the problem is that dna intercalates dye ETBR proportional to its length so the 800 base fragment only has 800/13000 or about 6% signal strength compared with the whole plasmid. So either run a larger volume or check that it has cut with a small sample and then run the main sample only a short distance. The large bands will not separate much but the 800 band should separate from the rest and have a stronger visibility because the band will not have broadened much in the running of the gel,

Also do not spend too long looking at the band as small bands lose thir signal destroyed by the uv light and the band seems to disappear. Take your picture once and quickly and cut out the band using as little uv light as possible

the problem is that dna intercalates dye ETBR proportional to its length so the 800 base fragment only has 800/13000 or about 6% signal strength compared with the whole plasmid. So either run a larger volume or check that it has cut with a small sample and then run the main sample only a short distance. The large bands will not separate much but the 800 band should separate from the rest and have a stronger visibility because the band will not have broadened much in the running of the gel,

Also do not spend too long looking at the band as small bands lose thir signal destroyed by the uv light and the band seems to disappear. Take your picture once and quickly and cut out the band using as little uv light as possible

If all you need to do is verify the presence of the insert, then just run a comparison of digested plasmid that doesn't have the insert. Finding the three expected large bands from the insert shows that your plasmic must have the insert. The 898 band is much smaller and therefore much less bright than the other bands. Don't waste your time trying to find it.

You haven't failed, you are just learning about the realities of molecular biology.

@Paul: Thanks! But, I have a doubt. What do you mean by more volume and then small volume. Do you want me to run twice? Lastly, I did look at bands under UV for 1.5 minutes. Of course, I was taking breaks but maximal was 30 seconds.

I meant that if you want to see all of your bands in one gel track then you will have to run a larger sample. If you just want to see that you have the 800 fragment then you could run a small volume of sample which will show you the larger fragments and prove that the sample has cut, Then you run a small sample but for only a short time and you will see the 800 band but the separation of the larger bands will be very poor but he first run assures you that the sample has cut properly so yes either run twice or load the samples on one gel and view and photograph early to see the 800 band and then later to see the larger bands ( but the 800 will be faint now),

I think that 1.5 minutes is too long and you may be getting photo quenching of your signal, Take a picture quickly and look at that to protect your sample

Incidentally if you want to know if the insert is present just running a pcr on the plasmid dna with inset specific primers would work

You can also take several pictures with different exposure times. The larger bands will be much brighter than the expected small band so over-exposing the picture to the point where the large bands are too bright may allow you to see the smaller band.

Do you need to gel-extract your DNA or just verify the presence of the insert?

@katie: just verify the insert!

@Paul: Should I make the gel thick or thin? I did try what you told but still not able to see the 800bp band. Should I reduce the DNA amount to 1ul?

Thank you so much! I tried to optimize the the following parameters:

1. gel thickness

2. DNA volume

3. Enzyme concentration

I am able to find all three together now. Gel (1% agarose with 100 ml 1xTAE); DNA volume (1-1.5 ul); and enzyme (1.5-2ul) depending on DNA volume. I was able to see 900 bp band after 25 minutes and three separated larger bands (~4kb) after 1.5 hours. My experiment is successful after combining these two images.