one of the most common methods for visualizing and identifying dna fragments is called agarose gel electrophoresis with just a small gel like this which feels a bit like thick jello we can explore the world of dna i'm dr alex danis with mini pcr bio and today we're going to explore this important laboratory technique electrophoresis is a long word that means carried by electricity in the lab it refers to the movement of molecules like dna rna or protein mobilized by an electric field through some kind of substance one of the most common uses of electrophoresis is to use an agarose gel to separate pieces of dna in order to visualize them and determine their sizes today we're going to take an in-depth look at that process in any gel electrophoresis setup there are two electrodes a positive electrode near one side of the gel and a negative electrode near the other when we turn the power supply on the two electrodes create a difference in charge on the two sides of the gel this creates an electric field through the gel how electrophoresis separates molecules is affected by the molecule's size and charge charge causes a molecule to move through an electrophoresis gel as it is attracted to the oppositely charged pole positively charged molecules are pulled towards the negative electrode negatively charged molecules are pulled towards the positive electrode and neutral molecules won't move at all because dna is negatively charged it will always move towards the positive electrode in an electric field with no obstacles all fragments of dna would move at the same speed towards the positive electrode but scientists want to separate dna fragments by size so in gel electrophoresis they add them to a gel full of irregular holes and pores almost like a sponge when moving through such a complex substance the size of the dna fragment determines how quickly it moves short pieces of dna will move quickly through the gel zipping through all of the pores without difficulty while long pieces of dna will encounter more hurdles moving through the small pores making them move more slowly through the gel the short pieces will travel quickly towards the far side of the gel while the longer pieces will move more slowly and travel a smaller distance in the gel in this way we can use gel electrophoresis to separate a dna sample based on size now that we know what happens in gel electrophoresis let's talk about how we actually perform this technique in the lab first we need to make our gel dna electrophoresis gels are usually made from agarose a long polysaccharide molecule extracted from seaweed making a gel is a bit like making jello you dissolve a powder in a liquid boil it and allow it to cool and thicken in a mold to create an agarose gel we dissolve agarose in an electrophoresis buffer boil it and add it to a gel casting tray typically agarose comes as a powder but it also sometimes comes as a pre-weighed tablet we usually also add a dna stain at this step to make visualization of our samples easier later on to learn more about gel pouring you can watch our how to pour a gel video linked below in order to see our sample in the gel we first need somewhere to add the dna to accomplish this we place a comb at one end of the gel here we have poured two gels when the gel cools and hardens we pull this comb out of the gel and small wells are left behind the wells are like little pockets in the gel and they are how we put our dna into the gel at the start of an electrophoresis run when the gel is cooled we place it into a gel electrophoresis chamber we covered the gel with running buffer which helps to conduct electricity before adding a dna sample to our gel we mix it with a loading die though often this die is already added this dye is more dense than the running buffer that the gel sits in so when we carefully pipet the mixture into the wells at one end of the gel the dna will sink to the bottom the color of the dye lets you see that your samples have been loaded properly into the wells the dye is also negatively charged and tinted so that we can more easily track the movement of molecules through the gel once our samples are loaded we will close the lid and turn on the power here we're using the blue gel from mini pcr bio which combines an electrophoresis chamber and visualization system the blue gel will take about 20 minutes to run once the gel has run we need a way to visualize our dna many different dna stains can be used for gel electrophoresis but they all bind to dna and make the dna visible these stains are different from the loading dyes we discussed before because they bind directly to the dna using fluorescent stains we can visualize our dna just by turning on a safe blue light here in our blue gel electrophoresis system we can simply turn on the light to visualize our dna and directly capture images using a smartphone without transferring the gel to a second location using a dark hood can help to see the bands in a bright room we can even use our phones to make a movie of our gel as it is running because the dna runs in a straight line from the well towards the far end of the gel we call each region of the gel that a single dna sample runs through a lane here the lanes in the middle of the gel represent the dna in each of our samples here we have a lane with two bright stripes called bands each band is actually billions of dna fragments all of the same length that all moved through the gel together at the same speed because of their identical sizes all of this dna started in the well here and traveled in this direction through the gel how quickly a dna fragment moves through the gel compared to another can tell us how big they are in comparison to one another for example in this lane this band labeled a has moved farther through the gel than band b so i know that the dna in band a is smaller than the dna in band b but usually we want to know the actual length of the fragments of dna we are separating to better assess the size of our dna fragments we typically add a dna ladder to one of the wells in this gel the ladder is in the leftmost lane a ladder is a sample of prepared dna fragments of known lengths that acts like a ruler we can later compare our dna samples to the smallest fragment which is only 100 base pairs will move the farthest through the gel then the 200 base pair fragment the 300 base pair fragment etc to determine the size of each band we can compare them to our ladder one band contains dna that is about 250 base pairs long and the other contains dna that is about 150 base pairs long if we look in the next lane we can see one band that is about 400 base pairs long dna electrophoresis allows you to check and see if a piece of dna of a specific size is present in your sample or not this can help you figure out the likely identity of that piece of dna helping to confirm an infection identify an individual by dna fingerprinting and more it is especially useful after pcr to confirm whether or not you amplified a desired piece of dna you can learn more about pcr by watching our video linked below gel electrophoresis is an invaluable tool in the molecular biology lab allowing us to visualize and analyze dna blue gel and gelato electrophoresis and visualization systems for mini pcr bio make this process efficient easy and economical to find out more about the blue gel system and mini pcr bio learning labs that can help to bring gel electrophoresis to your lab or classroom you can visit minipcr.com you