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-dCRequest quote
5-Me-dC✓
 
dI✓✓
dU✓✓
N6-Me-dARequest quote
8-oxo-dG✓Request quote
Reverse abasicRequest 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.

Chemical structures and technical specifications

  Click images to enlarge

 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 ACN  NA
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)

Ordering information

Applied Biosystems and AKTA synthesizer (serum vial) compatible products
Expedite synthesizer compatible products

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.

Chemical structures and technical specifications

  Click images to enlarge

 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)

Ordering information

Applied Biosystems and AKTA synthesizer (serum vial) compatible products

For quotes, flexible/bulk packaging, custom services, or items not listed above, please contact us or submit your inquiry

Resources

For Research Use Only. Not for use in diagnostic procedures.