Oligo Modifications
Support and Educational Content

Need a library of related DNA or RNA oligo sequences?

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

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 noncat@idtdna.com 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.

Oligo Entry

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 noncat@idtdna.com 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.

Additional resources

OligoAnalyzer® Tool—One of IDT’s most highly accessed design and analysis tools, this free, online program identifies oligonucleotide properties, including melting temperature, hairpins, dimers and mismatches. Mixed base positions within a sequence are also taken into account.

Need a nonstandard modification?—Review a list of the common modifications IDT can add to oligonucleotides here. Not finding a modification you need on the IDT website? No worries. IDT offers 89 modifications that are not listed in our online catalog. A few of the more popular modifications are described along with information on how to order them. IDT will consider any modification you have in mind. Just send a request to noncat@idtdna.com.

Libraries of double-stranded DNA fragments—Learn about obtaining double-stranded DNA fragment libraries that contain up to 18 consecutive N or K bases for generating up to 418 sequence variations.

Author: Amanda Bowersox is a research scientist at IDT.

© 2016 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.

IDT web tools for oligo properties

Free, online tools for oligo design, secondary structure, dilution, and resuspension.

Try them now ≫

Related Articles

DNA Oligonucleotide Resuspension and Storage

Guidelines and recommendations for how to resuspend and store newly synthesized oligonucleotides.

Read more ≫

Calculation Tips for Resuspending and Diluting Nucleic Acids

Easy guidelines for making a 100 µM solution; calculating nmoles, µg, copy number, and concentration; and determining concentration equivalencies.

Read more ≫

Understanding Melting Temperature

Advice on considerations for better oligo design: oligo concentration, salt, and SNPs.

Read more ≫

Oligonucleotide Modifications: Choosing the Right Mod for Your Needs

Guidelines on selecting specific oligonucleotide modifications and how they can help you in your research.

Read more ≫

Which Biotin Modification to Use?

Applications of each of the different biotins available from IDT.

Read more ≫