurs by irradiation with near-UV light (300-350 nm, >90% cleavage occurs within 5-25 minutes. Try using a Black Ray XX-15 UV lamp (Ultraviolet Products Inc., San Gabriel, CA) at a distance of 15 cm (emission peak 365 nm, 300 nm cut-off, 1.1 mW intensity at~31 cm).



References
1. Huisgen, R. Angew. Chem. Int. Ed. (1963), 2: 565-568.
2. Rostovtsev, V.V., Green, L.G., Fokin, V.V., Sharpless, K.B. A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective Ligation of Azides and Terminal Alkynes. Angew. Chem. Int. Ed. (2002), 41: 2596-2599.
3. Kumar, R., El-Sagheer, A., Tumpane, J., Lincoln, P., Wilhelmsson, L.M., Brown, T. Template-Directed Oligonucleotide Strand Ligation, Covalent Intramolecular DNA Circularization and Catenation Using Click Chemistry. J. Am. Chem. Soc. (2007), 129: 6859-6864.

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