Oligonucleotide Applications in Research

Oligonucleotides are most used for polymerase chain reaction (PCR). PCR is the technique of taking a DNA template and generating thousands or millions of copies of that DNA for use in other downstream applications (i.e., cloning, sequencing, etc.). Oligos used in PCR are usually between 20–35 bases long and are called primers.

Additional applications of custom DNA oligonucleotides in research are quantitative PCR (qPCR), gene editing and over-expression, site directed mutagenesis, fluorescence resonance energy transfer (FRET) assays, in situ hybridization (ISH), and single nucleotide polymorphism (SNP) assays. Oligonucleotides are also used in gene-targeted therapies. All these applications require custom DNA oligos (or RNA oligos) that are synthesized with user-specified sequences.

Modified oligos have always had an important job across many different life science applications, especially in clinical-based applications like molecular diagnostics and therapeutics. Adding modifications to an oligo can enhance the biological reactions related to that oligo, which is sometimes necessary. For example, there are certain modifications that can increase or improve the specificity of oligo hybridization to target sequences, resist against nuclease degradation, or create binding affinity to another molecule (Table 1).

Modifications can be added during the synthesis process utilizing phosphoramidite chemistry, or after the synthesis process is complete by NHS Ester chemistry. They can be added at the 3’ end or the 5’ end depending on what the oligo needs to accomplish. Typically, adding modifications to an oligo will decrease its final yield, which is why modified oligos are often synthesized in scales greater than 25 nmol.

There are many modifications available with a wide variety of applications:

Based on your application, the options for modifications can be narrowed down for your specific oligo. Thermo Fisher Scientific offers over 200 different modification options, including both catalog and custom modification synthesis offerings.

The accessibility researchers have to custom design their oligos for their experiments has opened new doors in fields like molecular biology and synthetic biology. These advancements help to continue the ground-breaking research that is making our world healthier, cleaner, and safer.

Custom oligos can be ordered using the options below. Simply enter your oligo name, sequence, select modifications from the drop-down lists provided, and select your synthesis scale (remember final yield does not equal synthesis scale!) and purification option. If you need a modification that is not listed, a guaranteed final yield, or special processing, be sure to contact our technical support team. For more information on our custom oligo services, please visit the links below.