What are Label Phosphoramidites and Their Applications?

What are Label Phosphoramidites?

Label Phosphoramidites are a class of chemical reagents used in DNA and RNA synthesis to introduce various markers or modifying components into the nucleic acid sequence. These markers can include molecules such as biotin, amino groups, other functional groups, etc. that provide specific properties or detection capabilities to the synthesized nucleic acids. Since labeled phosphoramidites have a phosphoramidite group, this allows them to react with the hydroxyl group of the nucleotide structural unit. Labeled phosphoramidites are usually added at specific positions in an oligonucleotide sequence for site-specific labeling.

Types of Labeled Phosphoramidites

• Biotin Phosphoramidites

Biotin is a small molecule that binds specifically to streptavidin or affinin. Biotin phosphoramidite contains a DMT group that allows quantitative coupling. It is soluble in acetonitrile and provides a valuable tool for adding biotin tags to the 3' or 5' position of an oligonucleotide sequence. Biotin phosphoramidite contains a 15-atomic spacer arm that minimizes potential barriers to biotin binding. It is complementary to commonly used biotin phosphoramidites that do not contain a DMT group and can only be added at the 5'-end, thus terminating synthesis.

• Spacer Phosphoramidite

Spacer phosphoramidites are used to place spacer arms into oligonucleotides. C3, C6, and C12 spacer phosphoramidites contain aliphatic junctions and can be added to oligonucleotides that require long spacer arms. Typically, spacer phosphoramidites are used during oligonucleotide synthesis to introduce spacers into the sequence, bridging the parts of the oligonucleotide.

• Amino Junction Phosphoramidites

Aminojunction products can be coupled to standard synthesis schemes, such as DNA monomeric phosphoramidite coupling schemes. The base-unstable TFA group is easily cleaved by concentrated ammonia during cleavage and deprotection steps. No additional deprotection step is required. Using an acidic decontainment solution, the DMT moiety can be cleaved more readily than the MMT moiety on a synthetic apparatus for supportive labeling schemes. 5'-DMT amino junctions can be handled by normal deprotection and cleavage methods.

• Other Functional Phosphoramidites

Specialized phosphoramidites can be used to dope other functional groups than those described above, such as cholesterol, phosphates, etc. These functional groups enable specific chemical reactions and downstream applications, such as affixation to other molecules or surface immobilization.

Characteristics of Labeled Phosphoramidites

• Selectable Markers

Labeled phosphoramidites can selectively introduce specific markers or modifying groups to specific positions in the DNA or RNA strand.

• Tunable Labeling Density

By adjusting the amount of labeled phosphoramidite input, the density of the marker in the nucleic acid chain can be controlled. This is important for experiments and applications that require precise control of the amount of marker.

• Compatibility

The use of labeled phosphoramidites in DNA and RNA synthesis is compatible with conventional synthesis methods and does not significantly affect the process of amplification and extension of the nucleic acid chain.

Application areas for Labeled Phosphoramidites

• Molecular Diagnostics

The introduction of specific markers, such as biotin, enables highly sensitive and specific molecular assays.

• Genomics and Genetics

Genotype analysis, gene expression analysis, mutation detection, etc. can be realized by introducing markers.

• Biochip Technology

Through the introduction of markers, high-throughput nucleic acid detection and analysis can be realized, such as gene expression microarrays, SNP typing microarrays and so on.