Frequently Asked Questions
used for a variety of genomic and proteomic applications. A key feature of magnetic beads is
that they can be easily captured from liquid and re-suspended in liquid
by attaching and detaching from a magnet, respectively. Furthermore, the surface
of the bead may be modified to capture a specific target. PSS has developed and
patented MAGTRATION® Technology for automated DNA/RNA purification,
and has commercialized a variety of systems utilizing this technology.
In addition, recently PSS has expanded Magtration® Technology into Proteomics applications.
Q What are the magnetic beads composed of?
A Magnetic beads are usually made of silica impregnated with iron.
Q What is the basis for DNA-magnetic bead binding?
A Under chaotropic conditions, DNA has an affinity for silica coated beads. The DNA is released from the beads by addition of a low ionic strength buffer and heat.
Q What are paramagnetic beads?
A Compounds that posses magnetic quality only when exposed to a magnetic force.
Q How large are typical magnetic beads?
A Generally 3-10 microns in diameter.
Q Can the beads be re-used?
A We do not recommend re-use of magnetic beads
Q Can the beads be coated with other materials
A Yes. For example, streptavidin coated beads may be used to isolate biotin labeled proteins.
Q Can alkaline lysis protocols be used to release DNA?
A Yes, although some modifications may be required for compatibility with MAGTRATION Technology.
Q What types of nucleic acids can be purified with MAGTRATION Technology?
A Genomic DNA, mRNA, total RNA, plasmids
Q What types of samples can be analyzed?
A Whole blood, dried blood, buccal swabs, cell cultures, PCR clean up, dye terminator removal.
Q How does one calculate the purity and quantity of a DNA sample?
A. Quantity and quality of DNA is accomplished by measuring absorbance at A260 (DNA), A280 (protein) and A320 (background).
For DNA quantitation: A260 A320 = corrected DNA quantity. 1 absorbance unit at A260 = 50 ng/ml (be sure to correct for any dilutions)
For DNA purity (protein carry over) measure A260-A320 / A280-A320. The final value should be between 1.7 and 1.9
Q Is it possible extract nucleic acids from a sample other than whole blood?
A. It is possible to extract nucleic acidsfrom various samples such as cells, animal tissues,bacteria, plants and viruses after
pretreatment of sample.Contact us for details.
Q. What is the Magtration?
A. Magtration is a PSS's proprietary technology of handling and separating magnetic beads particles with a uniquely shaped
tip in reactionsthat use magnetic particles. It is a term we newly created, of which derived from abbreviating "Magnetic Filtration" It means to separate and fractionation the sabstances by use of a magnet.
Q Is MAGTRATION true walk away technology?
A Yes. Once the samples and reagents have been loaded onto the instrument, just start the protocol and no additional intervention is required through to collection of the purified nucleic acid.
Q How does MAGTRATION differ from other magnetic bead based systems?
A PSS has patented a special pipetting tip that traps the bound DNA to the inner wall of the tip when a strong magnetic force is applied. This differs form other systems that collect the bound DNA on the bottom of a reaction well. The patented PSS technique facilitates washing and recovery of the target DNA.
Q What are the power requirements for MAGTRATION systems?
A AC 100~120V or 200-240V, 400VA and 50/60Hz
Q Is a computer included?
A No computer is supplied with the SX-6G, SX-8G or SX-96GC
Q What are the computer requirements?
A OS: Windows XP ~ Windows 7 (32bit)
CPU: Pentium dual core processor / AMD Atlon II X2 or higher
Memory: 2G byte or higher recommended (1Gbyte minimum)
HDD: 500 Mbyte available space
Q What is the strength of each magnetic?
Q. What type of material is the deck made of?
Q What type of material are the tips made of?
Q Are the tips disposable?
A Yes, to prevent cross contamination
Q Is the system ventilated?
A Both the upper chamber and the power supply have an active ventilation system
Q Do the instruments accept standard 48-and 96-well microtiter plates?
A The SX-6G accepts a PSS original design 42-well plate. The 8G Compact, SX-8G, M1200and SX-96GC will accept standard 96-well microtiter plates
Q Why are there cooling and heating blocks?
A Heating is necessary to release purified DNA from the magnetic beads (in conjunction with a low ionic strength buffer). Cooling is used to reduce evaporation of stored samples.
Q How is heating and cooling achieved?
A Peltier devices
Q Is there any right combination of reagent and IC card?
A There is a favorable combination of reagent and IC card.
Inappropriate combination may lead to malfunction and troubles of the system.
Use an IC card suitable for the reagent
Q How should we clean up the system?
A. Clean the system by wiping it with Kimtowel<span class="rMark">®</span> (paper towel for laboratory use) wetted with 70% ethanol.
Avoid the area where electronic parts are located and where grease is
coated.<br>*The nozzle area may have a black silicone ring coated with silicone
grease, depending on the systems. Please note that the removal of the silicone
grease may lead to inadequate fitting of the pipetting tip and leakage (liquid
QIs the system maintenance necessary?
A Regular maintenance by the customer is recommended for long time and reliable use of the apparatus. For details, see the related pages in the instruction manual of each device. Paid maintenance is also available, and please contact us, if you desire.
Q What is Biostrand?
A. Regular maintenance by the customer is recommended for long time and reliable use of the apparatus. For details, see the related pages in the instruction manual of each device. Paid maintenance is also available, and please contact us, if you desire.
Bio-StrandR is a new analytical technology proposed by PSS. It performs SNP analysis and quantitative analysis of genes with a device called "Bio-Strand tip" carrying hundreds of DNA fragments for detection immobilized at a constant interval onto a plastic thread or natural resin thread (diameter: 50 to 100μm, length: 2 to 3 m). Since it is possible to do operations such as hybridization and washing only by repeating aspirating and dispensing of reagent into a tip, the system may be automated easily.
Q. What is BIST?
A. BISTR, an abbreviation of "Beads array In Single Tip", is a PSS' proprietary detection method allowing simultaneous analysis (multiplex processing) of up to 18 analytes (9 SNPs in the case of SNP analysis), in which each of the beads sealed in a straw-shaped plastic tip corresponds to a particular test item.
Q What type of software runs the instrument?
A PSS HiMICO software is used for instrument programming and control
Q Is there a graphical user interface?
Q Can other applications be run while using HiMICO software?
A No. We do not recommend that any other applications be open or running while the HiMICO application is in operation.
Q Can we use original application
A Any protocol may be prepared, if the apparatus is an open-platform apparatus. Special-order machines are also available. Contact us for details.
Q. The yield dropped almost to half after extraction?
A. The extraction result may be influenced, if an un-fresh reagent is used. Use reagents after purchase without storage for an extended period of time.
Q The system makes noise during operation, after the installation site is moved?
A. The axis of the system may be disoriented during move, for example, by impact. Operation of the system in such a state may result in troubles and failure of the system. The system should be readjusted after move of the system (especially with impact). Please contact us.
Q. A sample or reagent is sucked into the nozzle? Is it OK?
A. Use of the apparatus, after the reagent or sample is aspirated into it, may lead to leakage and fluctuation of aspirating/dispensing amount. It affects system operation and extraction result, and thus, please contact us as soon as possible.
Q It is hard to make a hole in the alminum seal for the (prepackaged) reagent?
A. Deterioration in piercing efficiency for example by corrosion of the piercing pin end may lead to easier piercing defect of the aluminum seal. Use of it, as it is, may lead to failure of the system. As it will demand maintenance of the system, please contact us.
Q. Stainless steel parts such as reagent tank rack are corroded?
A. Stainless steel is used for example for reagent tank rack, and will cause rusting on it when used chlorine sanitizer during cleaning. If a chlorine sanitizer is used, make sure to wipe the surface with alcohol or water, so that no chlorine sanitizer remains on the stainless steel position.
Q. The extraction yield of Plasmid DNA is low?
A. The yield becomes smaller, when the copy number of plasmid DNAs in sample is low. Increase the amount of the microbe used. (The system is compatible with 1 ml of culture solution having an O.D.660 of up to 9.0.)
Q. The purity of the extracted DNA is low?
A. When an excessive amount of sample is used, magnetic particles become hardly dispersible in the steps of adsorption and washing process for nucleic acids and the purity of the extract may decline. Use a microbial cell suspension with an O.D.660 of 9.0 or less
Q. The processing in the following step by using the extracted Plasmid DNA does not proceed well?
A. It may be because of inhibition by ethanol present in a trace amount in the extract. The extract, when used in an amount of more than 1/5 of the sequencing or PCR reaction solution, may inhibit the reaction and thus, reduce the amount of the extract used. Alternatively in the case of the inhibition by ethanol, heating of the extract (75°C, 40 minutes) may reduce the inhibition.
Q. The eluate is colored?
A. The extract seems brown in color, if it is contaminated with magnetic particles. Although there is no adverse influence on downstream steps, it is preferably to centrifuge the solution (10,000 g, 1 minute) for removal of the magnetic particles.
Q.The extraction yield of genome DNA is low?
A. Make sure that there is no problem in the storage temperature of the blood sample use. Please use the sample in extraction operation, after it is heated up sufficiently to room temperature. In the case of a blood sample stored refrigerated, the yield may become smaller when the storage period is elongated. Make sure that there is no problem in storage temperature and place of the reagents. Storage of reagents in a place under vibration may lead to deterioration in performance of the magnetic particles. Avoid storage in a place under excessive vibration
Q. PCR does not proceedwell?
A. When Tris-HCl is selected as eluate, there may be some influence, depending on the PCR reaction condition. In such a case, use the sample after extraction operation carried out by using distilled water as the eluate.
Q. The extraction yield of total RNA is low?
A. There are many possible causes. (1) Excessive amount of sample Use of a sample in an amount more than a particular value does not lead to increase, but leads to decrease of the yield. Reduce the sample amount. In the case of a cell sample, use it at a concentration of 1×106 cells/200 μl or less, while in the case of a tissue sample, use it at a concentration of 10 mg or less/150 μl. (2) Insufficient solubilization and homogenization of sample Agitation or homogenization of the sample may be insufficient. Extraction treatment in the state where solid matters remain in the solution because of insufficient homogenization may cause tip clogging during extraction operation, leading to decrease of the yield. (3) Tip clogging Some tissues contain many muscle fibers and thus, make sure to conduct homogenization operation sufficiently. (4) Condition of prepacked reagents Tap or shake the reagent cartridge gently, when the cartridge reagent contains air bubbles or when there is deposition of reagents or water droplets in the reagent-sealing region or in the upper region of internal cartridge well. Processing with residual air bubbles may prohibit complete aspirating of the reagent and cause, for example, foaming during agitation, which often results in deterioration of the yield.
Q. The purity of extracted total RNA is low?
A. The purity may decline, when an excessive amount of sample is used. Reduce the sample amount before extraction operation (click here to see relevant Q A/FAQ). When the RNA concentration in the extract is low, the A260/A280 value may decline. Contamination of magnetic particles in the extract may lead to increase of background (A320) or generation of noises. Use the supernatant after centrifugation (10,000 g,1 minute) in absorbance measurement and various electrophoretic analyses.
Q. The extracted total RNA is decomposed?
A. The RNases may not be inactivated sufficiently, if an excessive amount of sample is used. Reduce the sample amount before extract operation (click here to see relevant Q A/FAQ). Sample-collecting operation, storage state and homogenization-solubilization condition also have an influence on decomposition of RNAs, and close attention should be given to these parameters as well. In addition, avoid storage of the extract for a long period andstore it soon in a deep freezer(-80C).
Q. RT-PCR does not proceed well?
A. If there are intron-less genes and genes very similar in sequence on genome, influence by the genome DNA should be taken into consideration. Use a total RNA extracted by a protocol including DNase treatment. When an excessive amount of sample is used, it may influence on the extraction yield, purity and decomposition of total RNA
Q. Processing in the following step by using the extracted DNA does not proceed well?
A. Extraction reagents and sample impurities may remain in and exert an influence on the next steps, depending on the state of the sample (storage period, storage temperature, etc.). Please confirm that the desired genome DNA is extracted without any problem by electrophoresis or absorbance measurement
Q. The system is tuned off by power failure. Is it possible to resume operation continuously?
A. The system is reset to the initial state during resumption after power failure. It is thus impossible to resume continuous operation. Would you please set samples, consumables and others and start operation from the first once again.
Q The system is tuned off suddenly?
A. Make sure to confirm that the AC power source cable is connected to the plug socket and the apparatus reliably. Use the AC power cable attached. If there is no power supply even when the AC power cable is connected, the fuse of the apparatus may be disconnected. Contact us in such a case
Q The number of the samples processed is desirable increased during processing?
A. The number of the samples cannot be increased during processing. Please do not open the door or place your hand or consumables into the apparatus during operation, because it may result in failure of the apparatus and injury of the operator.