Custom Degenerated Oligo Synthesis

As a professional oligonucleotide synthesis company, BOC RNA relies on the reverse translation of protein subsequences to synthesize limited degenerate oligonucleotides. BOC RNA provides quality assured oligonucleotides using state of the art technologies at a short turnaround time at affordable cost for your research needs. In addition, our scientists will provide you with free consultation and technical support for your research needs in molecular biology, diagnostics and drug discovery.

Introduction of Degenerated Oligo

  • What is Degenerated Oligo

If a certain DNA fragment represents a unique sequence, it is called specific; If it represents a unique set of sequences, it is called degenerate, e.g. the amino acid sequence "YHP" can be encoded by "TATCATCCC", "TACCATCCA", or "TACCACCCG". All of these are unique sequences, which can be summarized using the IUPAC code as the "degenerate" nucleotide sequence "TAYCARCCN".

  • How to Synthesize Degenerated Oligo

The conventional method for synthesizing degenerate oligonucleotide sequences (DOS) is to use mixed phosphoramidites at specific positions in the oligonucleotide.

  • What is DOP-PCR

Polymerase chain reaction (PCR) is a nucleic acid synthesis technology that uses the principle of DNA double-stranded replication to rapidly expand a large number of target DNA fragments in vitro. Degenerate oligonucleotide-initiated PCR (DOP-PCR) is a suitable approach to overcome the limited amount of genomic DNA available for genetic research by efficiently implementing whole genome amplification, thus increasing the number of templates available for microsatellite repeat marker genotyping (Fig. 1). Especially for those small quantities of DNA, DOP-PCR can be amplified 200-600 times.

Cloning strategy by PCR amplification of BCP54 cDNA using DOS as primers.Fig. 1 Cloning strategy by PCR amplification of BCP54 cDNA using DOS as primers. (Cooper D L, 1991)

The general process of DOP-PCR. During the first five PCR cycles at low annealing temperatures, a single degenerate primer is used which allows for random initial priming across the target DNA. In subsequent cycles, more stringent conditions are then used to amplify the first PCR product.

  • What Are the Applications of DOS

DOS has been used as a probe for Northern and Southern blotting, as well as for cDNA screening and genome mapping studies. DOS appears to be non-species specific, therefore the use of DOS primers is intended to cover all possible combinations of specific primer sets for nucleotide sequences encoding specific protein sequences, meaning that DOS primers can also be applied to amplify unidentified gene family members and homologues in different species.

What Are Our Custom Degraded Oligo Synthesis

BOC RNA degenerate site modifications can be incorporated into any position of the oligos. If you have any needs, please feel free to contact us.

Degenerate BaseCodePrice
2'-O methyl Inosine2-OMe-IInquiry
2-Amino Purine2dAPInquiry
2-Amino Purine Ribose2rAPInquiry
5-methyl Isodeoxycytosine5-Me-Iso-dCInquiry
Iso deoxyguanosineiso-dGInquiry
Mix BasesR=A+GInquiry

Advantages of Custom Degraded Oligo Synthesis

  • High quality - Meets stringent quality control standards for oligonucleotide synthesis.
  • Stability - ensures batch-to-batch consistency and traceability of oligonucleotides.
  • Cost effective - competitive pricing and highly customizable service.

Service Process


  1. ISERTE J A; et al. Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides. Biotechnol Res Int. 2013, 2013: 383646.
  2. Cooper D L; et al. Degenerate oligonucleotide sequence-directed cross-species PCR cloning of the BCP 54/ALDH 3 cDNA: priming from inverted repeats and formation of tandem primer arrays. PCR Methods Appl. 1991, 1(1): 57-62.
* Only for research. Not suitable for any diagnostic or therapeutic use.
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