Decorative

Oligonucleotides, or oligos, are short strands of synthetic DNA or RNA. Custom oligos are made by a process called solid-phase chemical synthesis. Oligo synthesis involves the sequential addition of the nucleic acids cytosine (C), guanine (G), adenine (A), thymine (T) for DNA, and uracil (U) for RNA, to a growing chain of nucleotides. To create the chain, the nucleic acids must be built on their phosphate backbone and the chain is synthesized in the 3’ to 5’ direction. When synthesis is complete, the oligo is typically desalted (removes all salts used during synthesis) and/or purified (removes non-full-length material).


Common oligonucleotide applications

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.


Applications of modified oligonucleotides

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:

Table 1. Table of modification categories by modification type and common application

CategoryModificationApplication
AttachmentAmino Linkers, Biotin, Phosphate, ThiolAttachment of labels or conjugation with other molecules post synthesis
FluorophoresFAM, Fluorescein, Alexa Fluor dyes, TAMRA, RhodamineDetection assays such as in situ hybridization (ISH), FRET, sequencing, etc.
SpacersPEG, C3, C18Create distance to eliminate steric hindrance
PhosphorothioatesPhosphorothioate bondsIncreases resistance to nuclease degradation
QuenchersDabcyl (Dabsyl), BHQsCommonly paired with fluorophores for FRET studies

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.


Ordering custom oligos

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.

Table 2. Ordering categories with associated yields, options for modifications, purification, and delivery formats

Standard oligos in tubes
  • 25 nmol–10 µmol scale 
  • Up to 100 bases
  • Modifications
  • Purification options available
  • Standard or next-day delivery
Bulk order standard oligos in tubes
  • Up to 200 sequences in single upload
  • 25 nmol–10 µmol scale 
  • Up to 100 bases
  • Modifications
  • Purification options available
  • Standard or next-day delivery
Standard oligos in plates
  • Single selection of synthesis scale (25 nmol–10 µmol), modifications, and purification across the plate
  • Up to 100 bases
  • 96- or 384-well plate format
  • Standard delivery

Value oligos

  • Priced per oligo rather than per base
  • 5–40 bases
  • 25 or 50 nmol scale
  • No modifications
  • Purification options available
  • Standard or next-day delivery

Resources

Molecular Biology Resource Library

Access valuable support for standard molecular biology techniques from our library of webinars, videos, articles, and more.

Molecular Biology Web Tools

Utilize free online tools for primer analysis, reaction setup, biochemical conversions, and calculators.

Product selection guides

Molecular Biology Handbook

Optimize your experiments. Our latest edition is improved with more technical tips, educational tools, and guidance to select the right molecular biology products.

 Molecular Biology Mini Catalog

Find the right products for your experiments. Our mini-catalog features the most popular Thermo Scientific molecular biology products.

Molecular Biology Product Discontinuations

Find an alternate to a discontinued molecular biology product.

Molecular Biology Services and Support

Email or call our Technical Application Scientists for additional questions regarding molecular biology products.

For Research Use Only. Not for use in diagnostic procedures.

For Research Use Only. Not for use in diagnostic procedures.