“QIAcube HT is an automated nucleic acid extraction unit. Here I am sharing my personal experience working with the present instrument.”
DNA extraction is one of the most critical steps of molecular biology, from diagnostics to research and development (R&D). DNA is the primary material required for the majority of molecular biology experiments.
I have experience working in a molecular biology laboratory for the last six to seven years. One of the challenges I faced was to extract high-quality DNA in sufficient quantities.
Manual methods can extract DNA with high concentrations, but these methods are very time-consuming, and also quality of DNA is lower. Manual methods have protocols of 1 to 2 days to extract the DNA from biological samples, but due to human limitations, we can not process a large number of samples at a time.
It raises a question are manual DNA extraction methods still relevant?
To ease the process of DNA extraction, several automated DNA extraction machines have been developed by companies like ThermoFisher and Qiagen. I have worked with many of these automated DNA extraction machines.
But one instrument that has been revolutionizing the molecular biology field is the QIAcube automated DNA extractor. In this article, I will share my personal experience working on this instrument, its positives and negatives in my opinion.
Stay tuned.
Disclaimer: This review is based on my personal experience with the QIAcube machine. It is not sponsored, and all opinions expressed are solely my own.
Key Topics:
What is QIAcube HT @96?
The QIAcube HT is an automated DNA extraction unit developed by QIAGEN, one of the leading bioscience companies. It is a mid to high throughput nucleic acid extraction unit, capable enough to extracting DNA, RNA and miRNA from various biological samples.
All the steps, lysis, elution, and purification, are performed in this 1-meter-square automated nucleic acid unit.
Physical overview
It is a benchtop machine available in QIAGEN’s unique blue and silver color. On the front side, it contains a hood, an on and off and QIAGEN branding.
I will not go into more technicalities but explain to you the components of the machine in brief.
On/off button:
As I explained, the very end of the machine has a single button for power on and off.
Robotic arm:
Once we open the hood, there is a robotic arm, which is the main part of the QIAcute HT automated nucleic acid extraction unit. It helps mix the reagents, samples and perform various pipetting steps without human interference.
UV lamp:
The machine is also equipped with a UV lamp to decontaminate the machine after completion of the run.
HEPA filter:
Provides a clean and positive air pressure.
Reagent turf:
Reagent turf is used to load the reagent in the machine, various buffers and other reagents.
S-block:
S-block is our sample block, where we place our sample. Usually, we can proceed with 8, 16, 24, 32, 40, 48,…., 88, 96 samples in a single run.
Elution plate:
Then there is an elution plate to elute the DNA in the last step.
Filtertips:
We also have to place the filter tips in their dedicated place in the machine, so that the robotic arm uses them for pipetting.
Vacuum chamber:
Create a vacuum for DNA elution. The vacuum chamber contains a waste chamber and an elution chamber. The waste is collected in the waste chamber, whereas the DNA is eluted in the elution chamber.
Tip Chute:
Through the Tip Chute, the used tips are ejected into the tips disposal box.
First look and installation:
The machine looks amazing from outer as well as inner, seeing it for the first time, one might think that this will be difficult to handle and to process the samples. But it is not the case, the machine comes with well-defined handbooks for operating, which are very easy to understand for the person working in the molecular biology lab.
The machine requires QIAcube HT Prep Manager Software to be installed on the computer that is connected to the machine. At the time of installation of the machine team of engineers from Qiagen comes, they connect the computer with the machine and then they will do the calibration of the robotic arm of the machine, which acts as an automated micropipette.
They will install the QIAcube HT Prep Manager Software, which contains protocols for DNA extraction.
Additional requirements:
The machine requires QIAamp 96 DNA QIAcube HT Kit and QIAcube HT Plasticware; these two kits need to be purchased from Qiagen, which contains reagents and equipment required for DNA extraction.
Along with these two kits, we also have to purchase the additional reagents as well as equipment such as Pipettes and disposable pipette tips with aerosol barriers (20–1000 µL), Isopropanol (100%), Ethanol (96–100%), and a Vortexer.
Principle:
The machine works on the principle of the spin-column nucleic acid extraction using the silica membrane. Cell lysis is done using Qiagen Proteinase K, then after 2 to 3 efficient washes, contaminants are removed as only DNA binds with the QIAamp membrane. Then, according to the requirements, DNA is eluted in 50 to 200 µL elution buffer.
Then, lastly, a single-step vacuum is applied to elute the DNA from the membrane to the elution plate. All these happen on the machine without human interference.
The obtained DNA is of high quality, i.e., Purified DNA has 260/280 ratios of 1.7 to 1.9.
Preparation of reagents:
For cell lysis, Proteinase K is supplied within the QIAcube HT kit. Proteinase K is ready to use, but at the time of use, it needs to be mixed with Buffer VXL in a 1:4 proportion.
VXL buffer is a lysis buffer that enhances the activity of Proteinase K, which is supplied in the Kit. The proteinase K is stable for 1 year at 15 to 25°C, but it is recommended to store it at 2-8°C. Buffer ACB is prepared in 100% isopropanol; the amount of isopropanol required is always mentioned on the bottle of reagent. This buffer is required for the precipitation of the DNA. Expiry dates are mentioned on the bottles, and it can be stored at 25°C.
AW1 and AW2 buffers are wash buffers supplied with the QIAcube HT Kit, which remove the micro and macro contaminants from the sample. These buffers are diluted by adding 96–100% ethanol; the amount of ethanol required for dilution is mentioned on the reagent bottle.
Expiry dates are mentioned on the reagent bottles, and they can be stored at 25°C.
Lastly, the AE buffer is required for the elution of the DNA from membranes. AE buffer is supplied with the QIAcube HT kit, which is ready for use. It can be stored at 25°C.
1 DNA QIAcube HT Kit and 1 QIAcube HT Plasticware contain reagents and equipment for the five DNA extraction protocols of 96 samples, i.e., 96*5.
Sample preparation:
Blood samples were collected/received in EDTA tubes. For optimal results, all the samples need to be shaken well using a shaker.
S Block preparation:
Blood samples are loaded into the wells of the S block. S block contains 96 wells, so we can process 96 samples at a time. After mixing well, 200 µL of the blood samples was loaded into the wells.
Machine setup:
QIAcube HT Prep Manager Software needs to be opened and linked with the machine. Protocols designed for 96 blood samples opened, the Protocol displays the amount of reagents required as well as the place of the turf of each reagent. Reagents are added to the turf, and the turf is placed on the places displayed in the protocol.
Once reagents are added, the QIAamp 96 Elution microtubes rack, the Elution plate, and filter tips are placed into the machine according to the places mentioned in the protocol.
At last, the vacuum chamber needs to be attached to the machine properly to build up sufficient vacuum in the Elution microtubes rack, which contains silica membranes to facilitate DNA binding and removal of contaminants.
After the machine setup, the protocol is run, and automated DNA extraction begins.
Automated Extraction Process:
The automated extraction process begins with cell lysis followed by precipitation of DNA. The protocol contains 2 to 3 washing steps, each of which is followed by a vacuum.
The last elution buffer is added, followed by vacuum. After 1.5 to 2 hours of protocol, DNA will be eluted in the elution plate. DNA can be stored at 2 to 8°C till further use.
Advantages:
The machine reduces the time required to extract the DNA from large numbers of samples. One can extract the DNA from 400 to 500 samples easily.
The machine is capable of extracting the DNA with consistent quality, i.e., 260/280 ratios between 1.7 to 1.9, with high concentrations.
The full automation of the machine, UV light, and HEPA filter minimizes the chances of contamination.
The protocol and machine setup are very user-friendly.
The flexible auto sample calibration saves time, cost and reagent, as the software automatically detects with 8, 16, 24,…., 88, 96 samples are processed in the machine and accordingly manages the solution and other utilities.
Disadvantages:
Sample loading needs to be done manually, which can lead to human errors.
Instruments and reagents are costly compared to reagents used in manual methods of DNA extraction.
The machine requires regular maintenance, cleaning, and checks.
Timely calibration of the robotic arm is required as it may sometimes be stuck or work abnormally.
If blood samples are clotted, then they will be stuck in the Elution Microtubule Rack, as clotted blood will not be removed during washing steps, and DNA will be contaminated.
Related article: Comparison between manual vs spin column vs automated DNA extraction.
Wrapping up:
QIAcube HT is an excellent choice for producing high-throughput results in less time. It is one of the best instruments for blood DNA isolation in labs that require high-throughput data.
In my opinion, labs dealing with high sample loads and microbial testing must have to go for the QIAcube HT. However, it is not meant for smaller or college-level laboratories.
I hope this review will help you to understand the importance of QIAcute HT in genetic research.
Resources:
QIAGEN QIAcube HT– product detail, service plans, resources, FAQs.
