The problem is not the percent agarose - you can 'see' just about any size band in any gel. The agarose  % is varied to optimize resolution in order to be able to estimate the size. The problem is that your smaller fragment is only 1.25% of the mass of your larger fragment. In order to be able to visualize the smaller band, you will have to load at least a couple of micrograms of digested vector (= 25 ng of smaller fragment). You will see both bands but the larger fragment will be a massive blob. If you really need to verify the sizes of both fragments, you will need to run 2 gels.

0.5-0.7 % agaorose gel you can use for 8 kb and for 100bp you have to use 2% agarose gel.

yes... even 1.5% would suffice for 100bp ... 

The problem is not the percent agarose - you can 'see' just about any size band in any gel. The agarose  % is varied to optimize resolution in order to be able to estimate the size. The problem is that your smaller fragment is only 1.25% of the mass of your larger fragment. In order to be able to visualize the smaller band, you will have to load at least a couple of micrograms of digested vector (= 25 ng of smaller fragment). You will see both bands but the larger fragment will be a massive blob. If you really need to verify the sizes of both fragments, you will need to run 2 gels.

All of these guys are right... if you need to confirm the size of your bands, you should run 2 separate gels. However, if you just want to see presence/absence of your bands, and you are sure that there won't be any other fragments, I would suggest you to run a 1% gel for 15-20min at 110V. You will be able to see both bands, but you probably won't distinguish the ladder clearly. I hope this is helpful!

I agree with all of the answers above, however I would suggest a very slow migration on a 1% gel. Depending on your conditions (for me TEA) I started at 100V for 5min and then decreased to 25V until the gel is run. It's long but it works.

If you have the possibility make a long gel so you have a better resolution.

0.8% agarose gel is better..

I think 2% agarose gel is better 

i always use 2 % gel for 100bp

Hey, The percentage of agarose is indeed important, but I will give you an additional tip. 

Because your 100nt band is smaller, it will present a smaller intensity than your 8Kb band because it will have less BET (because of the size, it will retain less). Also, because BET is charged positively, it will be attracted by the negative pole of your electrophoresis bath, which means that there will be a bigger concentration of BET on the top of the gel (where your 8Kb band is) and less in the bottow of you gel (where your 0.1 Kb band is). Therefore, in order to increase the intensity of the small band, I pour 1 or 2 drops of BET at the bottom of the bath (Positive pole), that way, this new BET will migrate towards the negative pole and run into your small band. 

Good luck.

You can use 1.5% agarose gel.

Agree with Shankar Loganathan

You can Use 1.5% to see the Bands clearly.

I can use 1.5 % too

1.5% to 2%, but like Craig said, you might be better off running 2 gels after cutting out the 100 bp region. This small fragment is likely to run with the dye front, so you might need to be very careful with your gels.

Agarose at 1.5 % in TBE is OK.

Dear Mahesh,

You can see the bands of any size of DNA in whatsoever %age of agarose gel you will use. But optimum resolution can only be achieved by using the optimum %age of agarose. I am sharing a table of recommended % agarose and optimum resolution of linear dna with you for your convenience... (source: promega)

0.5% 1,000 - 30,000 bp

0.7% 800 - 12,000 bp

1.0% 500 - 10,000 bp

1.2% 400 - 7,000 bp

1.5% 200 - 3,000 bp

1.8% 100 - 2,000 bp

2.0% 50 - 2,000 bp

You should always pick the gel percentage according to the smallest linear dna fragment for better resolution... and in your case it is 100 bp... so 1.5 - 1.8% agarose gel would suffice your need.

All the best