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5'-TFA-Amino C6 Modifier (TFA-6-Aminohexyl Amidite)

5'-TFA-Amino C6 Modifier (TFA-6-Aminohexyl Amidite)

Phosphoramidite for the incorporation of an amino function at the 5' end of an oligonucleotide.
  • Incorporates primary amine to 5' end of an oligonucleotide, for subsequent conjugation.
  • Base labile trifluoroacetate (TFA) group useful where purifcation "handle" is not necessary.
  • The shorter C6 linker may be used to attach compounds where proximity to the oligonucleotide causes no problem.
Item ID NACG1-021
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Product information

Incorporation of a primary amine reactive functional group at specific sites within an oligonucleotide allows for subsequent post-synthesis conjugation of the oligo with a number of different affinity, reporter or protein labels, depending on the application. Such labels need to be reactive towards the incorporated functional group: for example, NHS esters or isothiocyanates will react with primary amines. This approach is often necessary where the desired label or tag is either not available as a phosphoramidite, or is sensitive or unstable to the conditions of oligonucleotide synthesis or deprotection. A common example is the attachment of a rhodamine dye using the TAMRA NHS ester. Functionally-derivatised oligos can also be covalently attached to surfaces such as glass slides or gold microspheres for use in various microarray or nanoelectronic applications. One of the most common modifications is the incorporation of a primary amine at the 5'-terminus of the oligonucleotide using an ‘amino-linker’ phosphoramidite, protected with either the base labile trifluoroacetate (TFA) or the acid-labile monomethoxytrityl (MMT) groups. The choice between the MMT and TFA-protected amino modifiers is dependent on the purification strategy used on the oligo, or whether on-column or solution-phase conjugation is required. If the oligo is purified, the MMT protection is preferable since the trityl group, stable to the basic cleavage and deprotection conditions, can be used as a ‘handle’ in e.g. cartridge purification where the MMT group is removed during the purification process. Otherwise, the TFA protection is perfectly suitable. The MMT group can also be removed by extended deblocking on the synthesizer, allowing a solid-phase conjugation of a label containing e.g. an activated carboxylic acid. However, in this case it is important to remember that the conjugate must be stable to the subsequent cleavage and deprotection conditions. The shorter C5 or C6 carbon chain linkers may be used to attach compounds where proximity to the oligonucleotide causes no problem. The longer C12 analogue has specific applications in e.g. affinity chromatography, where the oligo must be sufficiently distanced from the surface, and in some cases labelling with fluorescent tags, where close interaction may lead to partially quenched fluorescence.


  • Formula: C17H31F3N3O3P
  • Molecular Weight: 413.42
  • Appearance: colorless oil

Product usage:

  • Dilution: 100 µmol/mL
  • Deprotection conditions: The deprotecting conditions for this amidite will be depend on the types of amidites used for the synthesis of the oligo. If using fast deprotecting amidites deprotect in concentrated NH4OH for 1 hour at 60°C. If using standard amidites deprotect in concentrated NH4OH for 5 hours at 60°C. The TFA group will be eliminated during ammonia deprotection.
  • The base labile protecting group comes off during ammonia deprotection. The crude functionalized 5’ amine oligo may be reacted with the labeling compound and then purified using RP Cartridge purification.Image of cleaved and deprotected structure:

Storage and handling:

  • Storage conditions: -20 °C, desiccated

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