this is not primer dimer which is small ( around 30-50 bases) and diffuse. You should always run a negative control because it picks up post pcr product contamination which is what you do have. Some pcr product is contaminating one of your reagents or pipettes or just your wouking area. You should change everything and clean up your working area and pipettes or set upa pcr with borrowed reagents and in a different part of the laboratory. One way of getting round contamination is to design primers one of which is outside the amplified product then it cannot interfere. Even the very tiniest amount of contamination is a big problem as it amplifies very efficiently as it is short and has perfect homology with the primers. Every 10 cycles you have 1000 times more product so it can overwhelm a reaction and you just end up amplifying the wrong template every time. A primer dimer and a 150 base product will separate very well on a 0.8-2% agarose gel...it will not be a problem distinguishing them but you do not have a primer dimer.

Wan Ling,

I would suggest to use filter tips and move to different room for PCR mix preparation (sure, with new reagents). We had once similar problem, and it was caused by one careless co-worker who was running the gels.

Alex  

i suggest to change the taq enzyme , working place , tips , pipettes and water .run again and check ??  

I am agree with Alex lgnatov....contamination can be happen (first to last part), your tubes can be the reason....

you can check your intend band,by PAGE too. and dimer primer can't possible as Paul said because your primer are shorter than your final band.

Thanks everyone for the suggestions. I have ordered new Taq and will try again with everything cleaned, new and fresh.

Dear Ling,

You may try these-

1. As mentioned above use filtered, autoclaved tips. In addition to this, prior to setting up PCR, UV irradiate the tips, any contamination DNA will have thymidine dimers and will not be amplified by your polymerase during PCR.

2. Run a PAGE to check the sequence and integrity and purity of your primers. Also check your template in nanodrop and in agarose gel for its purity.

3. ALong with no template control, you can have a no primer control. You may or may not run the PCR with it, but afterwards along with your sample PCRs, run an agarose gel with the unamplified reaction mix to check whether it is omnipresent from the beginning, or it is being picked up during the PCR. If you get a band as intense as you are getting in the sample (amplified) then, it is neither coming from your primers nor from the reaction. One of your reagent is contaminated with it. If you see a faint band of the similar size in the unamplified no primer control and see an amplification of the band (brighter than unamplified) then the band is picked up by non specific amplification by your primer set. 

4. Lastly, PCR is a very sensitive reaction. DNA from any source present in extremely low amounts may be amplified and result into non specific bands. To avoid such amplifications, you may vary the concentration of KCl in your buffer to see if it helps eliminate this annoying amplification.

You may refer to some previously discussed questions regarding this in Researchgate.

Hope it helps! 

https://www.researchgate.net/post/Taq_Buffer_with_KCl_or_Taq_Buffer_with_NH42SO4

https://www.researchgate.net/post/What_role_does_each_of_the_components_present_in_pfu_polymerase_buffer_play_in_PCR?_tpcectx=qa_overview_asked&_trid=RNlKdlm2KqulIFhmB7aZj2Ob_

Whenever you see bands for your negative control, it generally means there was some form of contamination as Tomas has suggested. However, it does depend on the size of the bands. If the bands for the negative control show products much smaller than the samples or positive control, it could possibly be primer dimer. But, if the band is the same or similar size as the positive control, it probably means there is some template contamination. Any one of the reagents could be contaminated, or it could be the pipetter or tips as Taras suggested.

The simple solution would be to re-setup the reaction using new reagents. If you want to find the source of the contamination, then you would need to change only one reagent at a time and set up a series of identical reactions where one reagent was change in each one. Filter tips could eliminate the possibility that the pipetter is the source of contamination. But you may also get by by cleaning the pipetter well since filter tips are more expensive.

Are the reagents and pipetting equipment shared by others? This also could be a source of contamination.

Good luck

What does it mean if negative control during PCR also shows bands on agarose gel? - ResearchGate. Available from: https://www.researchgate.net/post/What_does_it_mean_if_negative_control_during_PCR_also_shows_bands_on_agarose_gel [accessed Jun 19, 2016].