I did not get your question ??

There was a difference in the migration why?

Its a normal gel

are you measure the concentration and the purity of your samples because If the species are negatively charged (DNA) they will migrate towards the positively charged "anode" ,. maybe you have an error during extraction !

Does the bacterial DNA move towards the cathode? If so, my bet is your eukaryotic samples have histones, which are positively charged (in agreement with everyone above).

Have you taken any precautions for stripping histones (or protein in general) from your eukaryotic DNA prep?

I agree with Zinah,

Before you started the electrophoresis, how did you "isolate" the DNA? Centrifugation? how much rpm did you use?

As Michael told they may contain the histones otherwise it is impossible that the purified DNA moves in different directions..

Re isolate the DNA carefully according to the protocol and then check again what was the problem.

@Miguel-we used 3000rpm for centrifugation.

We need more detail. In which direction are the bacterial and eukaryotic preps moving? What are you using to stain the DNA? Did you incorporate the stain in the gel or staining afterwards? If the former, can you monitor the progress of the different preps to make sure nothing strange is happening?

How many times did you do the extraction? If once, then you should repeat the extraction.

I agree with Alicja, maybe your DNA sample is contaminated.

To extract DNA from bacterial samples, we use the heat shock protocol (water bath, 98°C, 10min, immediately followed by -20°C, 10 min) and only after this we centrifuge, but using 14000 rpm in our centrifuge model. It has worked fine for us.

If possible, try to do the extraction once more and see how it goes.

Best luck!

It is true that samples move to opposite current - positive ions move towards cathode and negatively charged towards anode. So ensure that the extracted bacterial DNA is pure.

You need to clean up your sample.

Normally, DNA is negatively charged, then it will migrate towards the positive pole "anode" . I think that you have something wrong.

Is it the DNA moving in the opposite direction, or is it the dye front? If it's the DNA, then it is contaminated with DNA-binding material (eg. protein). If it's the dye front, then your sample is contaminated with something, but the DNA will still migrate correctly. Either way, your DNA prep is contaminated and needs to be cleaned.

Any Kind Of contamination-proteins, lipids etc in the sample will directly affect your results. might have not done the drying properly at appropriate temperature

I agree with Gaber,I Think that you have something wrong,some times we connect anode & cathode correctly but our buffer tank maybe on not right position.

Surely there might be something carrying the +ve charge, are u going for precipitation of nucleic acid directly after the lysis? If so then treatment the lysate with 25:24:1n phenol:chloroform:iaa to remove the protein debris and other impurities. Then only proceed for precipitation step also wash the pellet with 70% ethanol two times if precipitation solution contains higher conc. of salts. Probably this will solve your problem. All the best.

Usually, nucleic material does not run to the cathod unless strongly modified to contain positive charges. However, some highly positive-charged protein do. check the protein contamination in your sample :ratio OD260/OD280 nm should be higher than 2. You may want to use proteinase K to get rid of all protein components !

i agree with Brumeanu, you must ensure from purity of bacterial DNA sample by measuring the sample ratio at OD260/OD280 nm.

I dont' quite get the question either. But most possible answer in my experience with many students....are you sure you plug the chamber in the correct orientation? (I assume that the bacterial DNA is run on a different gel/chamber from the other DNA prep). My suggestion is run it again with good DNA size marker...and show us the picture. Including your protocol of how did you extract the DNA will be good. If the problem still exist, then we might discover some weird phenomenon that the DNA sometimes can be positively charged after extraction (which I think its highly unlikely).

I suggest you do an experiment. Load your sample of bacterial DNA in one lane of a gel. Load another lane with the loading dye only. If the fluorescent material is in the loading dye, discard it. If the fluorescent material is in the sample of DNA, the preparation has an impurity. I once had a similar observation which turned out to be a compound thought to be a carotene. Once I had fluorescent material with a positive charge that was in all lanes of the gel, even those lanes that were not loaded with anything. I had taped the ends of the gel tray to pour the gel. Once the agar was set, the tape was removed and the gel was run as usual. But a fluorescent dye from the tape migrated into the gel. I simply changed brands of tape to get rid of the problem. DNA, regardless of its source, always migrates toward the positive electrode. If DNA moves in the wrong direction, the electrodes are plugged into the power supply incorrectly and reverse polarity is being used.

Be sure that your sample that is moving in an opposite direction is indeed the DNA.Check the optical density at 260 nm plus at 280 nm. The 260/280 ratio should be around 1.8.

1. Do the extraction again & check the purity by OD at 260/280 ratio by spectrometer.

2. Check your buffer . (TAE)

3. Check your connections and voltage for the run

4. Check your Tracking dye.

Go step wise and you will trace the error.

Can you please post an image of one of these gels?

Then: I assume you load your samples into the loading pockets created by the well. If the would run reverse, they would leave the gel after about 1cm or so and you will never be able to see them, so I don't thinkt this has happened (although I see this usually once every semester in the beginners lab course).

How do you prepare you gel? Do you add Ethidiumbromide after cooling the gel?

What kind of loading dye do you use?

Perhaps your sample is contaminated proteins. Nucleic acid molecules migrate toward the anode, due to the net negative charge of the sugar-phosphate backbone of the nucleic acid chain. Protein molecules in solutions with a pH less than the isoelectric point of the protein is positively charged and move in the electric field towards the negative pole - cathode.