Specialty Phosphoramidites

Thermo Fisher Scientific offers non-standard, structural phosphoramidites for synthesis of modified oligonucleotides.  Oligos with these modifications can then be used as primers, probes, or in structural studies.

Stability and melting point of oligo duplexes can be altered by incorporation of N4-Ethyl dC, 5-Me dC, dI, or dU into the sequence, while mutagenic effects from methylation of an exocyclic amine can be studied by the incorporation of N6-Me-dA. Similar studies may be performed utilizing 8-oxo-dG, which mimics an oxidized guanine.

Structural phosphoramidites can be custom manufactured with base or sugar (2′, 3′ or 5′ positions) modifications.

Structural phosphoramidites by synthesizer compatibility

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Modified Phosphoramidites - 5-Me-dC, dI, and dU

Thermo Scientific modified nucleoside 5-Me dC, dI, and dU phosphoramidites are used in specialty applications requiring high quality and performance. The unique deoxy-Inosine (dI) phosphoramidite structure facilitates pairing with all four bases, and is often utilized as a degenerate base for oligo probes/primers. 

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Cat. No.27-174827-174427-1738
Phosphoramidite Description5′-O-(4,4'-Dimethoxytrityl)-N4-Benzoyl-5-Methyl-2′-Deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-O-(4,4'-Dimethoxytrityl)-2′-Deoxyinosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-O-(4,4'-Dimethoxytrityl)-2′-Deoxyuridine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
AppearanceColor intensity not to exceed Pantone #P1-4U or #P4-2UNA
Molecular weight847.95 g/mol754.8 g/mol730.8 g/mol
CAS #105931-57-5141684-35-7144385-59-1
Solution ClarityFree from undissolved particulate at 0.2M in ACN  NA
HPLC purity≥ 98%≥ 98.0%≥ 98.0%
31P NMR purity≥ 98%≥ 98%≥ 98.0%
Water content≤ 0.3% (by KF method)
Shipping/Storage conditionAmbient/–20 °C
Material Originnon-animal source (no TSE/BSE risk)

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Modified Phosphoramidites - N6-Me-dA, N4-Ethyl-dC, and 8-oxo-dG

Thermo Scientific modified nucleoside N6-Me-dA, N4-Ethyl-dC, and 8-oxo-dG phosphoramidites are used in specialty applications requiring high quality and performance. Modified phosphoramidites are used to synthesize oligonucleotides with base modifications that can alter the stability and melting point of duplexes.

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 N4-Ethyl-dC CEPN6-Methyl-dA CEP8-oxo-dG CEP
Cat. No.27-174327-174627-1424
Amidite Description5′-O-(4,4'-Dimethoxytrityl)-N4-Ethyl-2′-Deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-O-(4,4'-Dimethoxytrityl)‑N6-Methyl-2′-Deoxyadenosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-O-(4,4'-Dimethoxytrityl)‑N2-isobutyryl-8-oxo-deoxyguanosine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Molecular weight757.85 g/mol767.9 g/mol855.9 g/mol
CAS #195535-80-9105931-58-6143060-53-1
Solution ClarityFree from undissolved particulate at 0.1M in ACN
HPLC purity≥ 98%≥ 98.0%
31P NMR purity≥ 98%≥ 98.0%
Water contentNA≤ 0.3%
Shipping/Storage conditionAmbient/–20 °C
Material Originnon-animal source (no TSE/BSE risk)
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Process and supply chain control

  • A controlled raw material supply chain and established vendor partnerships ensure consistency and security of supply
  • Purity of each phosphoramidite lot is assessed by HPLC and 31P NMR analyses
  • Rigorously controlled manufacturing processes minimize levels of reactive P(III) impurities which could be incorporated into the oligonucleotide and result in the accumulation of by-products
  • Processes are monitored from material procurement through final QC and product release, providing batch-to-batch reproducibility

Flexible packaging

  • Common oligo synthesizer pack sizes are available for immediate delivery
  • Custom and bulk packaging are also available. Contact us to learn more.

Custom services

  • Custom manufacturing services are available to assist in the development or scale-up of phosphoramidite compounds
  • Specialty phosphoramidites can be manufactured with base or sugar (2′, 3′ or 5′ positions) modifications


Not finding what you are looking for? We also offer DNA phosphoramiditesRNA phosphoramiditesdye-labeled phosphoramidites2′-modificationslinker and spacer phosphoramidites, and succinates and CPG support synthesis supportsContact us to learn more!