Dear Syeda, while it is not exactly clear what Syber Safe agarose staining product and agarose gels you are using Syber Green is usually not added into the wells mixed with your product. Please find parts of the official guide for Syber Safe gel staining:
1. Staining Nucleic Acids after Electrophoresis
1.1 Soak the gel in SYBR® Safe stain. If using SYBR® Safe gel stain concentrate, dilute 10,000X in TAE or TBE buffer (as appropriate) prior to use. Place the gel in a plastic container, such as a pipet-tip box lid or a household food-storage container. Do not use a glass container, as the dye in the staining solution may adsorb to the walls of the container, resulting in poor gel staining. Add sufficient SYBR® Safe DNA gel stain to cover the gel. A 50 mL volume is sufficient for staining most standard mini gels. To stain larger gels, increase the volume of staining solution in proportion to the increased gel volume, and ensure that the entire gel is fully immersed during staining.
1.2 Incubate for 30 minutes. Protect the gel and staining solution from light by covering it with aluminum foil or by placing it in the dark. Gently and continuously agitate the gel at room temperature (e.g., on an orbital shaker at 50 rpm). No destaining is required.
2. Precasting SYBR® Safe Stain in Agarose Gels
2.1 Prepare the agarose gel directly in SYBR® Safe DNA gel stain. SYBR® Safe stain is provided in the buffer; simply substitute SYBR® Safe stain for the buffer when preparing the molten agarose. If using the 10,000X SYBR® Safe stain concentrate, dilute the concentrated stain 1:10,000 in agarose gel buffer (e.g., 1X TBE or 1X TAE) and add the buffer plus stain mixture to the powdered agarose. For example, if you run TBE gels and require 30 mL of molten agarose for your tray, add 3 µL of 10,000X SYBR® Safe stain concentrate to 30 mL of 1X TBE and mix well. Add this stain–TBE mixture to the powdered agarose. The agarose/SYBR® Safe stain mixture may be heated in the microwave. As with precasting gels with ethidium bromide, the mobility of nucleic acid fragments in the gel may be somewhat slower when run in these gels, compared to their mobility in the gel without stain.
2.2 Run the gel. Use a running buffer appropriate to the SYBR® Safe gel stain formulation. No post-staining or destaining is needed.
Personally, I prefer the second method as it makes it possible to interrupt the electrophoresis
The most loading dyes that you mix your product are only intended to make your product heavier than water to load into the comb and it also prevents dissolution of the product in the running buffer but they usually don't contain any fluorescent agent to visualize your products in agarose (please see above). Again you did not provide the information what loading dye you are using.
3. PCR troubleshooting
Another possibility is related to your PCR process and primers used as you mentioned that you were able to visualize the ladder but not any products. In order to troubleshoot this stage of the process, I suggest to run 1 ul of any plasmid that you have in your lab. Plasmids don't require any PCR amplification and typically produce the bright single band. You can also try to run whole extracted DNA without PCR which will be visible in the gel as one large bright band with a smear to test if the gel staining is correct.
4. DNA extraction
I assume you have measured your DNA concentrations with Nanodrop or similar spectrophotometer so we can exclude failed DNA extraction or DNA degradation process.
5. Filter in the gel imaging system
Finally, you have not provided the information how you visualize your gels. In some imaging systems, it is required to manually install the filter or switch the filter wheel in order to properly image the Syber Green gels it is common in older gel imaging system that has the double purpose of chemoluminescence/fluorescence detection. You can confirm this step using just UV light to observe your cells visually, for instance, using your lab gel cutting UV source.
Hope it helps in troubleshooting your agarose process. I will need more information to help you further.
i am using 6X loading dye ;https://www.thermofisher.com/order/catalog/product/R0611,this gives very week bands when i stain my gel with sybre safe.
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