Destain your gel in water. Give it a gentle shake every 10-15 minutes or so and re-image after 30 min. You might need longer destaining but it should reduce the background greatly - you have DNA (and contaminating RNA, I think...or is that primer?) in there. Do NOT leave a DNA gel destaining overnight or for too long because the DNA will diffuse and your sharp bands will get fuzzy (and then disappear altogether). Good luck.

Apologies. I did read your question but forgot you said "PCR". The fuzzy bands at the bottom of each PCR reaction are primer (most likely) and not RNA.

First, do you put EtBr directly into the gel or do you soak the gel afterwards?  We always make the gels with EtBr after cooling the gel to 65oC add EtBr and then pour the gel.  Second, it looks like your gel is to low percentage for the small bands.  Try a higher percent agarose gel to visualize bands less than 500 bp.  You can use regular agarose up to 2% or metaphor agarose up to 4%.  This will give much clearer bands. 

you can use less ETBR but the important thing is to fully melt your agarose before adding the etbr, There are signs that some lumps of agarose are left in your gel and these are trapping etbr. You can run the gel without ETBR and then stain it but this is really too much trouble and the dna runs about 10% quicker if you do this.  Your bands are fine but you do have a primer dimer (PD) problem. pd occurs when the 2 primers anneal to each other and form a short and very easy to amplify product, This removes primer and lowers your amplimer yield. You can use less primer or a hot start enzyme to get rid of this and increase your yield and make sure that you do not leave the pcr reaction mix hanging around with the enzyme added for too long before starting cycling

It appears as though most of the interference was due to contact between the gel and my gloves. I didn't know this would cause such an effect. I will also try destaining later. Thank you for all the advice!  

when using etbr, use nitrille gloves and not latex or something else.

Etbr penetrates other gloves then nitrille quite fast.

Best way for etbr gells is melt agarose first, add etbr to the cooled down (mix well by swirling the bottle), but still liquid agarose and pour it into your gelcasting tray. Better is to change Etbr to something more safe like sybr safe, or gel red or whatever is on the market where you are. They have exactly the same function as Etbr, but are so bulky that they cannot penetrate cells like Etbr can. Thus not carcinogenic. In theory you would be able to handle them without gloves, in practise i would not advise to that and would recommend you to use gloves when handling such gells, you never know.

The problem is that Etbr is sooo cheap, it is even cheaper then common NaCl in the lab.

Run the gell. Because of the adding of Etbr in the gell, there might be a slight offsett between your sample and the molecular marker. But this doensnt weight up to the mess of staining and destaining afterwards (wich takes time and makes your DNA dffuse, creating ambiguent results).

Another way to reduce your primer dimers (which has been correctly identified in previous posts) is to increase your annealing temperature (Ta) by 1°C (can be more, but you need to test that in seperate runs to optimise your reacton). The higher Ta makes the formation of off targets more difficult, so decreases also dimerformations. Do not go to high since then your aplicon will not form either :). You can combine decreasing primer concentration, with Ta increase etc. to find the optimum reaction.

Also, above is mentioned that your gell has a to low percentage for your target region. I also agree to this, there is no seperation anymore on your marker in the lower region where your amplicon is. So better to increase your gell percentage.

In practice, you hardly ever need to go above 2% agarose.

Your second gell has different size amplicons then your first, so I assume different assays?, but there your rection is quite weak you have very faint bands on the picture. If it is an assay you will use often in the future, put some effort in it t increase its efficiency, you will thank me later since otherwise you might have to redo quite a lot of reactions just to be absolutly sure that what you see is in fact what you have.

All the above is no means of htting you on the head, since your new to PCR and all of its components, it is logical you do not know these things. Whe are here to help you if you are not getting to teaching or information in your own lab. You may always ask me directly (probably others too) if you have more questions regarding this topic.

Hello Lorenz,

I experienced the same phenomenon wth powdered latex gloves in the past. Use powder-free gloves and the problem should be solved.

best wishes

Dirk

Wear a clean gloves , take apt amount of TAE buffer and agarose.Boil it, cool it and then add a drop of EtBr. Do not use stock solution, always dilute it.Regards

It looks to me that your press gel with gloves, try to be more gently

It seems you put so much EtBr. How do you stain your gel?

"I have tried removing excess EtBr after submerging using a paper towel but so far no results. Maybe I should mention that I don't wash the gel after EtBr-staining"--> this might be the reason for the white spots/backgrounds. 

Do pre-staining(mixing EtBR after boling agarose-I do always), or post staining for few min by submerging gel in a tray filled with EtBr solution. In both cases, I have never wiped gel with paper towel. Go for scanning. good luck.

And I want to mention, destaining of EtBr gel was not necessary to me (a rinse with water wont affect though). But just keep in mind, it is not coomassie blue stain, to  destain the excess!

I suggest to prestain your gel.  After boiling, wait for 5 minutes, add 5 of EtBr (1mg/ml) for 30 mL agarose solution and cast your gel.

Bands are crisp but too much noise. My best guess, too much EtBr..  review thickness of gel.. thinner gels give better resolution. and easy to wash off the the non-specific die binds.. good luck

Use less EtBr, before casting the gels. Also, it is better to decrease the thickness of your gel. It effectively increase the contrast and quality of your figures. 

Your problem may be solved using one of the following:

1. immerse your gel in water or buffer for longer period to wash excess stain.

2. change and renew your stain solution and make solution with lower concentration of dye.

3. change and renew the buffer of your gel and tank.

Regards 

I had this problem before. After staining in EtBr solution you need to submerge gel in water for like 10 min or so. It depends on how long you will be staining your gel.

Good luck :)

You are putting more EtBr than required.

Lower the concentration and mix very well before pouring, 

Your problem would be solved. 

Or make the fresh EtBr stock, someone might have contaminated it using wrong tip. 

Make sure you dissolve the agarose well in 0.5xTBE (or 1xTBE, 1xTAE buffers) and then cool your gel in an homogenous way before adding EtBr (use a stirrer bar for a few min, until the flask is hand warm). Remove the stirrer bar and then add your EtBr. Mix well and only then pour the gel. Double check the final concentration of the EtBr that you are supposed to use

The key thing is to destain thoroughly

pre stain your gel After boiling, wait for 5 minutes, add

5 µl of EtBr (1mg/ml) for 30 ml agarose solution and cast your gel.

I aggre with Thakku. I get the same problem when the agarose is not well melted. Make sure you dissol the agarose well. It should be clear and transparent like water

This is due to poor melting of agarose and presence of excessive amount EtBr.