Our Oligo Synthesis Services

Oligo Synthesis FAQs

Below are some frequently asked questions about our Oligo Synthesis services. Should you have any questions other than listed below, feel free to contact us at synthesis@biobasic.com and we will be happy to clear your thoughts.

  1. 1. What is "HAP?"
  2. 2. What is "O.D." (OD)?
  3. 3. Can you synthesize long oligos?
  4. 4. I am not familiar with the O.D. system can I order in "nmol" scale?
  5. 5. I’ve ordered in "nmol" scale, why did I receive less?
  6. 6. How do I order?
  7. 7. What’s your turnaround like?
  8. 8. Can I order more than 10 OD?
  9. 9. Do you have "X" modification(s)? (i.e. modifications not listed on our website)
  10. 10. What formats are available for the oligo deliverables?
  11. 11. Is there a minimum requirement for oligos in 96-well plates?
  12. 12. How do I calculate the accurate Molecular Weight?
  13. 13. What is the average Molecular Weight per base?
  14. 14. How do I reconstitute the oligos?
  15. 15. To what concentration should I reconstitute the oligos?
  16. 16. How stable are the oligos?
  17. 17. What type of gels can I use for DNA electrophoresis analysis?
  18. 18. How can I measure the DNA concentration? Can I measure the OD value in the same way?
  19. 19. What is the ideal range of OD reading?
  20. 20. Are the ends of the oligos phosphorylated?
  21. 21. What are the Terms and Conditions for Oligo Synthesis?
1

What is "HAP?"

HAP stands for "High Affinity Purification"; it is a patented, novel purification method for custom oligos developed by Bio Basic. After synthesis the DMT-ON-oligo in the crude oligo mixture is selectively absorbed on a high affinity resin within a HAP column, this allows incomplete oligo fragments pass through while keeping majority of the full length oligos. The full length oligo is retrieved by removing the DMT protection group under mild acid conditions. The HAP process provides two major advantages, higher purity and a low cost comparable to PAGE or HPLC methods.

2

What is "O.D." (OD)?

O.D. stands for Optical Density units; it is based on absorbance readings at 260nm. For synthesis facilities that use phosphoramidite synthesis, O.D. measurements are a means to quantify the amount of available oligo after purification i.e. the FINAL YIELD of the oligo. As a rough estimate 1 O.D. ~ 33 ug. When comparing oligo synthesis services, the O.D. should be compared (the final yield) and not the initial synthesis scale (in "nmol") which is the quantity of the starting material required before synthesis of the oligo. From this, the final "nmol" yield will vary on the length, sequence and molecular weight of the individual oligo.

3

Can you synthesize long oligos?

We can synthesis oligos up to 130 bases in length. Due to manufacturing restrictions we only offer synthesis under PAGE or HPLC purification. Note, there is a size restriction for our desalted and HAP oligos between 11-59 bases.

4

I am not familiar with the O.D. system can I order in "nmol" scale?

You can order by "nmol" reference but note that "nmol" is assumed to be the initial amount of material used to synthesize an oligo unless otherwise noted. This is not accurate means to compare oligos between facilities as our manufacturing procedures are likely different and therefore the corresponding final yield and price rates will differ. If you’re switching providers and aren’t quite sure what to pick, don’t hesitate to ask and we will be happy to match an equivalent or better oligo service.

5

I’ve ordered in "nmol" scale, why did I receive less?

The "nmol" references refers to the initial amount of material used for each base in the oligo sequence. Like with all chemical reactions 100% completion is not possible. The average yield cycle is ~98%. The longer an oligo is, the increased likelihood of an error being introduced in the sequence. For example a 60-bases long oligo the yield of full length oligos is 0.98^(60-1) or 30.36% of full length material available. There are additional reductions in yield due to purification and minor loses due to material transfers and quality control analysis.

6

How do I order?

Fill out one of our order forms and submit it to synthesis@biobasic.com. Note these orders are NOT confirmed. You will receive a quotation within 24 hours which is non-obligatory (commitment free). Order will only be confirmed upon your review and approval of the quotation. Likewise you can estimate the cost of your oligos using our pricing list.
If you wish to proceed with the order as outline in the quotation sent to you, have your billing details ready (PO, Credit Card or Wire) along with confirmation to proceed.

7

What’s your turnaround like?

On average it takes about:
2 business days for standard oligos (Desalt and HAP).
+2-3 days for PAGE or HPLC purification.
+1-2 days for longer oligos (longer than 60 bases).
Turnaround times will vary on current throughput, volumes and complexity of the order.

8

Can I order more than 10 OD?

Yes you can! May we recommend down-packing your oligo? Oligos are most stable left in their lyophilized state. If you’re not using all your oligo at once we can offer down packing for your oligos at no extra cost to you;
Please let us know when placing your order (we recommend a max. of 20-40OD down-packed in a single tube if you plan to work within that given tube).
Otherwise, the max. quantity of oligo we can down-pack in each tube are:
Standard Tube (2ml) : 200 OD
Special Tube (5ml) : 1000 OD

9

Do you have "X" modification(s)? (i.e. modifications not listed on our website)

We have a large variety of common modifications. You can find our full list on our oligo modifications page. If you cannot find the modification you’re interested in, don’t hesitate to contact us. Note that some of our modifications may have alternate names as some modification names are propitiatory, therefore we are not allowed to list them on our website. You can always contact us at synthesis@biobasic.com to request an equivalent.

10

What formats are available for the oligo deliverables?

Oligos are lyophilized in microcentrifuge tubes or lyophilized in 96-well plates for automated operations.

11

Is there a minimum requirement for oligos in 96-well plates?

A minimum of 48 oligos must be ordered for the 96-well Plate format.

12

How do I calculate the accurate Molecular Weight?

Accurate MW: MW=(A bases x 313.2)+(C bases x 289.2)+(G bases x 329.2)+(T bases x 304.2)-61.

13

What is the average Molecular Weight per base?

Average MW: Average MW per base = 324.5.

14

How do I reconstitute the oligos?

To reconstitute: Centrifuge the tube for a few seconds to collect the DNA in the bottom of the tube. Carefully open, add an appropriate volume of distilled water, close, rehydrate for two minutes and vortex for 15 seconds.

15

To what concentration should I reconstitute the oligos?

It is recommended that oligos be reconstituted at concentrations > 10u molar and stored at -20°C.

16

How stable are the oligos?

When kept at -20°C, the stability of the lyophilized material is >1 year and the stability of reconstituted material is >6 months.
When kept at 4°C, the stability of reconstituted material is little over 1 week.

17

What type of gel can I use for DNA electrophoresis analysis?

De-natured polyacrylamide gel in the presence of 7M urea is recommended for oligo DNA electrophoresis analysis. Agarose gel is not recommended.

18

How can I measure the DNA concentration? Can I measure the OD value in the same way?

EB staining is suitable for measuring DNA concentration, but not suitable for measuring OD value of oligos, as A, C, G and T have different binding capacities with EB.

19

What is the ideal range of OD reading?

The ideal range of OD reading in UV spectrometer at 260 nm is from 0.3 to 0.8 OD. If the solution is too diluted or too concentrated the measured total OD units may not be correct.

20

Are the ends of the oligo phosphorylated?

No, they are not phosphorylated. Both ends of the oligo have a free hydroxyl group.

21

What are the Terms and Conditions for Oligo Synthesis?

Please click here for the terms and conditions for our Oligo Synthesis services.

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