Degenerate bases refer to the possibility of multiple bases in a particular location, as is often the case when DNA sequences originate from amino acid sequences with codon-based sequences. BOC RNA provides oligonucleotide synthesis using degenerate base modification and provides several degenerate site-enhanced oligonucleotide primer synthesis methods. These degenerate generic base analogues can replace any of the four DNA bases without creating base pairing bias or destabilizing base pair interactions.
What are Degenerate Bases?
A degenerate base is a symbol that replaces two or more bases based on codon merging.
According to the degeneracy of codons, a symbol is often used to replace two or more bases. For example, there can be 4 codons for transcoding alanine: GCU\GCC\GCA\GCG. At this time, for the convenience of biology, the letter N is used to refer to the four bases of UCAG, so the codon for compiling alanine is GCN, where N is a degenerate base.
When the primer is usually biologically designed for DNA cloning based on protein sequences, Some bases on the primer of the design are marked with degenerate bases due to codon mergers. In synthesis, all kinds of bases are distributed in equal quantities, that is, A synthetic degenerate primer is a collection of many kinds of primers, the difference being degenerate bases.
Degeneracy: The number of types of degenerate primers are equal to the number of all degenerate bases in the degenerate primer, that is, how many different primers there are, only one of which is truly paired with the template.
What is Degenerate Primer?
Degenerate primers are mixtures of primers that represent all the different base sequence possibilities encoding a single amino acid. To increase specificity, PCR can refer to codon use tables to reduce degeneracy based on base use preferences of different organisms. The lower the degeneracy, the stronger the product specificity. When designing primers, try to choose amino acids with small degeneracy and avoid degeneracy at the 3' end of the primer.
Password Degeneracy Table
The number of amino acid codons
- M and W refers to one
- C, D, E, F, H, K, N, Q, Y refer to 2
- I 3
- A, G, P, T, V means 4
- L, R, S stand for 6
(Note: The selected peptide chain should avoid amino acids with 4 to 6 codons)
Advantages of BOC RNA's RNA Modified Services
- Salt-free or HPLC-purified oligonucleotides with wobbles can be ordered. (However, any HPLC purification of a wobble oligonucleotide results in the loss of a particular sequence resulting from the wobble. BOC RNA does not recommend further purification of wobbles oligonucleotides.)
- Oligonucleotides with non-isomolar wobbles mixtures can be synthesized at the 5 'end or internally. Custom wobbles Contact the Technical Support Specialist for BOC RNA for more information.
BOC RNA's oligonucleotide synthesis business can support and provide a wide range of modified monomers and custom synthesis. BOC RNA's experienced chemists have many years of experience in synthesis, from small trials to process optimization and scale-up, and are able to communicate with customers in a timely manner to provide "customer-oriented" services. Please contact us for more details.
Source: https://rna.bocsci.com/products-services/degenerate-bases.html
