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.
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".
The conventional method for synthesizing degenerate oligonucleotide sequences (DOS) is to use mixed phosphoramidites at specific positions in the oligonucleotide.
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.
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.
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.
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 Base | Code | Price |
| 2'-O methyl Inosine | 2-OMe-I | Inquiry |
| 2-Amino Purine | 2dAP | Inquiry |
| 2-Amino Purine Ribose | 2rAP | Inquiry |
| 5-methyl Isodeoxycytosine | 5-Me-Iso-dC | Inquiry |
| 5-Nitroindole | 5N-Indoe | Inquiry |
| K-2'deoxyribose | dK | Inquiry |
| P-2'deoxyribose | dP | Inquiry |
| 2'-deoxylnosine | dI | Inquiry |
| Inosine | rl | Inquiry |
| Iso deoxyguanosine | iso-dG | Inquiry |
| Mix Bases | R=A+G | Inquiry |
| Y=C+T | Inquiry | |
| M=A+C | Inquiry | |
| K=G+T | Inquiry | |
| S=G+C | Inquiry | |
| W=A+T | Inquiry | |
| H=A+T+C | Inquiry | |
| B=G+T+C | Inquiry | |
| D=G+A+T | Inquiry | |
| V=G+A+C | Inquiry | |
| N=A+C+G+T | Inquiry |
Degenerate oligonucleotides are commonly used in PCR amplification to detect multiple gene variants or homologous sequences across different species. They can also be employed in genome mapping and cDNA screening.
DOP-PCR is a technique that uses degenerate primers to amplify low amounts of genomic DNA, often for whole genome amplification. It allows researchers to efficiently increase DNA template availability, even from small samples.
Degenerate oligonucleotides are used as primers in PCR for cloning unknown genes or gene family members. They can amplify a broad range of gene variants that are related across different organisms.
Degenerate oligonucleotides can be modified with various base substitutions like 2'-O methyl Inosine or 5-methyl Isodeoxycytosine to enhance specificity and stability. These modifications allow for a broader application in genetic research.
BOC RNA uses advanced synthesis platforms to produce highly specific and high-yield degenerate oligonucleotides with full quality control. Each product undergoes rigorous analysis to ensure purity and consistency for your research needs.
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