Dimer phosphoramidites are chemically synthesized dinucleotides—two nucleoside units covalently linked via a phosphodiester bond and equipped with a 3'-phosphoramidite group for coupling to a growing oligonucleotide chain. These reagents are strategically used in solid-phase RNA synthesis to bypass the sequential addition of individual monomers, thereby reducing the number of synthetic steps and minimizing cumulative side reactions such as depurination and strand scission.
The general structure of a dimer phosphoramidite includes two ribonucleotides with protective groups at the 2'-hydroxyl (commonly TBDMS or TOM), a 5'-DMT group on the terminal nucleotide, and a 3'-phosphoramidite group suitable for chain elongation. These dimers deliver better coupling results while producing higher purity products, which is especially beneficial for synthesizing complex or lengthy RNA sequences.
Figure 1. A practical approach to dinucleotide phosphoramidite chemistry for de novo DNA synthesis[1].
In solid-phase RNA synthesis, each nucleotide addition cycle involves multiple steps: deprotection, activation, coupling, capping, and oxidation. By using dimer or trimer phosphoramidites instead of monomers, multiple nucleotides can be added in a single coupling step. This reduces the total number of cycles required and correspondingly lowers the chance of incomplete coupling or side product formation.
| Comparison | Monomer Phosphoramidites | Dimer/Trimer Phosphoramidites |
| Coupling steps per 30-mer | ~29 | ~15 (dimers) / ~10 (trimers) |
| Risk of depurination | High (cumulative) | Reduced |
| Product homogeneity | Lower | Higher |
| Overall synthesis time | Longer | Shorter |
| Coupling efficiency | Variable | More consistent |
Alfa Chemistry supplies a wide array of dimer and trimer phosphoramidites that are pre-validated for high-yield, high-purity RNA synthesis, facilitating rapid assembly of biologically relevant RNA fragments, including siRNA, aptamers, and ribozymes.
The creation of dimer phosphoramidites needs precise control of stereochemistry along with a protection strategy together with base compatibility. Key considerations include:
Figure 2. Dimer phosphoramidite synthesis (TBDMS protection)[1].
Alfa Chemistry provides custom-designed dimer and trimer phosphoramidites with tailored protection strategies, enabling sequence-specific synthesis solutions even for highly modified or labile RNA sequences.
Dimer phosphoramidites are extensively employed in the synthesis of therapeutic oligonucleotides and chemically modified RNA analogs. They are particularly beneficial in:
A. siRNA and shRNA Construction: Rapid assembly of sense/antisense strands for gene silencing.
B. RNA Aptamer Synthesis: Precision in structural motifs such as loops and stems.
C. Splice-Switching Oligonucleotides (SSOs): Enhancing stability and sequence fidelity.
D. miRNA Mimics and AntagomiRs: Synthesizing functional double-stranded RNA segments with exacting base composition.
These applications demand not only precision but also reproducibility, which Alfa Chemistry supports through stringent quality control and batch-to-batch consistency of its dimer and trimer phosphoramidite products.
Alfa Chemistry offers a comprehensive catalog of dimer and trimer phosphoramidites that are rigorously tested for:
Additionally, Alfa Chemistry provides custom synthesis services for non-standard dimers, including modified bases (e.g., 2'-OMe, 2'-F, pseudouridine) and isotope-labeled variants. These reagents are optimized for use in both automated synthesizers and manual protocols, ensuring compatibility across various laboratory platforms.
Q1: What are dimer phosphoramidites used for?
Dimer phosphoramidites are used in RNA synthesis to incorporate two nucleotides in a single coupling step, reducing synthesis time and improving product purity.
Q2: Can dimer phosphoramidites be used in DNA synthesis?
They are primarily optimized for RNA synthesis due to their 2'-OH protection, but specially modified dimers can be applied in DNA synthesis with adjusted protocols.
Q3: How do dimer phosphoramidites differ from trimer phosphoramidites?
Trimer phosphoramidites incorporate three nucleotides per coupling step, offering even greater synthesis efficiency compared to dimers.
Q4: What are the typical protective groups on RNA dimer phosphoramidites?
Common protective groups include DMT on the 5'-hydroxyl and TBDMS or TOM on the 2'-hydroxyl, with cyanoethyl protection on the phosphite moiety.
Q5: Why are dimer phosphoramidites more stable during synthesis?
They reduce the number of deprotection and coupling cycles, thus minimizing exposure to acidic and oxidative conditions that could degrade RNA.
Q6: Where can I purchase high-purity dimer phosphoramidites for RNA synthesis?
A: Alfa Chemistry offers a wide selection of high-purity dimer and trimer phosphoramidites designed for efficient RNA synthesis in research and industrial applications.
For more details or custom synthesis inquiries, contact our oligonucleotide synthesis division directly.
References
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