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Structural Phosphoramidites |
Designed for oligonucleotide synthesis for diagnostic research and development
Structural, nonstandard phosphoramidites are 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.
Applications of modified oligonucleotides with structural phosphoramidites
Duplex stability: Stability and melting point of oligonucleotide duplexes can be altered by incorporation of N4-ethyl deoxycytosine (N4-Et-dC), 5-methyl deoxycytosine (5-Me-dC), deoxyinosine (dI), or deoxyurosine (dU) into the oligonucleotide sequence.
Mutagenesis: 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.
Available structural phosphoramidites by synthesizers
| Applied Biosystems/ AKTA synthesizer | Expedite synthesizer | |
|---|---|---|
| N4-Et-dC | Request quote | |
| 5-Me-dC | ✓ | |
| dI | ✓ | ✓ |
| dU | ✓ | ✓ |
| N6-Me-dA | Request quote | |
| 8-oxo-dG | ✓ | Request quote |
| Reverse abasic | Request quote | |
For items not listed above, quotes, flexible/bulk packaging, or custom services, please contact us or submit your inquiry
Our structural phosphoramidites are supported by:
- Technical expertise—over 40 years of partnership, customization, and scale-up experience
- Secure and consistent supply—5x capacity expansion in 2022 to support emerging therapeutics and diagnostic assays
- Service excellence—48 hours or less response to orders, >98% delivery to customer at promised date†
- Flexible packaging—custom and bulk packaging available upon request
- Refined quality—ISO 9001:2015–certified quality management system that has been refined in partnership with our customers since 1995
† May not be applicable in all regions.
Quality manufacturing and documentation
Processes are monitored from material procurement through final QC and product release for batch-to-batch reproducibility. Purity of each phosphoramidite lot may be assessed by HPLC, NMR, and water determination by Karl Fischer methods. Our rigorously controlled manufacturing processes help minimize levels of reactive impurities which could be incorporated into the oligonucleotide during synthesis and result in the accumulation of by-products.
N4-ethyl-dC, 5-methyl-dC, dI, and dU for duplex stability studies
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.
Click images to enlarge
N4-Ethyl-dC CEP
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) | |||
Ordering information
For quotes, flexible/bulk packaging, custom services, or items not listed above, please contact us or submit your inquiry
N6-methyl-dA, 8-oxo-dG, and reverse abasic for mutagenesis studies
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) |
Ordering information
For quotes, flexible/bulk packaging, custom services, or items not listed above, please contact us or submit your inquiry
Resources
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仅供科研使用，不可用于诊断目的。