I am using the product for sequencing, I tried to reduce the amount of the template but I got weak bands. I know that we can use gel extraction, but does anyone have suggestion on how to minimize smearing in my samples?
lower primers concentration or/and different temperature - strong dimers at the bottom of the gel - maybe different less self specific primers
cutting band from the gel is a good idea, but you have to remember that product loss during gel-out could be very high, so you need much stronger band than these ones on photo. next extremely important thing is to remember that UV light damage DNA, so try not to cut bands on UV transilluminator, blue light is better but it needs different dye
Since the cost of DNA synthesis is very low (less than 5USD per pair) and PCR optimization process can be very tedious, I feel it might be a good option to try alternative PCR primer sets. If not work, try alternative PCR kit or Taq enzyme.
I think, bands of PCR product depends upon quality of your DNA /template. Please check 1st that what is concentration/quality of your template.
If quality of template is good then plz increase the MgCl2/ MgSo4 in preparation of PCR Reaction/ Cocktail.
If you have pure extracted template then plz decrease 2 degree anealing tempearture of primers.
If still you face the same problem then please chnage the primer set from any other available facility like invitrogen. Because in the gel at the end near dye there is no presence of well band of primer dimer. It means primers quality is not good.
very simple go for different Gradient temperature's to avoid uncessary amplifications of small fragments of DNA. You will definitely get one desired fragments of your gene.
Seema, Fatoon is not facing problem of non-specific amplification. He/she needs help to get the PCR product with good intensity. Gradient temperatures also good option, but he required good template and other optimzations as I suggested. In past, I optimized this sort of problems. Fatoon, if you want to solve this problem, please reply me on my suggested points. I will help you more regarding this matter.
The PCR gel pic shown is having clean bands, smear often do not affect your sequencing results if your pcr product has gone through proper exo sap and ethanol wash cleaning treatment. Then surely you will get good results, still you have a problem.... then, pls enlist your thermal cycler program and pcr protocol, both are interdependent. we might help you to suggest some solution after looking @ it.
After watching your image of PCR product, I would suggest to increase the number of cycle of your conditions as the bands look quite good but the intensity of your bands is low which can be increased by increasing product density.
Another thing you can do is increase the time for your annealing temperature so that your primer may get threshold time to bind with target DNA.
Part of your problem is a high fluorescent background in the gel. There are several ways to reduce this . First and simplest, are you making sure that there is no background lighting that is lightening the whole picture. The uv source and camera needs to be in a dark room or a dark box. If, in the dark, the agarose is autofluorescent without any ethidium bromide or other intercalating dye, then you need to buy better agarose, and/or to throw it out without re-use. If not, then you are probably using your flourescent dye at too high a concentration. Try half the current concentration in the gel and one tenth the concentration in your running buffer.
Turning to the DNA. You have a perfectly good PCR product in slightly lower quantity than for some products, but with a contaminating high molecular weight smear and also some primer dimer. The high molecular weight smear is likely to be your template DNA - I assume you are using genomic DNA. You will probably be able to sequence the band simply by purifying the PCR using a clean up kit that removes primers, as the number of moles of primer binding sites in the template is very small. But if this gives poor sequencing quality, just cut some of your PCR band out of a TAE buffered agarose gel ( taking the minimum amount of agarose trimmed tightly to contain only the DNA band) and clean up for sequencing using a gel purification kit such as Qiagen's Qiaquick gel extraction kit.