Core chemicals for oligonucleotides

Oligonucleotides (or “Oligos” for short) are short strands of nucleic acids, specifically DNA or RNA, that consist of a sequence of nucleotide building blocks. They are typically composed of around 10 to 100 nucleotides in length.
 

Oligonucleotides serve as essential tools in various areas of molecular biology research, diagnostics development, and therapeutics development. They are utilized for a wide range of applications, including DNA amplification, sequencing, gene expression analysis, gene editing, biomarker detection, nucleic acid-based assays, and drug development, among others.
 

What are the important factors when performing oligonucleotide synthesis?
 

There are several important factors to consider when performing oligonucleotide synthesis. These factors include the length and sequence of the oligonucleotide, the purity and yield of the product, the presence of any modifications or labeling, the turnaround time and cost of the service, and the quality and reliability of the supplier.
 

Additionally, you may also require specific technical support and expertise in designing and optimizing oligonucleotide synthesis protocols for their specific applications. By addressing these factors and providing high-quality, reliable services, suppliers can effectively meet the needs of their customers and establish a strong reputation in the industry.
 

How and why are chemicals used for oligonucleotide synthesis?
 

In oligonucleotide synthesis, a variety of chemicals are used to facilitate the synthesis process, and the process of producing the target oligomer sequence takes several cycles consisting of specific synthetic steps.
 

These chemicals typically include CAP A and CAP B, activators, oxidizers, deblocking reagents, solvents and phosphoramidites.
 

Activators and oxidizers are used to promote the coupling and oxidation steps, respectively, to help ensure efficient formation of phosphodiester bonds.
 

Deblocking reagents are employed to remove the protecting groups from the nucleotides, enabling subsequent addition of the next nucleotide in the sequence.
 

Solvents, such as acetonitrile or dichloromethane, are used to dissolve and mix the various reagents during the synthesis process.  Acetonitrile is particularly important as it is used in every step of the synthetic cycle as a washing solvent.
 

Phosphoramidites are the building blocks used to add individual nucleotides to the growing oligonucleotide chain. Amidites are used to protect the reactive groups on the nucleotide building blocks during synthesis.
 

As part of the synthesis cycle, capping reagents are used to convert unreacted OH groups to acetate groups to prevent them taking part in the synthetic cycle thereon. They can then be removed in the purification step. This prevents the formation of n-1 oligomers in the final product.
 

It is important to note that the specific chemicals and protocols used may vary depending on the synthesis platform and the desired application of the synthesized oligonucleotides.