N4-Ethyl-dC CEP
Structural phosphoramidites are nonstandard amidites used to synthesize modified oligonucleotides. Oligos with these specialty phosphoramidites are often used as primers, probes, or in structural studies. Structural phosphoramidites can be custom manufactured with base or sugar (2′, 3′, or 5′ positions) modifications.
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N4-ethyl-dC, 5-methyl-dC, dI, and dU for duplex stability studies
The stability and melting point of oligonucleotide duplexes can be altered by incorporating N4-ethyl deoxycytosine (N4-Et-dC), 5-methyl deoxycytosine (5-Me-dC), deoxyinosine (dI), or deoxyurosine (dU) into the oligonucleotide sequence.
Availability by compatible synthesizer model
| Common application | Duplex stability studies | |||
|---|---|---|---|---|
| N4-Et-dC | 5-Me-dC | dI | dU | |
| Applied Biosystems/AKTA Synthesizer | Custom orders available. Request quote | 27-1748-04 | 27-1744-04 | 27-1738-03 |
| Expedite Synthesizer | ||||
| Request quote | 27-1744-10 | 27-1738-08 | ||
Technical specifications for N4-ethyl-dC, 5-methyl-dC, dI, and dU phosphoramidites
Thermo Scientific N4-Et-dC, 5-Me-dC, dI, and dU β-cyanoethyl phosphoramidites (CEP) are used in specialty applications such as duplex stability studies. Thermo Scientific dI CEP facilitates pairing with all four bases as a degenerate base in oligo probes and primers and can also provide the oligos nuclease resistance.
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5-Me-dC CEP
dI CEP
dU CEP
| N4-Et-dC CEP | 5-Me-dC CEP | dI CEP | dU CEP | |
|---|---|---|---|---|
| Cat. No. | 27-1743 | 27-1748 | 27-1744 | 27-1738 |
| Phosphoramidite description | 5′-O-(4,4'-dimethoxytrityl)-N4-ethyl-2′-deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | 5′-O-(4,4'-dimethoxytrityl)-N4-benzoyl-5-methyl-2′-deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | 5′-O-(4,4'-dimethoxytrityl)-2′-deoxyinosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | 5′-O-(4,4'-dimethoxytrityl)-2′-deoxyuridine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| Formula | C41H52N5O7P | C47H54N5O8P | C40H47N6O7P | C39H47N4O8P |
| Molecular weight | 757.85 g/mol | 847.95 g/mol | 754.8 g/mol | 730.8 g/mol |
| CAS # | 195535-80-9 | 105931-57-5 | 141684-35-7 | 109389-30-2 |
| Solution clarity | Free from undissolved particulate at 0.2 M in ACN | NA | ||
| HPLC purity | ≥98.0% | ≥98.0% | ≥98.0% | ≥98.0% |
| 31P NMR purity | ≥98.0% | ≥98.0% | ≥98.0% | ≥98.0% |
| Water content | NA | ≤0.3% | ||
| Shipping / storage condition | Ambient / –20°C | |||
| Material origin | Nonanimal source (no TSE/BSE risk) | |||
Compatible products by synthesizer model
Structural phosphoramidites for duplex stability are compatible with the following oligonucleotide synthesizers:
- Applied Biosystems and AKTA Synthesizer
- Expedite Synthesizer: Custom order only; contact us for a quote
Applied Biosystems and AKTA synthesizer
Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.
Expedite synthesizer
Available catalog SKU is supplied in 30 mL amber bottle with a 20-400 finish neck style.
N6-methyl-dA, 8-oxo-dG, and reverse abasic phosphoramidites for mutagenesis studies
Mutagenic effects from methylation of exocyclic amine can be studied by incorporation of N6-methyl deoxyadenosine (N6-Me-dA) into the oligonucleotide sequence. Similar studies may be performed with 8-oxo-2'-deoxyguanosine (8-oxo-dG), which mimics an oxidized guanine, and reverse abasic, which introduces abasic sites.
Availability by compatible synthesizer model
| Common application | Mutagenesis studies | ||
|---|---|---|---|
| N6-Me-dA CEP | 8-oxo-dG CEP | Reverse abasic CEP | |
| Applied Biosystems/AKTA Synthesizer | Custom orders available Request quote | 27-1424-04 | Custom orders are available Request quote |
| Expedite Synthesizer | |||
| Request quote | |||
Technical specifications for N6-methyl-dA, 8-oxo-dG, and reverse abasic phosphoramidites
Thermo Scientific N6-Me-dA, 8-oxo-dG, and reverse abasic phosphoramidites are used to synthesize oligonucleotides with base modifications for mutagenesis studies.
Click images to enlarge
N6-Methyl-dA CEP
8-oxo-dG CEP
Reverse abasic CEP
| N6-Me-dA CEP | 8-oxo-dG CEP | Reverse abasic CEP | |
|---|---|---|---|
| Cat. No. | 27-1746 | 27-1424 | 27-1998 |
| Amidite description | 5′-O-(4,4'-dimethoxytrityl)‑N6-methyl-2′-deoxyadenosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | 5′-O-(4,4'-dimethoxytrityl)‑N2-isobutyryl-8-oxo-deoxyguanosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | 3-O-(4,4’-dimethoxytrityl)-1,4-anhydro-2-deoxy-D-ribitol-5-O-(β-cyanoethyl-N,N-diisopropyl) |
| Formula | C41H50N7O6P | C44H54N7O9P | C35H45N2O6P |
| Molecular weight | 767.9 g/mol | 855.9 g/mol | 620.72 g/mol |
| CAS # | 105931-58-6 | 143060-53-1 | NA |
| Solution clarity | Free from undissolved particulate at 0.1 M in ACN | Free from undissolved particulate at 0.2 M in ACN | |
| HPLC purity | ≥98.0% | ≥98.0% | ≥98.0% |
| 31P NMR purity | ≥98.0% | ≥98.0% | ≥98.0% |
| Water content | NA | ≤0.3% | ≤0.5% |
| Shipping / storage condition | Ambient / –20°C | ||
| Material origin | Nonanimal source (no TSE/BSE risk) | ||
| 5′-O-(4,4'-Dimethoxytrityl) |
Compatible products by synthesizer model
Structural phosphoramidites for duplex stability are compatible with the following oligonucleotide synthesizers:
- Applied Biosystems and AKTA Synthesizer
- Expedite Synthesizer: Custom order only; contact us for a quote
Applied Biosystems and AKTA synthesizer
Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.
Looking for additional size options, customization, or packaging solutions?
For Research Use Only. Not for use in diagnostic procedures.
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