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 applicationDuplex stability studies 
 N4-Et-dC 5-Me-dCdI dU 
Applied Biosystems/AKTA SynthesizerCustom orders available.
Request quote		27-1748-0427-1744-0427-1738-03
Expedite Synthesizer
Request quote27-1744-1027-1738-08

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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 N4-Et-dC CEP5-Me-dC CEPdI CEPdU CEP
Cat. No.27-174327-174827-174427-1738
Phosphoramidite description5′-O-(4,4'-dimethoxytrityl)-N4-ethyl-2′-deoxycytidine-3′-O-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite5′-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
FormulaC41H52N5O7PC47H54N5O8PC40H47N6O7PC39H47N4O8P
Molecular weight757.85 g/mol847.95 g/mol754.8 g/mol730.8 g/mol
CAS #195535-80-9105931-57-5141684-35-7109389-30-2
Solution clarityFree from undissolved particulate at 0.2 M in ACNNA
HPLC purity≥98.0%≥98.0%≥98.0%≥98.0%
31P NMR purity≥98.0%≥98.0%≥98.0%≥98.0%
Water contentNA≤0.3% 
Shipping / storage conditionAmbient / –20°C
Material originNonanimal 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

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.

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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 applicationMutagenesis studies
 N6-Me-dA CEP8-oxo-dG CEPReverse abasic CEP
Applied Biosystems/AKTA SynthesizerCustom orders available
Request quote		27-1424-04Custom 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.

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 N6-Me-dA CEP8-oxo-dG CEPReverse abasic CEP
Cat. No.27-174627-142427-1998
Amidite description5′-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)]-phosphoramidite3-O-(4,4’-dimethoxytrityl)-1,4-anhydro-2-deoxy-D-ribitol-5-O-(β-cyanoethyl-N,N-diisopropyl)
FormulaC41H50N7O6PC44H54N7O9P

C35H45N2O6P

Molecular weight767.9 g/mol855.9 g/mol620.72 g/mol
CAS #105931-58-6143060-53-1NA
Solution clarityFree from undissolved particulate at 0.1 M in ACNFree 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 conditionAmbient / –20°C
Material originNonanimal 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

Compatible catalog product is ready-to-ship in amber bottles with serum vial neck style.

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Resources

Phosphoramidite Learning Resource

Access webinars, videos, articles, and more to optimize your success in oligonucleotide synthesis for diagnostic and therapeutic manufacturing process development.

mRNA Production Learning Library

Browse the educational assets related to raw materials selection, process development using in vitro transcription, scale-up synthesis, and the latest trends in mRNA production.

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