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dT-5' CE-Phosphoramidite

dT-5' CE-Phosphoramidite

CAS No.:134031-86-0

Phosphoramidite for incorporation of an (otherwise unmodified) reverse (5’ to 3’) dT nucleobase within an oligonucleotide.
  • Stringent QC includes testing for synthesis coupling efficiency
  • Available pre-packaged for common synthesizers
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Product information

The chemical synthesis of DNA using the phosphoramidite method proceeds in a 3’ to 5’ direction principally as a consequence of the use of building blocks activated as 3'-O-phosphoramidites. The primary 5'-OH group is significantly more reactive than the secondary 3'-OH (or 2'-OH) group, making it straightforward to protect with the DMT group leaving the 3'-OH available to form the phosphoramidite. In contrast, ‘reverse’ oligonucleotide synthesis (i.e. in a 5’ to 3’ direction) has not been utilised to nearly the same extent.

Nevertheless, there are several applications of this chemistry, most notably in nuclease resistance.

An interesting addition to the protection of antisense oligonucleotides is to modify the terminal linkages from the natural 3'-5’ to 3'-3’ and/or 5'-5’ linkages. In this way, the oligonucleotides are protected against exonuclease activity, especially 3'-exonuclease activity which is by far the most significant enzymatic degradation route, resulting in nucleosides with no toxicity concerns. This strategy has been applied by Beaucage and co-workers who have used 5'-O-phosphoramidites in the formation of oligonucleotides having alternating 3'-3’ and 5'-5’ linkages to maintain effective hybridisation. (1) A simpler approach is in fact to modify only the linkage at the 3’ terminus. (2) This is conveniently carried out and results in effective resistance with minimal disruption to hybridisation.

We provide a range of 5'-3’ “reverse” (or “inverse”) phosphoramidites and CPGs, with a variety of pore sizes and linkers consistent with our unmodified DNA and RNA CPG products. The protecting group strategies are compatible with the usual DNA and RNA chemistries.

Ref:

  1. (a) Alternating α,β-oligothymidylates with alternating (3'-3’)- and (5'-5’)-internucleotidic phosphodiester linkages as models for antisense oligodeoxyribonucleotides, M. Koga, M.F. Moore and S.L. Beaucage, J. Org. Chem., 56, 3757-3759, 1991; (b) Synthesis and physicochemical properties of alternating α,β- oligodeoxyribonucleotides with alternating (3'-3’)- and (5'-5’)-internucleotidic phosphodiester linkages, M. Koga, A. Wilk, M.F. Moore, C.L. Scremin, L. Zhou and S.L. Beaucage, J. Org. Chem., 60, 1520-1530, 1995.
  2. (a) Antisense effect of oligodeoxynucleotides with inverted terminal internucleotidic linkages: a minimal modification protecting against nucleolytic degradation, J.F.R. Ortigao, H. Rosch, H. Selter, A. Frohlich, A. Lorenz, M. Montenarh and H. Seliger, Antisense Res. & Dev., 2, 129-146, 1992; (b) Oligonucleotide analogs with terminal 3'-3'-internucleotidic and 5'-5'-internucleotidic linkages as antisense inhibitors of viral gene-expression, H. Seliger, A. Frohlich, M. Montenarh, J.F.R. Ortigao and H. Rosch, Nucleosides & Nucleotides, 10, 469-477, 1991.

Applicable Products

LK2020 dT-5'-CE Phosphoramidite
LK2021 iBu-dG-5'-CE Phosphoramidite
LK2022 Bz-dA-5'-CE Phosphoramidite
LK2023 Bz-dC-5'-CE Phosphoramidite
LK2093 dmf-dG-5'-CE Phosphoramidite
LK2294 dT-5'-SynBase™ CPG 1000/110
LK2298 iBu-dG-5'-SynBase™ CPG 1000/110
LK2355 iBu-dG-5'-SynBase™ CPG 1000/110
LK2356 Bz-dC-5'-SynBase™ CPG 1000/110

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.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

LK2020 C40H49N4O8P 744.83 304.20 3.36 6.71 13.43
LK2021 C44H54N7O8P 839.94 329.21 2.98 5.95 11.91
LK2022 C47H52N7O7P 857.95 313.21 2.91 5.83 11.66
LK2023 C46H52N5O8P 833.93 289.18 3.00 6.00 11.99
LK2093 C43H53N8O7P 824.92 329.21 3.03 6.06 12.12
LK2294 - - 304.20 - - -
LK2298 - - 329.21 - - -
LK2355 - - 313.21 - - -
LK2356 - - 289.18 - - -

Coupling

No changes are required from the standard method recommended by the synthesiser manufacturer. Coupling is as per standard nucleoside amidites and supports.

Cleavage & Deprotection

Standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo synthesised using these products.

Storage & Stability

All phosphoramidites are stored refrigerated at a maximum of 2-8°C. Their stability in solution is the same as standard dA, dC, dG and dT phosphoramidites. CPGs are stored in the fridge or freezer.

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