How to Place a Sigma-Aldrich Oligo Order

Custom oligonucleotides, or “oligos,” are short, single-stranded DNA or RNA molecules synthesized to a specific sequence. They are foundational to molecular biology applications like Polymerase Chain Reaction (PCR) and DNA sequencing. Their utility comes from their ability to bind to complementary nucleic acid sequences, acting as primers for DNA replication or as probes for detecting genetic targets. Sigma-Aldrich is a long-established supplier of these custom biological tools.

Preparing Your Order Information

Before beginning the online ordering process, gathering all necessary specifications for your oligo ensures accuracy. The primary piece of information is the nucleic acid sequence, which is the precise order of bases (A, C, G, T) that defines the oligo. This sequence dictates the oligo’s function and must be entered without error. This planning helps prevent mistakes that could impact experimental outcomes.

Another parameter is the synthesis scale, which refers to the starting amount of material used for synthesis, not the final amount of oligo you will receive. Common scales include 25 nmol, 50 nmol, 200 nmol, and 1.0 µmol. The choice of scale depends on the intended application; a 25 nmol synthesis is sufficient for routine PCR, while larger scales are better for applications requiring a greater quantity of oligo.

You will also need to select a purification method. The required level of purity is dictated by the downstream application. Options range from standard desalting for many PCR applications to more stringent methods like High-Performance Liquid Chromatography (HPLC) and Polyacrylamide Gel Electrophoresis (PAGE) for sensitive experiments.

Finally, consider the delivery format. For researchers ordering a small number of sequences, receiving the oligos as a dried-down pellet in individual tubes is standard. For high-throughput applications involving many oligos, ordering them pre-arranged in 96-well or 384-well plates is a more practical option that simplifies sample handling.

Navigating the Sigma-Aldrich Ordering Portal

To begin an order, access the custom oligo ordering tool through the Sigma-Aldrich website. From the main homepage, users can find a link for “Custom Products” or “Oligos & Peptides.” This directs you to a specialized page where you can select the type of oligo you need, such as standard DNA oligos, and proceed to the ordering interface.

Once in the ordering tool, you will be presented with fields to input your oligo details. For individual sequences, this involves manually entering or pasting the oligo name and sequence. A more efficient method for large orders is the bulk upload option. This feature allows you to upload a pre-formatted spreadsheet with the names, sequences, and specifications for all your oligos.

After your sequences are entered, the interface will prompt you to select the specifications you determined earlier. Using dropdown menus, you will choose the synthesis scale, purification method, and delivery format. This is also the stage where you would add any chemical modifications from a provided list. The interface updates dynamically, showing how choices may affect the turnaround time and cost.

The final step before purchase is a thorough review of your order. The system generates a summary page that lists all entered oligos, their sequences, modifications, and all selected specifications. It also provides calculated data such as the oligo’s melting temperature (Tm) and a final price quote. Carefully check this information for errors before proceeding to checkout.

Understanding Oligo Specifications and Modifications

The choice of purification method directly impacts the purity of the final oligo product, a consideration for sensitive applications. The default option, desalting, removes residual salts from the synthesis process but does not effectively remove shorter, incomplete oligo sequences, known as failure sequences. This method is sufficient for standard PCR primers, where the presence of some failure sequences is unlikely to interfere.

For applications demanding higher purity, such as quantitative PCR (qPCR) or cloning, more advanced purification is necessary. High-Performance Liquid Chromatography (HPLC) separates the full-length oligo from failure sequences based on hydrophobicity. An even more stringent method is Polyacrylamide Gel Electrophoresis (PAGE), which separates nucleic acids by size with single-base resolution. PAGE purification is recommended for oligos longer than 40 bases or for demanding applications like gene synthesis.

Beyond sequence and purity, oligos can be ordered with a wide array of chemical modifications that add specific functionalities, typically added to the 5′ or 3′ end. An example is the addition of a biotin molecule, which is used for immobilizing or purifying the oligo and its binding partners. Another modification is the attachment of a fluorescent dye, such as FAM, HEX, or Cy5.

These fluorescently-labeled oligos, called probes, are used in applications like qPCR and fluorescence microscopy to detect and quantify specific DNA or RNA targets. In qPCR probes, the fluorescent dye is paired with a quencher molecule. The quencher absorbs the fluorescence of the dye when they are in close proximity. During the PCR reaction, enzymatic cleavage of the probe separates the dye from the quencher, resulting in a measurable increase in fluorescence proportional to the amount of target sequence.

Post-Delivery Handling and Storage

Upon arrival, your oligos will be accompanied by a technical datasheet or Certificate of Analysis. This document details the oligo name, sequence, and the final yield delivered, reported in Optical Density (OD) units, nanomoles (nmol), and micrograms (µg). It also provides calculated values such as the oligo’s molecular weight (MW) and its theoretical melting temperature (Tm).

The oligos are shipped in a lyophilized (dried) state and must be resuspended in a suitable liquid before use. First, briefly centrifuge the tube to collect the small pellet of dried oligo at the bottom of the tube, preventing any loss when the cap is opened. Use a sterile, nuclease-free buffer, such as TE buffer (Tris-EDTA), or nuclease-free water to resuspend the oligo to a desired stock concentration.

Properly calculating the concentration and storing the oligos are practices that maintain their integrity. A standard laboratory practice is to resuspend the oligo to create a stock solution of 100 micromolar (µM). From this stock, smaller amounts can be diluted to create working solutions, typically at 10 µM. This practice of creating aliquots minimizes the number of freeze-thaw cycles the main stock undergoes. For long-term storage, both stock and working solutions should be kept at -20°C.