Define electrophoresis List factors that affect movement of

Define electrophoresis. List factors that affect movement of a charged molecule in an electrophoresis field.

Solution

Factors that affect movement of a charged molecule in an electrophoresis field:

Nature of the agarose gel

Charge, size of the particle (DNA or protein)

The molecular sieving effects exerting on the isolating particle

Explanation:

On an electrophoresis power source, the anode (positive charge) is red and cathode (negative charge) is black. When you put your gel in the rig, the end with the comb/wells with sample DNA to be at the red because DNA is negatively charged and upon electrophoresis, it migrates towards anode (red) where positive charge located. This type of system is going to determine the “charge and various fragments” in the given sample. Black end is negatively charged (cathode) & positively charged molecules are going to migrate towards the cathode. Therefore, migration rate during electrophoresis in the sample of comb is completely based on “charge & size”. The tiny pores are in the comb acts as a sieve to allow migration of small molecules according to charge & resolve larger molecules to migrate to a lower distance.

A denaturing agarose gel is normally used in examining the “exact quality of any RNA preparation”. RNA yield will be maximum with this gel using a denaturing gel system. This type of gel system is being used in gel electrophoresis of RNA as “Majority of RNA produce extensive secondary structure through intramolecular base pairing”, finally this is going to avoid migration of RNA as per size. A positive control RNA is needed to prevent unusual results.

Native agarose gel loading usage for assessment of any RNA preparation through electrophoresis is not much recommended as “RNA secondary structure may completely changed on native gel” result in “no migration of 28S and 18S rRNA bands according their true size”. Finally, non-reliable bands may be obtained during analysis of RNA.

Native agarose gel electrophoresis may be sufficient to judge the integrity and overall quality of a total RNA preparation by inspection of the 28S and 18S rRNA bands. The secondary structure of RNA alters its migration pattern in native gels so that it will not migrate according to its true size. Bands are generally not as sharp as in denaturating gels, and a single RNA species may migrate as multiple bands representing different structures.