The movement of different sized dna particles through electrophoresis
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Smaller strands do in fact run faster than larger mass DNA molecules. Have you ever had one run off the end of the gel? Not uncommon. Sometimes you have to lower the run time just to catch all the fragments of say a digest or a PCR of small size DNA samples.
The reason is clear if we think of a gel as being another tool like a chromatography of some kind, HPLC for example or even a paper chromatography. The principle is differential migration in a charged field, for gel electrophoresis. The charge on the DNA is the electrical current applied to the buffer, and it acts on the polarity of the molecule. The polarity is due to the same principle that holds double stranded DNA together, namely hydrogen bonding. The molecule has net charge from the many hydrogen molecules of the backbone.
In a matrix such as gel, agarose or polyacrylamide, the molecules are physically hindered from traveling in the direction the current is pulling them. Either you are a small molecule that can fit thru the spaces of the matrix or you are a large folded molecule that can not pass thru the much smaller matrix spaces. Think of a tank driving thru a mine field versus a foot soldier, the former encountering much more surface area in the mine field and likely therefore not to pass thru.
Its not a bad idea to run a ladder, as well as a positive and negative control with your gel. The ladder demonstrates the principle well, smaller molecules at the bottom of your ladder and larger molecules at the top.
The principles of the gel matrix become even more obvious to those who have ever made a batch of gel incorrectly with too much or too little gel in solution. Gels are poured much like any other recipe or formula of known proportions. Get too much matrix in the gel and it becomes prohibitively dense for DNA to migrate thru, making run times seem askew.
Regards Vishal______(BhamBhamBhole)
__
#BeBrainly✌✌
The reason is clear if we think of a gel as being another tool like a chromatography of some kind, HPLC for example or even a paper chromatography. The principle is differential migration in a charged field, for gel electrophoresis. The charge on the DNA is the electrical current applied to the buffer, and it acts on the polarity of the molecule. The polarity is due to the same principle that holds double stranded DNA together, namely hydrogen bonding. The molecule has net charge from the many hydrogen molecules of the backbone.
In a matrix such as gel, agarose or polyacrylamide, the molecules are physically hindered from traveling in the direction the current is pulling them. Either you are a small molecule that can fit thru the spaces of the matrix or you are a large folded molecule that can not pass thru the much smaller matrix spaces. Think of a tank driving thru a mine field versus a foot soldier, the former encountering much more surface area in the mine field and likely therefore not to pass thru.
Its not a bad idea to run a ladder, as well as a positive and negative control with your gel. The ladder demonstrates the principle well, smaller molecules at the bottom of your ladder and larger molecules at the top.
The principles of the gel matrix become even more obvious to those who have ever made a batch of gel incorrectly with too much or too little gel in solution. Gels are poured much like any other recipe or formula of known proportions. Get too much matrix in the gel and it becomes prohibitively dense for DNA to migrate thru, making run times seem askew.
Regards Vishal______(BhamBhamBhole)
__
#BeBrainly✌✌
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