This web page will certainly display to erected and also run an agdeveloped gel for DNA samples. You should already be acquainted via the basic ethics of electropohresis, and also I will assume that you have already run an SDS-PAGE gel for proteins.

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You"ll perdevelop DNA electrophoresis numerous times in the time of the quarter. This page isn"t around one certain experiment; it describes the basic method that uses to all your DNA gels. For the details of the particular samples that go on a specific gel, see the lab overview.


We"ll usage the Bio-Rad Mini Below Cell GT for all our DNA electrophoresis this quarter. This form of gel unit is offered in nearly eexceptionally molecular biology lab; many manufacturers make comparable gel devices. To put up your gel, you"ll need to gain all the pieces of the gel apparatus, as displayed below.

The gel apparatus we"re using for DNA is less complicated than the SDS-PAGE apparatus, yet you"ll need to make your very own gel. We"ll usage agoccurred gels for DNA.


Set up your gel apparatus. Put the gel tray into the electrophoresis chamber. Keep in mind that tbelow are two sets of little slots in the gel tray to organize the comb. The tray goes in as displayed, via one collection of slots towards the babsence electrode of the gel box.

The black aluminum pieces are gel spreading gates; drop them into the slots in the chambr and also they will organize the melted agoccurred in the gel tray while it cools and also solidifies.

The comb must be close to the black electrode. The phosphate teams alengthy the backbone of DNA provide it an adverse charge; it will migrate toward the positive (red) electrode throughout electrophoresis. Note that tright here are 2 sets of slots wbelow you can put the comb. The middle place is tbelow so you might use two combs in one gel if you wanted. This would certainly double the variety of samples you can run on the gel, yet you"d only have the ability to run the samples a brief distance dvery own the gel. You will not need to use 2 combs in this lab.


The running buffer for DNA electrophoresis is 1x TBE. It contains Tris (a buffer), Borate salt to boost conductivity, and also EDTA to chelate cations. Dispense 40 ml TBE from the carboy right into a graduated cylinder. (In this lab, it"s constantly 40 ml for DNA gels. You"ll vary the amount of agemerged you usage for various gels, however the volume need to constantly be 40 ml to fit the gel tray.


Pour the TBE into a 125-ml Erlenmeyer flask. Don"t usage a beaker; the flask reduces evaporation and helps prevent the contents from boiling over in the next step.


Weigh out the correct amount of agoccurred. For each gel, you need the ideal amount of agarose to accommodate the sizes of the DNA fragments you"re trying to separate; bigger DNA pieces need a gel with bigger pores (lower agoccurred percentage), or the bands will certainly smear also much. Smaller DNA pieces reqire a gel via smaller sized pores (higher agoccurred percentage); otherwise, the DNA will certainly diffuse out and the bands will be fuzzy.

Typical agarose percentperiods for the Bio 6B lab:

Plasmid & lambda DNA: usage 0.7% to 0.8% agoccurred to prevent bigger fragments from smearing, yet about 1.5% if you desire to closely analyze the smaller fragments of a restriction digest.Small PCR assets, 200-300 bp: 2% agoccurred.

Agemerged portion is in regards to mass/volume; a 1% agoccurred gel would have actually 1 gram of agdeveloped per 100 ml buffer, or 0.4 g agarose/40 ml buffer for our gel devices.


Pour the agoccurred powder right into the flask through the TBE. Microwave your gel flask for roughly 1 minute. The agarose must melt totally, creating a clear solution through no chunks. Caution: after microwaving, the gel solution might be superheated; as soon as you swirl it, sometimes the warm solution boils over. Use a flask gripper to protect your hand also.

It"s best to microwave one flask at a time; doing two flasks at as soon as seems to take more than twice as lengthy, and it"s feasible that one flask will boil over prior to the other is completely melted.


Add the ethidium bromide after your agoccurred is fully melted.

Caution: ethidium bromide is considered perhaps hazardous (but view the web links at the bottom of this page for more information). If it isn"t done currently, put up a terminal for ethidium bromide on the earlier counter, via the ethidium bromide in its second container, a P-20 labeled for ethidium usage, a box of tips, and a beaker for waste tips. Do not carry the ethidium bromide bottle to your lab table; everyone need to go to the ethidium bromide station to do their pipetting.

Bring your flask to the terminal on the earlier bench and include 2 μl of the 10 mg/ml stock solution. Final concentration: (10 mg/ml)(2 μl)=(0.5 μg/ml)(40 ml). Swirl the flask briefly to disperse the ethidium bromide.

Do not microwave an agdeveloped solution containing ethidium bromide; heating the solution will certainly vaporize the ethidium.


Pour the melted agemerged right into the gel tray after it has actually cooled for a pair of minutes. Make sure the comb is positioned correctly, and the agemerged isn’t leaking through under the dams. The agoccurred will certainly circulation approximately the comb, producing the wells. Once you"ve poured it, do not relocate the gel box until the agoccurred is totally solid. This might take around 15 minutes.


Rerelocate the comb. Be certain the gel has actually solidified completely prior to you do this. The entire gel must have readjusted from transparent to translucent, and also it shouldn"t jiggle as soon as you tap the box. The underside of the gel unit must no longer feel warmth. Don"t rush this! If you pull out the comb also early, the wells will collapse, making it tough or difficult to put samples in your wells. You"ll need to start over with a brand-new gel.

Hold dvery own the gel tray while carefully pulling the comb up. It might help to pour a little TBE buffer on top of the gel prior to you perform this.


Remove the gel casting gates.


Pour 1x TBE running buffer right into the electrophoresis chamber, filling both sides until tbelow is just sufficient TBE to cover the gel. The TBE have to fill the wells.

Make sure your wells are correctly developed. Position your gel so the red connector is toward you, and look straight down right into the wells. You must check out cleanly characterized rectangular wells. If you don"t, it might be because the wells have actually fell down.

Almeans place the gel this means when you get prepared to fill samples right into it. By convention, gel photos are always shown via the wells at the height, and the wells are numbered from left to ideal. Positioning the gel this way to load it provides it easier to properly keep track of which sample is in each lane.

Mix each DNA sample via sample buffer before loading it right into a well of your gel. In many instances, it"s ideal to usage the Parafilm method for this. Cut out a tiny item of Parafilm (two squares is plenty) and spreview it out through the waxy side up. Gently pipet a 3 μl drop of sample buffer onto the Parafilm for each sample. (The precise amount of sample buffer isn"t important; you just require sufficient to make your samples sink right into the wells.)

Mix one sample with sample buffer and pack it on the gel prior to mixing the following sample. That method, you will not be able to confuse one sample through one more.

The volume of sample will certainly vary for various experiments, however you can use the same volume of sample buffer (2 or 3 μl) eextremely time.

You have the right to gain the entirety volume of sample + buffer from the parafilm to the gel in one shot. Suppose your sample volume is 20 μl. You have actually your pipetter set at 20 μl while you take up the sample and also mix it via the sample buffer. Then simply press the button a little harder (slightly previous the initially stop) so you can take up the 23 μl of sample + buffer without resetting the pipetter.


Load the samples into the wells. Sit dvery own via your elbows braced on the table, and usage two hands to stabilize the pipetter. Look directly dvery own into the wells. Don"t try to stick the pipet tip right into the bottom of the well. Hold the guideline at the mouth of the well and also gradually squeeze the thumb button; the sample will progressively sink to the bottom of the well.


The blue sample buffer makes the sample clearly visible as it sinks to the bottom. Don"t problem if a small bit of sample ends up on height of the gel; as lengthy as most of the sample is in the well, you"ll check out it. The small amount of sample on top will just disshow up.


Here"s another look at gel loading; in this photo, I"m making use of my left hand to stabilize the pipet guideline. Be certain you don"t poke the pointer into the gel. The agdeveloped is likely to plug the tip so the sample can"t come out -- or, in a worst-situation scenario, you might poke the reminder all the way with the bottom of the gel so the sample leaks out the bottom.


Run the gel. Put the lid on package. It will only fit one way, via the red lead connected to the red electrode on the gel. The DNA is negatively charged, so it will certainly run towards the red (positive) electrode. Make certain your gel is oriented properly within the box (wells towards the babsence electrode). If the gel is in backward, just lift out the gel tray and rotate it roughly. Plug in the lead wires — the red wire to the red plug on the power supply, black to black. It doesn"t issue which of the 2 red or babsence plugs you usage on the power supply.

Set the array to low and the screen switch to volts and also rotate on the power supply. Using the knob, readjust the voltage to about 70 Volts. You have to see bubbles creating in your electrophoresis chamber. Set the display switch to milliamps, and also it should check out roughly 40 mA. The specific amount of present isn"t vital, but make certain you have some existing running through your gel box.

Physics refresher: According to Ohm"s regulation, voltage = current x resistance, or: volts = amps x ohms. When you"re running a gel, the voltage is organized consistent by the power supply, regardless the existing. If you revolve on the power supply via no gel unit connected, you deserve to set the power supply to 70 V, however the existing will certainly be 0 mA. In truth, our power gives never before check out 0 mA; if there is nopoint connected, the display will certainly read roughly 003 mA. If your power supply reads 003 mA, tbelow is no existing running via your gel, and also the DNA isn"t going anywhere. This can occur if you forgot to add running buffer, for instance. It could likewise happen if one of the wires on the gel unit is damaged, which happens sometimes, specifically if someone bends the red or black wires where they connect to the lid. Be gentle.

How much to run the gel: Without UV light, you won"t be able to check out the DNA while the gel runs. You"ll primarily want to run your DNA gels for around 15-50 minutes. There"s no tough dominance around just how far to run your gel; you simply should run it far sufficient for the bands to be clearly separated. If you"re only expecting one band per lane (as on some of our PCR gels), you don"t have to run it much at all. For restriction digests via multiple bands, run it until the initially dye front gets about halfmethod down the gel. Running the gel much longer will separate your bands even more, yet it will certainly likewise cause the bands to come to be even more faint, and also they might disappear totally. If you"re not sure whether your gel has actually run lengthy enough, you deserve to constantly take it out, look at it on the UV transilluminator (as defined below) and also put it earlier to run much longer.

Another means to acquire a quick look is to usage a UV flashlight. The plastic lid of the gel unit blocks UV, so you"ll need to take it off.

When you think your gel has run much enough, put your gloves and security glasses back on; it"s time to take the gel out and acquire a snapshot. Follow these steps to get prepared for the photo:

Turn off the power supply and also unplug the red and black leads.Take the lid off the gel box.Spreview a piece of plastic wrap on the table for the gel.Lift the gel tray out of the box and also let the buffer drain off the gel, then slide the gel out of its tray onto the plastic wrap.Place the gel & plastic wrap on the UV transilluminator.Dry the edge of the plastic wrap through a paper towel and also compose your team name and the day on the plastic wrap with a fluorescent highlighter. Make certain the highlighter will be illuminated by the UV light, so it will be fluorescent. Make certain the plastic wrap is dry, or the highlighter will run into your gel and revolve it bappropriate yellow.Placed down the transparent lid on the transilluminator, rotate on the UV light, and also take a look at your gel.

Photo your gel. Once you"ve obtained your gel on the transilluminator and the plastic wrap labeled, don"t waste too a lot time looking at the gel; you"ll have the ability to view it much better in the photo on the computer system. Turn on the video camera, and also make certain the height dial is collection on C mode. Raise the transparent lid on the transilluminator and also put the camera on height. Make sure that the camera"s hood is all the means dvery own over the UV light. The UV light goes off when you lift the lid, but it comes earlier on as soon as the magnet on the electronic camera hood activates the switch.


Look at the picture of your gel on the camera"s display. Use the camera"s zoom lever before to zoom in a little, making sure that you incorporate your team name in the photo. Use the left and also best butlots to readjust the shutter speed, making the picture darker or lighter. For a DNA gel, the background have to be fairly dark, via bbest and plainly visible bands.

Once you"ve gained the ideal zoom and also exposure, organize dvery own the shutter release switch and provide the video camera some time to emphasis. It"s slow. Once it"s concentrated, press the shutter release switch all the means while holding the camera steady. The expocertain may be long, and also if you move the electronic camera, you might acquire a blurred photo.

Don"t leave the camera on the UV transilluminator longer than crucial. The heat from the UV light will make your gel steamy, and the camera"s lens will fog up.

Don"t try to use various other picture-taking settings, choose Program or Manual. That"s for suckers. The C mode contains the correct settings to help you obtain an excellent photo. You just should readjust the expocertain.

When you"ve obtained your picture, put the camera right into evaluation mode (the blue arrow) and also attach the usb cable to the lab"s lappeak. The computer should currently be put up to instantly copy your image to the proper folder on the computer and delete it from the electronic camera. If you took more than one photo, please delete all however one.

Turn off the cam as soon as you"re done. If it"s left in testimonial mode, it will not rotate off by itself, and also the batteries will certainly wear down.

When you view that you"ve acquired a good image, throw away your gel in the biodanger trash. Wear gloves and also safety glasses for this -- remember, the gel includes ethidium bromide.

Later, the instructor will certainly upload all the images to the lab"s flickr website, so you"ll have the ability to watch it and download it later on. It"s necessary to acquire everybody"s gel picture on flickr, so you deserve to compare your gel to others.

You could also desire to take a snapshot via your phone, yet be sure there"s a photo on the lab electronic camera.

Cleanup: Leave your gloves and safety glases on; you still need to do a small cleanup after you have actually your gel photo:

Wrap the gel in its plastic wrap and also throw it in the biorisk trash.Pour the TBE running buffer down the sink.Rinse the gel unit through deionized water, dry it carefully (watch out for those fragile electrode wires), and also put it earlier in addition to the gel tray inside.Put the comb and also the gel casting gates earlier in the correct box inside the cabinet with the gel unit.

Make sure you return all the components of the gel unit. If someone stops working to put the tools amethod effectively, you can not have the ability to run your next gel. Taking treatment of the tools is the students" duty, and also you will certainly be graded on it.


Terms & concepts

AgaroseEthidium bromideSample buffer (additionally called gel loading buffer)TBEVoltage and existing (amps or mA)

Resee questions

What determines just how a lot agemerged you should usage in your gel?What is the UV transilluminator for?How could you view your DNA while the gel is running?Why do you check out just DNA on the gel, and also not protein?How do you recognize which finish of the gel to location the comb?Suppose you turn on your power supply to run the gel and also uncover that the milliamps reading is cshed to zero. What would you check?If you want to make a gel through 0.8% agemerged, just how many grams of agarose must you use?What does sample buffer carry out in DNA electrophoresis?Why do you need to usage a buffer choose TBE in your gel and also in the electrophoresis chamber, rather of simply making use of ordinary water?


DNA electrophoresis approaches & videos

All these videos show the very same fundamental techniques; I"m not certain which one will assist you the majority of.

Agoccurred Gel Electrophoresis from AddGene. Technique web page via a video clip reflecting just how it"s done.

Agdeveloped Gel Electrophoresis from Bio-Rad. Good 4-minute look at the entire procedure.

How to make an agarose gel and How to fill an agdeveloped gel from Synthetic Biology One.

See more: Show Me Why You Deserve To Have It All, Filter By Rhyme

Ethidium Bromide

The Myth of Ethidium Bromide. Derek Lowe, Science Translational Medicine, 2016.