Structural 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.

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Structural phosphoramidites by synthesizer compatibility

Synthesizer	ABI/AKTA	Expedite	Mermade	Bulk
Specialty	5me-dC	-	Contact us	Contact us
	dI	dI
	dU	dU
	8-oxo-dG	-

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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5-Me-dC CEP

dI CEP

dU CEP

	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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ABI and AKTA Synthesizer (serum vial) Compatible

Expedite Synthesizer Compatible

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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 CEP

N6-Methyl-dA CEP

8-oxo-dG CEP

	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′-O-(4,4'-Dimethoxytrityl)

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ABI and AKTA Synthesizer (serum vial) Compatibility

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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 phosphoramidites, RNA phosphoramidites, dye-labeled phosphoramidites, 2′-modifications, linker and spacer phosphoramidites, and succinates and CPG support synthesis supports. Contact us to learn more!