Q: What is synthesis scale and why is it important?

A: When you order an oligonucleotide from Ella Biotech, you’ll need to select a synthesis scale. We typically offer 40 nmol and 200 nmol synthesis scales. Think of the scale as your starting pool of building materials – it’s measured in either nanomoles (nmol) or micromoles (µmol). For example, if you choose a 40 nmol scale, we will start with about 40 nmol of your first nucleotide (the one at the 3′ end of your sequence) attached to a solid support.

However, it’s important to understand that this starting amount is not what you will receive as your final product. The synthesis scale is just the beginning of the story.

Q: What affects the amount of oligonucleotide I actually receive?

A: The final amount of oligonucleotide you receive depends on several factors:

• Coupling efficiency: Think of building your oligo as putting together a chain. Each time we add a new nucleotide (a new link), there is a chance that some chains won’t attach their new link properly. The percentage of successful attachments is called coupling efficiency. Just as a chain is only as strong as its weakest link, an oligo needs every nucleotide to successfully attach to be complete.
• Sequence length: The longer your oligo, the more attachment steps are required. With each step, there’s a small chance that something won’t work perfectly. This is why longer oligos tend to have lower yields than shorter ones – there are simply more opportunities for something to go slightly wrong.
• Sequence complexity: Some sequences are inherently more difficult to synthesize than others. It’s similar to how some DNA sequences are harder to amplify by PCR than others.

Q: How much product can I expect?

A: At Ella Biotech, we want you to know exactly what to expect when you order your oligonucleotides. The amount of final product you’ll receive depends on several key factors that we carefully consider when calculating your guaranteed yields:

1. Your chosen synthesis scale
2. The length of your sequence
3. The sequence complexity
4. Your selected purification method

Let’s look at a practical example: For a standard primer (up to 45 nucleotides) synthesized at 0.2 µmol scale, we guarantee:

• 110 nmol yield with desalted purification
• 50 nmol yield with HPLC purification

For oligonucleotides with special modifications or complex designs, yields can vary significantly. In these cases, we’re happy to offer personal consultations to discuss expected yields and help you choose the optimal synthesis scale for your specific needs. This will ensure that you’ll have enough material for your experiments while remaining cost effective.

Q: What information is included in my oligonucleotide synthesis report?

A: Every order from Ella Biotech comes with a comprehensive synthesis report that includes:

• Oligonucleotide name and sequence (optional)
• Base composition and count
• Modifications (if any)
• Actual yield (nmol, µg and OD)
• Synthesis scale
• Delivery form
• Quality control method
• Purification method
• Molecular properties (Tm and molecular weight)
• Solution volume required for a 100 µM concentration

Q: How is the amount of my oligonucleotide measured?

A: We provide your yield measurements in three different units to make it easy for you to use in your experiments:

• Optical Density (OD)
• Nanomoles (nmol)
• Micrograms (µg)

We also include the concentration of your oligonucleotide solution, making it simple to use directly in your experiments or to make further dilutions as needed.

Q: What about quality and purity?

A: It’s worth noting that not all the material from your synthesis will be perfect, full-length oligos. Using our 40 nmol scale example for a 25 base oligo, at least 25% of the starting material may result in incomplete sequences. These are removed during purification to ensure that you receive high-quality, full-length products.

After purification, what you receive is primarily your desired full-length oligonucleotide. We then measure the final product by OD260 (optical density at 260 nm), which includes all DNA material present.