Home | Products | Oligo Technology | Fluorescent Probes | Modifications | Oligo Design Tools | Online Order

Oligo Modifications List | Oligo Modifications Reference Category
Modification : Inverted dA (reverse linkage)
Reference Catalog Number 26-6551
Category Minor Bases
Modification Code InvdA
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 313.21
Extinction Coeficient (ec) 15.4
Technical Info (pdf) PS26-6551.pdf
Catalog NoScalePrice
26-6551-0550 nmol$42.00
26-6551-02200 nmol$42.00
26-6551-011 umol$54.60
26-6551-032 umol$81.90
26-6551-1010 umol$436.80
26-6551-1515 umol$546.00

Discounts are available for Inverted dA (reverse linkage)!
Modification* Discount Price Structure
1 site/order List price
2 sites/order 10% discount
3 sites/order 20% discount
4 sites/order 30% discount
5-9 sites/order 50% discount
10+ sites/order 60% discount
*Exceptions apply

Related Modifications
3'-dT (2'-5' linked)
Inverted dG (reverse linkage)
Inverted dC (reverse linkage)
3'-dA (2'-5' linked)
3'-dC (2'-5' linked)
3'-rA (2'-5' linked)
3'-dG (2'-5' linked)
Inverted dT (reverse linkage)
Reverse synthesis can be achieved by incorporation modifications where the synthesis orientation can be changed as desired. Oligo can be designed for the production of 5'-5' or 3'-3' linkages or a combination of these in the same oligo. These modified phosphodiester linkage modified oligos are useful in antisense studies, or to synthesize oligonucleotide segments in the opposite sense from normal synthesis, for structural studies.

The CE phosphoramidite of 5'-3' reverse dA has the dimethoxytrityl (DMT) and phosphoramidite groups reversed from the normal case, that is, the DMT-group is attached to the 3'-OH, and the phosphoramidite attached to the 5'-OH, of the ribose. This reverse configuration allows for oligonucleotide synthesis in the 5' to 3' direction (instead of the standard 3' to 5' direction). Reverse synthesis is advisable in the following cases:

1. Formation of oligos containing hairpin loops with parallel strands. Oligos with hairpin loops are used for structural studies into duplex formation. Typically the strands of the stem of the hairpin are anti-parallel. However, by switching to 5'-phosphoramidites for part of the synthesis of such an oligo (for example, initiating the switch during synthesis of the loop portion of the hairpin), the strands of the hairpin stem will be in parallel orientation (1).

2. Formation of nuclease resistant (5'-5', 3'-3') linkages. Anti-sense oligos containing terminal 5'-5' or 3'-3' linkages are highly resistant to exonuclease degradation. For the terminal 5'-5' linkage, the appropriate 5'-phosphoramidite is incorporated at the 5'-end in the final synthesis cycle. For the terminal 3'-3' linkage, the appropriate deoxynucleoside-5'-CPG is used as the solid support for the 3'-end, followed by synthesis of the oligo in the standard 3'-5' direction to make the terminal 3'-3' linkage (2).

Having a single inverted base at the 3' position with a 3'-3' linkage imparts the oligo exonuclease resistance and prevents extension by polymerases as there is no free 3' hydroxyl group to initiate synthesis.

3. 3'-terminal base/moiety cannot be attached to a CPG. Examples include 2',3'-ddT or ddI.

References
1. van de Sande, J.H., Ramsing, N.B., Germann, M.W., Flhorstn, W., Kalisch, B.W., Clegg, R.C., Pon, R.T., Jovin, T.M. Parallel-Stranded DNA. Science (1988), 241: 551-557.
2. Ortigao, J.F.R., Rosch, H., Selter, H., Frohlich, A., Lorenz, A., Montenarh, M., Seliger, H. Antisense effect of oligodeoxynucleotides with inverted terminal internucleotidic linkages: a minimal modification protecting against nucleolytic degradation.Antisense Res. Dev. (1992), 2: 129-146.
Email
Question

Enter the letters you see above for verification:
Order Status | Customer Service | Site Map | Request Literature | About e-oligos | Contact Us |   Search
July 17, 2019 e-oligos(tm) is a brand of Gene Link. e-oligos(tm) and the binary helix(tm) All graphic art is a trade mark of Gene Link, Inc. Copyright 2019
    Terms and Conditions    Licenses    Privacy Policy