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Mixed bases

We offer oligonucleotides containing randomized or “mixed” bases. Mixed bases are ideal for binding primers to templates that contain variability or a mixture of sequences at the binding site. They can also be used to create diversity in clone libraries and in site-directed mutagenesis.

Two types of randomization are available—machine mixing and hand mixing, both of which can be ordered through online oligo entry tools by selecting the Mixed Base tab.

Standard machine mixing is the most popular and economical way of incorporating degenerate bases into oligo sequences. Machine-mixed bases can be inserted at any/all base sites within a sequence at no additional charge. At these wobble base positions, the synthesizer dispenses an equal ratio of the desired bases (e.g., a mix of A:C:G:T would be allotted 25:25:25:25); however, each base could be added at slightly different percentages, so there is no guarantee that all bases will equally represented in the full length product.

By requesting hand mixing of wobble bases, specific ratios of the desired bases can be defined (e.g., a mix of A:C:G:T could be allotted 85:5:5:5, 25:25:25:25, or any other custom ratio). Each nucleic acid is coupled at slightly different rates, and these coupling efficiencies are taken into account when manufacturing oligos with hand-mixed degenerate bases. Please contact customer care for prices for hand-mix, because pricing varies with synthesis scale and the number of degenerate insertions.

Standard mixed base sites

To include mixed bases in your oligo sequence, use the DNA or RNA Oligo Entry tool and enter required bases using the base codes indicated below:

Mixed bases requiredMixed-base code for DNAMixed-base code for RNA
A, C, T/UHrH
G, C, T (or U)BrB
A, C, GVrV
A, G, T/UDrD
A, C, G, T/UNrN