Linker Phosphoramidites

Linker Phosphoramidites

Molecular Formula: C16H29F3N3O3P Molecular Weight: 399.39 g/mol
Molecular Formula: C39H46N3O7P Molecular Weight: 699.78 g/mol
Molecular Formula: C38H53N4O5P Molecular Weight: 676.83 g/mol
CAS: 114616-27-2 Molecular Formula: C35H48N3O3P Molecular Weight: 589.75
CAS: 133975-85-6 Molecular Formula: C17H31F3N3O3P Molecular Weight: 413.42

BOC RNA provides linker phosphoramidites used for DNA/RNA synthesis. Use an amino linker to conjugate biotin, fluorescein, or other modifiers and a reporter group to the 5'end of the oligonucleotide or adheres to the surface.

Advantages of linker phosphoramidites

  • Providing a simple and effective method for preparing multiple oligonucleotides in a single solid-phase synthesis.
  • The cleavage of the linker between phosphoramidite and nucleoside releases products with only 3'-OH ends, and no additional cleavage or 3'-dephosphorylation steps are required.
  • These phosphoramidites can be used in lower concentrations and lower amounts than conventional phosphoramidites to adjust the number of oligonucleotides produced and reduce reagent costs.

Types and applications

As the DNA-based microarrays and multi-label diagnostic systems become increasingly important, the demand for easy preparation of functionalized oligonucleotides is also growing. At present, the most common modification is the primary amine at the 5'end of the oligonucleotide. TFA-protected and MMT-protected 5'-amino modifiers can be used in automatic synthesizers or manual coupling to connect various moieties to 5'-primary amines, including fluorescent dyes, biotin, and EDTA.

  • Monomethoxytrityl (MMT) protected amino linker
  • The acid-labile MMT protecting group is stable to basic cleavage and deprotection conditions and can be used as a "handle" for analysis in RP high-performance liquid chromatography to easily separate oligonucleotides from failed sequences. The MMT group is then removed using acidic conditions.

    The MMT linker is the best choice when purification by reversed-phase technique is required.

  • Trifluoroacetyl (TFA) protected amino linker
  • In the cleavage and deprotection steps, the alkali-labile TFA-group can be easily removed with concentrated ammonia. In the case of directly separating amino-modified oligonucleotides from cleaved and deprotected oligonucleotides, base-labile TFA moieties are used.

Main features of amino linkers

  • Completely soluble in acetonitrile
  • The MMT-amino linker has a lipophilic group, which helps to purify modified oligonucleotides after synthesis
  • The acid-labile MMT-group can colorimetrically determine coupling efficiency
  • It is recommended to deprotect the MMT-amino linker oligonucleotide in concentrated ammonia at a lower temperature (e.g., 40°C) for 24 hours
  • The MMT-group can be removed in an 80% acetic acid aqueous solution at room temperature after 24 hours
  • The TFA-amino linker is completely deprotected by concentrated ammonia. No additional deprotection steps required

Quality control

  • The entire process is monitored from material procurement to final quality control and product release, providing repeatability and security between batches
  • Assess the purity of each RNA phosphoramidite batch by HPLC and 31P NMR
  • The manufacturing process is tightly controlled to ensure minimal levels of impurities

Custom services

Custom manufacturing services are available to help develop or expand phosphoramidite compounds.

If you have any questions or requirements, please feel free to contact us.

* Only for research. Not suitable for any diagnostic or therapeutic use.
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