Need a library of related DNA or RNA oligo sequences?

Even nonstandard, modified bases can be used in Hand-Mixed Oligos

Product spotlight: Build variability into your oligo sequences by incorporating Mixed Bases. We offer mixes of multiple base types as well as nonstandard and modified bases.

Jan 29, 2016

Revised/updated Aug 24, 2016

Quick Facts:

Availability: DNA or RNA
Location: 5', internal, and 3′
Scales: 250 nmol to large scale
Purification: Standard desalt
Ordering: Please email all requests for nonstandard mixed bases to for review and quoting

Randomized sections of sequence

IDT offers oligonucleotides containing randomized, or “Mixed Bases”. Mixed Bases are used in primers to bind to templates that contain variability or a mixture of sequences at the primer binding site. Mixed Bases can also be used to create diversity in clone libraries and in site-directed mutagenesis experiments.

IDT offers two types of randomization, Machine-Mixed Bases and Hand-Mixed Bases. Machine-Mixed Bases can be made at any/all base sites at no additional charge. At these base positions, the synthesizer pulls an equal ratio of the desired bases; however, their different coupling rates do not guarantee an equal ratio of incorporation.

Hand-Mixed Bases use customer-defined ratios of the desired bases, where coupling efficiencies are taken into account. For each mixture, IDT can incorporate up to 100 residues on the 100 nmol and 250 nmol scales, and up to 40 residues on the 1 µmol scale, with a maximum of 4 distinct Hand-Mix formulations per oligonucleotide. When entering your sequence, use the Mixed Bases tab in the Sequence entry portion of the ordering page. It lists the IUPAC-IUB symbols and is where custom mix ratios should be entered.

art120-MH-Hand Mixes-Fig1

Figure 1. Select Mixed Bases when ordering your oligo.

Mixes of nonstandard and modified bases

In addition to IDT standard machine and hand mixing options for randomizing bases, we offer mixes of multiple base types (e.g., DNA, RNA, LNA*, or 2’O methyl) as well as modified bases. This allows incorporation of multiple base types or modifications from IDT’s catalog of modified base offerings into a single position on an oligo.

Please note that nonstandard mixed bases are considered Hand-Mixed Bases and are subjected to the maximum of 4 distinct Hand-Mixed Base formulations per oligonucleotide.

Submitting requests for oligos incorporating nonstandard mixed bases

IDT scientific experts meet regularly to review the complexity and feasibility of producing nonstandard sequence requests, such as oligos incorporating nonstandard mixed bases.

To submit a request for review, email with your name, organization, and sequence designs. Oligos containing nonstandard mixed bases can be ordered with HPLC purification or with standard desalt, providing modifications in the sequence do not require HPLC.