Currently Mobix Lab orders oligos from three Oligonucleotide Synthesis companies: Integrated DNA Technologies (IDT), Eurofins MWG Operon (Operon), and Sigma-Genosys.

Oligo synthesis proceeds in the 3' to 5' direction with the 3' base covalently attached to a solid support and utilizing cyanoethyl phosphoramidite nucleosides. As the coupling efficiency of each base addition step is less than 100% (normally between 98% and 99%) there is always a portion of short terminated oligos after synthesis.

Purification

Desalted oligos will contain the full-length oligo, as well as the smaller failed synthesis DNA fragments, which were capped due to failed incorporation of the next base.  These oligos are adequate for most applications, such as DNA sequencing, PCR amplification, etc. 

HPSF purified oligos were previously described as OPC purified and have similar purity levels (approximately 80%) and high yield. 

HPLC achieves a higher purity level (approximately 85%) but with a significant decrease in yield. 

PAGE purified oligos are the most pure (>90%) but yield is also quite low.

IDT Purification details

Operon Purification details

Sigma Purification details

Degenerate Primers

Degenerate oligos are synthesized to contain equimolar mixtures of two or more different bases at a given position within the sequence. Mixed bases are often incorporated into oligonucleotide probes designed to hybridize to an unknown gene that encodes a known amino acid sequence. Since the genetic code is degenerate (e.g., Histidine could be encoded by CAC or CAT), the oligo probe is prepared with C or T at the degenerate site. Oligos with mixed bases are also useful in random mutagenesis and combinatorial chemistry. Degenerate oligos are produced for no additional charge (except for degenerate bases, where a hand-mixed variant is desired (see IDT website)). Check the IUB codes for mixed bases.

IUB Codes