Phosphoramidites (often abbreviated as amidites) are building blocks used in chemical synthesis of oligonucleotides. Automated oligo synthesizers complete sequential chemical reactions using phosphoramidites to produce the nucleotide chains of synthetic oligos. Typically, oligo synthesizers add phosphoramidites from the 3′ to 5′ direction, the opposite of enzymatic synthesis. One advantage of synthesizing oligonucleotides chemically is that modifications or labeling of the building blocks necessary for final oligo function can be introduced easily.

Thermo Fisher Scientific offers a broad range of phosphoramidites, which 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 enable emerging diagnostic assays and oligo therapeutics
  • 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
  • Quality manufacturing and documentation—batch-to-batch consistency, minimal level of reactive impurities, and analytical documentation support
  • Refined quality—ISO 9001:2015–certified quality management system that has been refined in partnership with our customers since 1995

* May not be available in all regions

Quick tour of our manufacturing facility for phosphoramidites

At the Thermo Fisher facility in Milwaukee (WI, USA), we have been customizing and scaling up high-quality phosphoramidites for oligonucleotide synthesis, for over 40 years.


Purpose-built Thermo Scientific phosphoramidites

Explore the following categories of phosphoramidites to fit your varying needs of oligonucleotide manufacturing for the development of therapeutic, diagnostic, and research applications.

DNA amidite structure on teal background

DNA phosphoramidites

Find phosphoramidites with deoxyribonucleobases for synthesis of DNA oligos for diagnostic assays and therapeutic applications.

RNA amidites structure on teal background

RNA phosphoramidites

Find phosphoramidites with ribonucleobases for synthesis of RNA oligos for diagnostic assays and therapeutic applications.

2’ modified amidite structure on teal background

2′ modified phosphoramidites

Find phosphoramidites with common base modifications—such as 2′-MOE, 2′-OMe, and 2′-fluoro—for synthesis of antisense oligos and siRNAs for therapeutic applications.

Dye-labeled amidite structure on teal background

Dye-labeled phosphoramidites

Find phosphoramidites with fluorescent labels for synthesis of oligos for detection in molecular assays and microarrays.

Structural amidite structure on teal background

Structural phosphoramidites

Find phosphoramidites with modifications (e.g., 5m-dC, N6-Me-dA, N4-Ethyl-dC, 8-oxo-dG) for synthesis of primers, probes, or oligos for structural and mutagenesis studies.

Linker and spacer amidite structure on teal background

Linkers and spacers

Find phosphoramidites with linkers at 3′, 5′, or internal positions for NHS ester conjugation; and spacers to increase the distance between functional groups as well as to provide conformational support.

Succinate amidite structure on teal background

Succinates

Find DNA succinates for the derivatization of controlled pore glass, polystyrene, or other supports used in solid-phase oligo synthesis.


Options for base protection groups and package formats

Depending on your selected phosphoramidites, they may be available in one or more of these options. Please contact us if you do not find one that meets your needs.

Base N-protections to choose depending on your deprotection methods, their sensitivity to base hydrolysis, and their reactivity with tags and labels:

  • Benzoyl (Bz)
  • Isobutyryl (iBu)
  • Isopropyl-phenoxyacetyl (iPrPAC)
  • Phenoxyacetyl (PAC)
  • Acetyl (Ac)
  • Dimethylamino-formamidine (DMF)
  • No base protection

Package formats to accommodate your synthesis scales, synthesizers, and solvation methods:

  • Synthesizers 
    • Applied Biosystems synthesizer, AKTA synthesizer, MerMade synthesizer, Expedite synthesizer, and others
  • Capping
    • Screw cap, serum vial, bulk options, among others
  • Threading finish and neck size
    • GL-45, 38/430, 20 mm, 28/400, and more
  • Fill volumes
    • From 1 mg to 15 kg
  • Packaging materials
    • Borosilicate glass; glass type I, II, and III; HDPE; PETG; and more
Examples of some available packaging options
2 mL Sarstedt
skirted screw cap tube		10 mL
serum vial		125 mL screw
cap glass bottle		1 L polyethylene
terephthalate (PETG)
bottle		10 L NOWPak
stainless steel
container		5 gallon
plastic pail
Small metal screw cap tubeAmber serum vail with rubber capAmber screw cap, narrow-neck glass bottleClear square plastic bottle with white capCylindrical stainless steel containerWhite square plastic pail

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Custom services for oligonucleotide chemistry

In addition to our Thermo Scientific phosphoramidites, we offer custom services for oligonucleotide chemistry tailored to fit your needs in diagnostic and therapeutic applications. We are fully set up to provide customization of our existing phosphoramidites, synthesis of new compounds, and development of oligonucleotide delivery chemistries. Simply fill out this short form with your interest so that our representative can explore available options with you.

Advanced project management
  • Customer involvement 
  • Dedicated cross-functional project team
  • Project planning and execution tailored to each custom request
  • Manufactured in an ISO 9001–registered facility
  • Thoroughly documented processes provide consistent product quality with batch-to-batch consistency
Customization options
  • Base or base protection modification
  • Sugar modifications
  • Changes to phosphitylation, or phosphitylation of custom molecules
  • 5′ protection modification
Custom chemistries and capabilities
  • Chemistries: phosphoramidite and custom organics
  • Modifiers and linkers
  • R&D to large-scale manufacturing
  • Development of customized QC
  • Customer-driven specifications
  • Custom filling, labeling, and packaging
Phosphoramidite structure with customization options 



Phosphoramidite customization options

A. Dimethoxytrityl (DMT) substitution with alternate protecting groups

B. Base = A, C, G, T, or U protection modifications or base modifications

C. Sugar modifications and protection options

Request custom services

TheraPure services—access to customized materials for producing nucleic acid therapeutics

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Hear our scientists discuss Thermo Fisher's Milwaukee facility history, customer partnership, manufacturing process, quality improvement, mitigation of supply chain issues, and our recent response to global needs.

Related solutions: Oligonucleotide synthesis service | Oligonucleotide analysis tools

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