Plasmid Prep FAQs

Service Options

Our plasmid prep includes a standard-scale service with mini to giga scale preps, and a targeted yield service to deliver specific quantities of transfection-grade DNA. We also offer 96-well-mini-preps, custom large-scale preps, and AAV plasmid preps for your specific project needs. Plasmid prep can also be ordered using bacterial colonies or glycerol stocks from a Sanger sequencing order.
We offer a wide variety of analysis options with your plasmid prep order including DNA sequencing, restriction digest analysis, sterility testing, and much more.
We have proven a steadfast commitment to superior service over the last two decades, becoming a global leader in genomics services. With plasmid DNA preparation, we offer rapid turnaround times starting at just 2 business days, convenient online ordering, and a strict QC process with a wide range of analysis options to ensure high-quality plasmids.

Completing the Order Form


# of Aliquots: The table below shows how we aliquot your sample volumes into tubes. If you would like your sample aliquoted in any other way, by volume or yield, that can be done for you at an additional charge. Examples for custom aliquot requests are also listed.

Run Scale Sample Volumes
Mini 60μl mini tube or 96-well plate depending on order size
Midi 200μl in 2ml tube
Maxi 500μl in 2ml
Mega 1ml in 2ml tube
Giga (1ml in 2ml tube) x2
Normalizations 1.7ml per tube 2ml (leaving room for expansion if freezing) or mini tubes (<200ul)

Example 1: 50μl in one tube, the rest in a second tube.
Example 2: Split the order into 5 tubes.
Example 3: 50μg per tube.

Custom Tubes: If you would like your samples shipped back to you in specific tubes from your stock, that can be done for you at an additional charge. Simply include a stock of your tubes with your samples.


The table below provides guidance on selecting the appropriate cell line based on factors such as expression system, target protein, and downstream applications.

Strain Best for
DH5alpha Regular cloning and storage, uptake of large plasmids
Top10 Regular cloning and storage
Stable Lentiviral and retroviral plasmids, plasmids prone to rearrangement
AAV Proprietary cell strain used for our AAV-ITR plasmid production services, designed to maximize ITR stability

Sample Submission


  • Purified DNA: At least 5 µL of DNA at 200 ng/µL (minimum 100 ng). Additional charge applies.
  • Agar plate: Fresh (<3 days old) plate with single, well isolated colonies. Customer may indicate the colony (or colonies) to use, if desired.
  • Glycerol stock or media sample: At least 200 µL. We can streak colonies (additional charges apply) for isolation prior to starting the liquid culture upon request.
  • Cell pellet: Ship frozen on dry ice (direct to us via overnight carrier), with an indication of the culture volume, media used, OD600 at harvest, and cell pellet mass.
  • DNA on filter paper: This format is discouraged – please send as purified, wet DNA in a sealed tube via overnight shipping (or our courier, if available). Additional charge applies.
  • Other samples: Please contact our Technical Support team to discuss custom requirements.
We routinely stock Carbenicillin (Carb), Kanamycin, Chloramphenicol, Ampicillin, Tetracycline, Streptomycin, Spectinomycin, and Zeocin. We also supply Gentamycin, Hygromycin, Apramycin, and Erythromycins but do not keep them on hand, so some lead time will be necessary. An automatic upgrade of Ampicillin to Carbenicillin is included at no added charge. Other antibiotics may be submitted by the customer with their samples.

Fresher is better; < 3days old with well isolated colonies. Older plates can be freshly streaked for isolation upon request. Please note that this will add to the order timeline.

Please use caution in shipping agar plates during the cold winter months. The agar media may freeze in transit, rendering the plate unusable. Glycerol stocks are recommended as a substitute format during this season.

Our plasmid prep team accepts only BSL1 samples. Typical agar plates used for these strains, bearing well isolated colonies are usually acceptable.
Our Plasmid DNA Preparation service is for plasmids in the 3-15 kb range. We do not currently offer BAC or cosmid preparation services.
We do not currently offer BAC or cosmid preparation services. Plasmids requiring handling outside standard protocols are reviewed on a case-by-case basis. Additional charges may apply.
Please send at least 10 µL for each sequencing reaction using that primer. The primer concentration should be 5 µM.

Larger plasmids (>10 kb) and plasmids containing toxic or unstable sequences (such as long terminal repeats (LTR) found in viral expression vectors) are likely to produce better results when paired with cell lines engineered to maintain these difficult sequences.

We advise against using standard cloning strains for these plasmids, due to increased risk of lower yield and plasmid instability. We also suggest the selection of additional QC testing to verify unstable or toxic plasmids.

Please contact our Technical Support at with any questions and to discuss your project.

Turnaround Time and Troubleshooting

Typical turnaround time is 2-4 business days, depending on the order options selected. Additional testing or repeats may extend the timeline.

  1. Log into your account and view My Orders. From this main menu you can also see Order Status next to each individual tracking number.
  2. If additional help is needed, please e-mail, call 908-222-0711 ext.2, or live chat with our Technical Support team.
Upon request, we will store a sample of your starting material or final DNA for up to one year at no additional charge, to facilitate subsequent ordering. Please be sure to request this storage in your order comments and include the order tracking number when reordering preps.
Azenta Project Management stores a sample of your final DNA from a gene synthesis order for up to one year at no additional charge. To order preps from these projects, simply go to the gene synthesis results page, select the construct of interest in the checkbox, and click “submit prep order” to initiate an online plasmid prep order.

Our internal quality monitoring will trigger the automatic repeat of a plasmid DNA preparation when the yield is below a critical threshold, depending on the anticipated copy number for the plasmid. Yield variance above this threshold could be due to a variety of factors and may be intrinsic to the sample provided.

Plasmid DNA preparation orders are processed by run. For low copy or other low yield plasmids, we recommend ordering a larger preparation scale or multiple preps, depending on the amount of final material required.

To discuss troubleshooting or custom process modifications, please contact Azenta Technical Support.

GLP-level Plasmid Preparation

Our Quality System is developed in accordance with applicable FDA GLP regulations described in Title 21, Part 58 of the Code of Federal Regulations and EPA GLP regulations described in Title 40, Part 160 of the Code of Federal Regulations. We offer GLP services including GLP Plasmid Prep. For more details, please contact us at 877-436-3949, ext. 3350 or

AAV Plasmid Preparation

AAV plasmid preparation is our newly developed, proprietary process to propagate AAV plasmids while preserving the integrity of ITR regions. The service includes pre- and post-prep QC steps that leverage our AAV-ITR Sanger sequencing capabilities, while regular plasmid preparation kits and protocols still risk the loss of ITR integrity.
Pre-prep QC assesses your sample configuration for the presence of full-length intact or truncated ITRs, or a mixture of both. It allows selected propagation of intact ITR sub-population only, while post-prep QC ensures integrity of ITR regions in the final plasmids delivered to you.
If your sample contains only truncated ITRs, we can fix the mutation at an additional cost and prep the corrected plasmids. If a mixture of intact and truncated ITRs is present, we can separate the full-length intact ITR sub-population and propagate it.
Pre-prep QC can be skipped if you could provide the tracking number of your AAV-ITR Sanger sequencing order, or the .ab1 files associated with the current aliquot of your samples. Any new transformation and plasmid preparation on your end will require a pre-prep QC.
Currently, we only accept plasmid DNA. 10 µl at 200-300 ng/µl is recommended (minimum 200 ng/µl), in order to account for ITR sequencing as well. Please contact our Technical Support team at for possible options if you have insufficient sample quantities.
Final yield is dependent on the copy number of your sample(s), and a minimum yield cannot be guaranteed. Please indicate in the Comments section of the order form if your sample has a low copy origin of replication (ORI).

Have a specific question?

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