| Overview - (Click on Methods for greater detail) |
| Fast Deprotection Methods |
Monomers |
Cleavage and Deprotection Reagents |
Time/Temperature |
|
TAC Chemistry |
dA(tac), dC(tac), dG(tac), dT |
Concentrated ammonia* |
15 min. at 55°C or
2 hrs. at room temp. |
| AMA reagent** |
5 min. at 65°C or
30 min. at room temp. |
dG(dmf) Method
View Structure |
dA(bz), dC(bz), dG(dmf), dT |
Concentrated ammonia* |
2 hrs at 55°C or
1 hr. at 65°C |
Substitution of dC(bz) with dC(tac)
View Structure |
dA(bz), dC(tac), dG(ib), dT |
AMA reagent** |
10 min. at 65°C |
| * ≥ 25% ammonia in water |
| ** Mixture of ≥ 25% ammonia in water with 40% aqueous methylamine I/I, v/v |
1. TAC Chemistry |
Substitution of standard protecting groups with the labile TAC (tert.butylphenoxyacetyl) protecting group results in ultra-fast and easy deprotection under mild conditions, suitable for oligonucleotides with base-labile monomers and reporters as well as in-situ synthesis schemes on glass surfaces.
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| Key features of TAC Chemistry. |
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Deprotection of the TAC group is ultra-fast: complete deprotection in concentrated ammonia occurs within 15 minutes at 55°C or two hours at room temperature |
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TAC protecting groups are compatible with the AMA deprotection reagent (a mixture of ≥ 25% ammonia in water with 40% aqueous methylamine I/I, v/v) |
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TAC protected amidites are highly soluble in acetonitrile. There is no need to add co-solvents such as dimethylformamide or methylene chloride |
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TAC monomers are suitable for the synthesis of oligomers with base-labile units e.g. dyes and modifiers, because of less exposure to ammonia and the possibility of room temperature deprotection |
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No change is required in the reagents commonly used for DNA synthesis, except that Proligo Reagents’ Fast Deprotection CAP A solution is used instead of Cap A solution |
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The application of dA(tac) minimizes depurination and improves the quality of oligonucleotides |
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2. dG(dmf) Method |
Changing the dG protecting group to the dimethylformamidine (dmf) base-protecting group enables rapid synthesis of high-purity, high-yield oligonucleotide, thus increasing the efficiency of high-throughput production.
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| Key Features of dG(dmf) |
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dG(dmf) is deprotected faster than the conventional dG(ib): the deprotection time in concentrated ammonia is reduced to 2 hours at 55°C or 1 hour at 65°C |
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The dG(dmf)-monomer is especially suitable for G-rich sequences: incomplete deprotection is greatly reduced in comparison with the conventional dG(ib)-monomer |
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dG(dmf)-amidite is as stable in solution as the standard dA(bz)-, dC(bz)- and dT-amidites. |
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dG(dmf)-amidite can directly substitute for dG(ib)-amidite |
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No change is required in the reagents commonly used for DNA synthesis (except a low concentration iodine oxidizer i.e. 0.02M in iodine, should be employed) |
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3. Substituting the dC Protecting Group |
Changing the dC protecting group to the TAC protecting group leads to rapid synthesis of high-purity and high-yield oligonucleotides. Substituting the commonly employed dC(bz) monomer by the dC(tac) monomer enables the application of ultra-fast deprotection with the AMA reagent and provides a high-throughput method of oligonucleotide synthesis.
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| Key Features of Substituting the dC Protecting Group |
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The deprotection of oligonucleotide synthesis products with the AMA reagent is ultra-fast: complete deprotection requires 10 minutes at 65°C |
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Side reactions at C-monomers through transamination are eliminated |
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Not compatible with some base-labile modified nucleosides |
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dC(tac)-amidite can directly substitute for dC(bz)-amidite |
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No change is required in the reagents commonly used for DNA synthesis: acetonitrile is used to dissolve the amidite. The standard acetic anhydride capping reagent can be employed |
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| FAST Deprotection Phosphoramidites |
| Compatible with Expedite™ and Polygen® Instruments |
| Product No. |
Description |
Unit |
| A112081-12 |
DMT-dA(tac) amidite |
12 × 1 g |
| A112082-12 |
DMT-dA(tac) amidite |
12 × 2 g |
| C112081-12 |
DMT-dC(tac) amidite |
12 × 1 g |
| C112082-12 |
DMT-dC(tac) amidite |
12 × 2 g |
| G115081-12 |
DMT-dG(dmf) amidite |
12 × 1 g |
| G115082-12 |
DMT-dG(dmf) amidite |
12 × 2 g |
| G112081-12 |
DMT-dG(tac) amidite |
12 × 1 g |
| G112082-12 |
DMT-dG(tac) amidite |
12 × 2 g |
| Compatible with ABI™ Instruments |
| Product No. |
Description |
Unit |
| A112031-12 |
DMT-dA(tac) amidite |
12 × 1 g |
| A112032-12 |
DMT-dA(tac) amidite |
12 × 2 g |
| C112031-12 |
DMT-dC(tac) amidite |
12 × 1 g |
| C112032-12 |
DMT-dC(tac) amidite |
12 × 2 g |
| G115031-12 |
DMT-dG(dmf) amidite |
12 × 1 g |
| G115032-12 |
DMT-dG(dmf) amidite |
12 × 2 g |
| G112031-12 |
DMT-dG(tac) amidite |
12 × 1 g |
| G112032-12 |
DMT-dG(tac) amidite |
12 × 2 g |
| Compatible with MerMade™ Instruments (8oz 28/400 bottle) |
| Product No. |
Description |
Unit |
| C112081-12 |
DMT-dC(tac) amidite |
12 × 1 g |
| C112082-12 |
DMT-dC(tac) amidite |
12 × 2 g |
| G115028-06 |
DMT-dG(dmf) amidite |
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| Compatible with AKTA™ oligopilot Instruments (100ml septum bottle) |
| Product No. |
Description |
Unit |
| A112010-01 |
DMT-dA(tac) amidite |
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| C112010-01 |
DMT-dC(tac) amidite |
10 g |
| C112020-06 |
DMT-dC(tac) amidite |
6 × 20 g |
| G115005-01 |
DMT-dG(dmf) amidite |
5 g |
| G112010-01 |
DMT-dG(tac) amidite |
| Bulk Quantities (16oz 28/400 bottle) |
| Product No. |
Description |
Unit |
| C112010-01 |
DMT-dC(tac) amidite |
10 g |
| C112020-06 |
DMT-dC(tac) amidite |
6 × 20 g |
| G115021-06 |
DMT-dC(tac) amidite |
6 × 10g |
| FAST Deprotection CPG |
| Product No. |
Description |
Unit |
| |
500 Å, extent of labeling: 30-40 μmol/g |
| A302001-01 |
dA(tac)-CPG |
|
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1000 Å, extent of labeling: 25-35 μmol/g |
| A402001-01 |
dA(tac)-CPG |
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500 Å, extent of labeling: 30-40 μmol/g |
| C302001-01 |
dC(tac)-CPG |
1 g |
| C302010-01 |
dC(tac)-CPG |
10 g |
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500 Å, extent of labeling: 30-40 μmol/g |
| G305001-01 |
dG(dmf)-CPG |
1 g |
| G305010-01 |
dG(dmf)-CPG |
10 g |
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500 Å, extent of labeling: 30-40 μmol/g |
| G302001-01 |
dG(tac)-CPG |
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1000 Å, extent of labeling: 25-35 μmol/g |
| G402001-01 |
dG(tac)-CPG |
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SAFC and SAFC Proligo Reagents are trademarks of Sigma-Aldrich Biotechnology, LP.
©2006 Sigma-Aldrich Biotechnology LP. All rights reserved. Reproduction forbidden without permission.
Other trademarks are the property of their respective owners. |
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