Specialty Phosphoramidites

Thermo Fisher Scientific offers non-standard, specialty 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. 

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

Biotin-TEG can be placed throughout the oligo (3', 5', or internal) while also having a spacer arm, thereby minimizing steric hindrance between the biotin moiety and the oligo.  5'-Biotin amidite can only be synthesized to the 5′ end of the oligonucleotide. 

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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  5-Me-dC CEP dI CEP dU CEP
Cat. No. 27-1748 27-1744 27-1738
Phosphoramidite Description 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
Appearance Color intensity not to exceed Pantone #P1-4U or #P4-2U NA
Formula C47H54N5O8P C40H47N6O7P C39H47N4O8P
Molecular weight 847.95 g/mol 754.8 g/mol 730.8 g/mol
CAS # 105931-57-5 141684-35-7 144385-59-1
Solution Clarity Free 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 condition Ambient/–20 °C
Material Origin non-animal source (no TSE/BSE risk)
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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 CEP N6-Methyl-dA CEP 8-oxo-dG CEP
Cat. No. 27-1743 27-1746 27-1424
Amidite Description 5′-O-(4,4'-Dimethoxytrityl)-N4-Ethyl-2′-Deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite 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
Formula C41H52N5O7P C41H50N7O6P C44H54N7O9P
Molecular weight 757.85 g/mol 767.9 g/mol 855.9 g/mol
CAS # 195535-80-9 105931-58-6 143060-53-1
Solution Clarity Free from undissolved particulate at 0.1M in ACN
HPLC purity ≥ 98% ≥ 98.0%
31P NMR purity ≥ 98% ≥ 98.0%
Water content NA ≤ 0.3%
Shipping/Storage condition Ambient/–20 °C
Material Origin non-animal source (no TSE/BSE risk)
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  5′-Biotin CEP Biotin TEG CEP
Cat. No. 27-1793 27-1773
Phosphoramidite Description [1-N-(4,4'-Dimethoxytrityl)-biotinyl-6-aminohexyl]-2-cyanoethyl-(N,N-diisopropyl)-phosphoramidite 1-Dimethoxytrityloxy-3-O-(N-biotinyl-3-aminopropyl)-triethyleneglycol-glyceryl-2-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite
Formula C46H64N5O6PS  C52H76N6O11PS
Molecular weight 846.08 g/mol 1010.24 g/mol
Appearance White solid
HPLC purity ≥ 95.0% ≥ 90%
31P NMR purity ≥95.0% N/A
Solution Clarity 0.1M solution in ACN is clear
Shipping / Storage condition Ambient / -20 °C
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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!