Custom Oligonucleotides From Integrated DNA Technologies

Integrated DNA Technologies (IDT) synthesizes custom DNA and RNA sequences to order. As a molecular biologist, I buy a lot of primers. Most of my purchases from IDT have been pretty straightforward sequences: short oligonucleotide primers for PCR or sequencing. These are available in single tubes or in 96-well format, and can be ordered for same day or standard shipping. In addition to standard synthesis, IDT offers degenerate oligonucleotides, in which any given position in the sequence is synthesized with one of two or more nucleotides. Let’s say that you have a cDNA library from an organism that hasn’t been sequenced yet, and you want to synthesize a primer to fish out a gene encoding the amino acid sequence “PAINTING” (i.e. ProAlaIleAsnThrIleAsnGly) Using the DNA alphabet, you’d order a degenerate oligo of the sequence: CCNGCNAUHAAYACUAUHAAYGGN, which would be synthesized as a pool of 2304 oligos (every possible combination specified by the sequence). The degenerate oligos I’ve purchased from IDT have worked dependably.

IDT’s offerings are customizable in several additional ways: you have your choice of optional modifications (such as phosphorylation or fluorescent labels), scale of synthesis, and method of purification. I’ve used their phosphorylated primers to engineer custom multiple cloning sites in expression vectors and was very happy with the accuracy of the synthesis of these long oligonucleotides. After ligation of the phosphorylated primers into my vector, I analyzed 18 clones; each of them had all of the restriction sites I had specified (which had not been my experience with another vendor). Another product line offered by IDT is custom gene synthesis. IDT is able to synthesize double-stranded DNA sequences of 2 kb or more. This is useful for a variety of applications such as codon optimization of a sequence, or synthesizing a gene when you have access to the nucleotide sequence but not a clone.

The IDT field representatives have always been very helpful and reliably followed up on my inquiries. Ordering is done online, and the interface is fairly straightforward, especially when ordering one or a few sequences. The instructions for ordering multiple items indicate that the information should be saved as tab delimited text and then pasted from a text editor (such as Notepad). However, I’ve been able to skip those extra steps and cut and paste directly from Microsoft Excel. One criticism I had in the past was that the order entry didn’t automatically recognize the degenerate DNA alphabet, instead giving an error message. Someone must have told them about this glitch, though, because when I tested that feature today, the system recognized the degenerate letters as valid. IDT provides many software tools on the website for evaluating your primer sequences, permitting one to predict hairpins, melting temperatures, etc. IDT also offers online chat with IDT representatives as part of their customer service. Although I’ve never used the live chat it is nice to know that it’s available. In short, IDT is my vendor of choice for PCR and sequencing primers, linkers, and labeled oligonucleotides because their products are consistently accurate and shipped on time.