Genome Compiler's new gel simulation feature allows you to visualize the digest results on a running gel and save it as an image. This picture can assist you to analyze the results by simply comparing it to the actual gel results. In order to simulate the gel, digest your project and press on 'Gel Simulation':
- Digest – select your preferred restriction enzymes and click ‘Run Digest’.
- Press 'Gel Simulation'
- Set ladder - select a ladder from our supplied list to simulate the gel according to your preference. Each time you set a ladder the fragments will be arranged accordingly.
- Fragments length - hovering over the fragments will display the fragment's length. Note that fragments which do not separate on the running gel will be displayed as one white line with several sizes.
- Gel limits - fragments that fall outside the gel ladder limits will not be displayed in the simulation, a warning will appear specifying them. This can direct you to choose the right ladder for your experiment.
- Save Gel as Image - you can save the simulation to your computer as an image in order to easily compare it to your results or share with others.
About the technique:
Gel electrophoresis is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge. Gel Electrophoresis is mostly used for the following purposes:
- Estimating of the size of DNA molecules following restriction enzyme digestion. For example, in restriction mapping of cloned DNA.
- Analysing PCR. For example, in molecular genetic diagnosis or genetic fingerprinting.
- Separating restricted genomic DNA prior to Southern transfer, or of RNA prior to Northern transfer.
The results can be analysed quantitatively by visualizing the gel with UV light and a gel imaging device. The image is recorded with a computer operated camera, and the intensity of the band or spot of interest is measured and compared against standard or markers loaded on the same gel.
Using an electric field, molecules (such as DNA) can be made to move through a gel made of agar or polyacrylamide. The electric field consists of a negative charge at one end which pushes the molecules through the gel, and a positive charge at the other end that pulls the molecules through the gel. The gel is placed in an electrophoresis chamber, which is then connected to a power source. When the electric current is applied, the larger molecules move more slowly through the gel while the smaller molecules move faster and easily through the gel's pores in a process called sieving. The different sized molecules form distinct bands on the gel.
In most cases, the gel is a cross-linked polymer whose composition and porosity is chosen based on the specific weight and composition of the target to be analysed. When separating proteins or small nucleic acids (DNA, RNA, or oligonucleotides) the gel is usually composed of different concentrations of acrylamide and a cross-linker, producing different sized mesh networks of polyacrylamide. The gel forms a solid, yet porous matrix. Acrylamide, in contrast to polyacrylamide, is a neurotoxin and must be handled using appropriate safety precautions to avoid poisoning. Agarose is composed of long unbranched chains of uncharged carbohydrate without cross links resulting in a gel with large pores allowing for the separation of macromolecules and macromolecular complexes.
There are molecular weight size markers (ladders) available that contain a mixture of molecules of known sizes. If such a marker was run on one lane in the gel parallel to the unknown samples, the bands observed can be compared to those of the unknown in order to determine their size. The distance a band travels is approximately inversely proportional to the logarithm of the size of the molecule.
DNA may be visualized using ethidium bromide which, when intercalated into DNA, fluoresce under ultraviolet light, while protein may be visualized using silver stain or Coomassie Brilliant Blue dye. Other methods may also be used to visualize the separation of the mixture's components on the gel.