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ORIGINS by Elchrom Scientific / SEA 2000

The ORIGINS electrophoresis system in combination with AL´s pre-cast gels offers the following: high resolution, highest reproducibility and high throughput. The ORIGINS achieves these standards by a highly linear electric field, buffer circulation and temperature control.

  1. The results generated with the ORIGINS system are highly reproducible and reliable. Migration distances and times are fully predictable, hence no DNA fragments will be lost. Similarly, the resolution (distance between two neighboring fragments) can be accurately determined prior to the run using Elchrom´s Elquant software.
  2. Pre-cast gels guarantee very accurate gel dimensions and therefore make comparisons between different samples easy and DNA size estimations precise.
  3. The same running buffer can be used in consecutive, fast runs without compromising the results, mainly the reproducibility.
  4. Runs at a constant elevated temperature (55 oC) enable the most precise estimation of DNA size.
  5. Electrophoresis at 55 oC cuts the running time by half, therefore doubling the throughput. Closely spaced bands are best resolved at 55 oC in the majority of cases.
  6. With the S-4x13 and S-4x25 gels, DNA fragments that exit the first gel section do not enter the second (due to buffer circulation). Band patterns are clear and easy to interpret.

A2: Normally there is no need for special cleaning nor maintenance. After 4-5 runs, drain the buffer through the drain valve on the left side of the unit (Quick fit), and rinse the gel compartment with deionized water. TAE running buffer prevents the growth of most bacteria and fungi (due to presence of EDTA). When another buffer is used (especially phosphate buffers), empty the apparatus immediately after use and rinse it extensively with distilled water. In case, a contamination occurs, clean the buffer compartment of the ORIGINS with 0.1% SDS in TAE buffer at 55 °C for several hours or overnight with the pump switched on. For more severe contaminations, use 0.1 % SDS in 0.1 M NaOH. Incubate with the pump switched on at room temperature overnight.

A3: Common reasons for distorted bands are:

  • high salt concentrations in the samples. Dilution or dialysis will solve the problem.
  • the pump being switched off too late after the run.
  • the level of the running buffer is too low or too high. The optimal running buffer level is marked on the left hand side in each buffer compartment.

A4: AL' ORIGINS / SEA 2000® apparatus is CE marked (European Union electrical safety standards).

Precast Gels

Elchrom's pre-cast ready-to-use gels are made of a novel type of gel material. The gels were designed to resolve fragments in the range from 20 bp up to 20 kb with a resolution down to 1 pb for small fragments (below 150 bp). The gels are thermally stable and do not melt at 95 °C. They are also biochemically inert and do not inhibit enzymes in any downstream reactions. Thus, it is possible to use gel fragments containing the band of interest for direct re-amplification, sequencing or cloning.

Mini gels: 96 x 66 mm

Wide Mini gels: 96 x 131 mm or 40 x 131 mm

Thickness: 3 mm

Spreadex, Poly(NAT), GMA, Clearose, PCR CheckIT, Short Fragment Gels, Oligo Purification Gels

Formats of the gels Dimension (mm) Running distance (mm) wells/gel

Mini gels: 96 x 66 57 / 87 12 / 8 wells on the same gel

Wide Mini S-2x13 96 x 131 87 13

Wide Mini S-4x13 40 x 131 40 13

Wide Mini S-2x25 96 x 131 87 25

Wide Mini S-4x25 40 x 131 40 25

Wide Mini S-2x104L 96 x 131 16 104

Wide Mini S-2x104 96 x 131 8 104

Wide Mini S-2x200 96 x 131 8 200

Choosing the appropriate pre-cast gel is dependant on three criteria: the type of molecule (RNA or DNA), the total length of the fragments to be analysed and the required resolution. The electrophoresis system of Elchrom is designed to achieve particularly high reproducibility. The system also allows to predict the running distance of any given DNA / RNA fragment in any given pre-cast gel. Elchrom Scientific therefore offers a web-based software tool (http://www.elchrom.com/support/tools) to chose the optimal gel for every possible application. Simply enter the sizes of your fragments and the software tool will suggest the optimal gel either by shortest running time or best resolution. The software tool also allows you to predict the running time and distance for every pair of fragments separated by at least 1 mm.

All Elchrom's pre-cast gels must be stored at 4 - 8 °C. Do not freeze the gels! Freezing will destroy the matrix of the gel by the formation of microscopic ice crystals. Also, avoid storing the pre-cast gels at room temperature (expiry date is dramatically reduced).

Elchrom's gels are base on a novel, synthetic, non-toxic matrix. This matrix is susceptible to extreme and fast temperature changes. Such changes become most apparent by the formation of air bubbles inside the gel matrix. Therefore, all pre-cast gels need to be brought to ambient temperature before running. For an electrophoresis at high temperature, the gel has subsequently to be pre-warmed for 30 minutes. To do so, place the gel onto a catamaran inside the chamber (Do not submerge the gel in the buffer during pre-warming). For further information, go to movie.

Loading too much DNA per lane affects the migration of individual fragments rather substantially (overloading). Furthermore, the optimal concentration of DNA and therefore resolution also depends on the detection method: for Ethidium Bromide staining, the optimal concentration of dsDNA is between 2 and 20 ng per band; for SYBR staining, between 0.4 and 4 ng per band.

Spreadex, Poly(NAT), GMA and Short FragmentTM : 6 months*
PCR CheckIT and Clearose RNA: 18 months*

*if stored properly.

The expiry date is very critical for Elchrom pre-cast gels. With prolonged storage, hydrolysis influences the resolution by severely slowing down the mobility of DNA / RNA fragments. As an additional effect, expired gels also show a stronger background with SYBR dyes and they tend to swell detach from the plastic backing. We do not recommend to use any pre-cast gels after their expiry date

High buffer concentration reduces the staining sensitivity because the cations of the buffer compete with the dye to bind DNA. Salts, especially Calcium and Magnesium, displace the dye and decrease the sensitivity. Ideally, water of the highest purity should be used for staining and destaining.

Only PCR CheckIT gels can be air dried. All our other gels do, unfortunately, wrinkle and occasionally break. Vacuum drying has not been tested by us so far. For longer storage, we recommend freezing (except PCR CheckIT gels).

All pre-cast gels by Echrom Scientific show higher transfer efficiency than acrylamide gels. The transfer time is also faster compared to agarose gels (high voltage is applied):

• Transfer efficiency with acrylamide gels: max. 50% (in Southern blots)

• Transfer efficiency from Elchrom gels: close to 100% (in Southern and Northern blots)

Yes. More than 0.01 % SDS in your sample buffer will impair the resolution

All Gels are run in standard TAE buffer.

The final concentration of the running buffer should be 30 mM TAE (according to Maniatis this equals a 0.75 x solution).

Elchrom offers a standardised TAE buffer stock solution (P/N 3031).
One packaging unit consists of 20 x 50 ml tubes with 40 x TAE buffer (1.2M Tris-Acetate- EDTANa).

Borate buffer (TBE: Tris Borate EDTA Buffer) must NEVER BE USED, AS BORATE WILL DESTROY THE GELS! Even smaller traces of borate buffer will influence the property of the gel already.

Elchrom's pre-cast gels were developed to give highest resolution and reproducibility only in combination with ORIGINS and SEA 2000 electrophoresis units. In order to achieve such high quality results, the parameters of an electrophoresis need to be tightly controlled which is not the case in a regular unit. However, Elchrom's pre-cast gels can be run in standard units if they have a buffer volume of at least 600 ml. The running time needs to be optimised, though. When using a regular unit, the temperature of the running buffer increases with time. This results in faster migration of the DNA fragments. It is therefore impossible to predict the running distance of a certain fragment. The distance may even differ between different runs and consequently abolish any reproducibility.

Optimal loading volume: 4 - 8µl
Minimuml loading volume: 4 µl
Maximum loading volume for
- Mini: 18µl
- Wide Mini S-2x25, S-4x25, S-2x104L, S-2x200: 14 µl
- Wide Mini S-2x13, S-4x13, S-2x104: 25 µl

Bind-ET (TM)

The Bind-ETTM was designed to purify any inorganic solution (e.g. salt buffers used for electrophoresis, e.g. TAE, TBE) from certain chemical compounds such as DNA-staining dyes. Do not use the Bind-ET to purify solutions containing more than 10% organic solvents! Chemical compounds bind to resins inside the cartridge of a Bind-ET by an ion exchange reaction. This reaction is not limited to the binding of Ethidium Bromide (EtBr) but also eliminates other fluorescent dyes (such as SYBR Gold / Green) from the flow-through. However, it is crucial that the flow rate does not exceed 3 L per hour to guarantee complete removal of the compound from the buffer.

The cartridge is susceptible to blockage by pieces of agarose or other particles. This will eventually completely abolish the buffer flow. The Bind-ETTM is therefore equipped with a sieve in the lid of the reservoir. All solutions must be poured through the sieve to eliminate all particles or gel pieces.

Cartridges used for several months have been demonstrated to show a slower flow rate. However, this does not effect the binding efficiency of the cartridge. Similarly, the growth of bacteria or fungi inside the cartridge can not be entirely excluded if the cartridge has been used to purify phosphate containing buffers. Again, this does not affect the efficiency of the cartridge

The binding capacity of each cartridge is 2 g of Ethidium. Using a standard concentration of 0.5 ug /ml of Ethidium Bromide, the cartridge can purify up to 4'000 L of buffer. The concentration of Ethidium in the purified flow-through can be tested by UV-spectrometry at 220 - 400 nm or 280 nm (UV-transilluminator). Elchrom Scientific guarantees that the flow-through of the cartridge is below detection limit if used correctly for up to 2 g per cartridge.

Each cartridge can bind up to 2 g of Ethidium. We advise to keep a log-book for each cartridge. If saturated, cartridges can be disposed of by incineration which destroys Ethidium. The mantle of the cartridge is made of PP (polypropylene). Burning of PP does not release any dangerous gases.

The cartridge can theoretically be stored for a long time if properly sealed. The only factor that determines the life span is the amount of bound Ethidium (2 g). For long term storage, we recommend to keep the cartridge in its original plastic bag with the yellow plastic caps tightly attached to prevent drying. However, should the cartridge run dry, it can be rehydrated by placing it in a bucket of water overnight (place it in a upright position to allow the trapped air to escape). This will restore functionality completely.

Electrophoresis Accessories

The Catamaran frames are special tools to position and fix the gel in electrophoresis tanks such as the ORIGINS or the SEA 2000®. Catamaran frames also increase the uniformity of the electric field and they help to direct the buffer flow over the gel.

Six sizes of catamarans are available for the ORIGINS and SEA 2000®apparatuses:

2 catamarans for Mini gels: A) to run 12 samples across the short gels side, and B) to 8 samples across the long gel side.
For Wide Mini gels there are 5 different formats:
for half a Wide Mini gel presentation
for half a high throughput Wide Mini gel presentation
for the whole Wide Mini gel presentation
for the whole Wide Mini gel presentation in high throughput format
for Short fragment gels.

Peel-IT™ is a very helpful tool to easily remove the plastic backing of a pre-cast gel from Elchrom Scientific.

The gel is placed onto Peel-IT™ with the plastic backing facing down. Tighten the nylon string (included in every gel box) with both hands and press it onto the plastic backing overhang at the upper end of the gel. Subsequently, use the string to press the plastic backing onto the surface of PeelIT and slowly pull it along the back side of the gel to peel it off the. Eventually, grip the plastic backing with forceps and transfer the gel into an Easy Staining Gel Tray (P/N 2344 or 2344-L). The gel will stick to the plastic backing until it is washed off by the staining buffer. Easy Staining Gel Trays are designed to safely handle all pre-cast gels from Elchrom Scientific.

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eppendorf

gilson

mettler toledo

heidolph

neolab

satorius

systec

thermo scientific

zeiss