Yes--as long as you are going to use a detection method that is sensitive to single-stranded DNA. You can't use dyes like ethidium bromide or Sybr green that bind primarily to double-stranded DNA. On the denaturing gel, the DNA will be single-stranded, so these kinds of stains will not be helpful. If you are detecting your experimental samples with a radioactive label, you can also label your 50 bp ladder with radioactivity (see the suppliers recommendations on how to do that) and use it as a marker. Silver staining or staining with a single-strand binding fluorescent dye like SYBR-gold should also work--you'll need the right UV light source and orange filters to visualize the SYBR-gold stains. Make sure that you denature the marker completely before loading it--95 for 3 minutes in loading buffer, ice and then load quickly.

@david well there is no protocol for the ladder for denaturing in the leaflet they provided.. If i denature it will that be a problem.. After running how can i read the size?

What is your protocol for denaturing PAGE? Usually there is a loading buffer/dye mix that will contain something like formamide, to slow any possible re-annealing of the sample. If you mix a sample of 50 bp ladder with loading buffer, ready to load, and then heat that for 3 minutes at 95C--in your thermal cycler say--it will denature. You need to make sure that the samples are completely single-stranded before loading--otherwise they are likely to denature as they run--creating a smear or a blurry band. The 50 bp ladder consists of double-stranded DNA fragments. When they denature, they will still represent the same sizes, but each band will be single-stranded DNA.

Ok i got it.. Yes i use formamide loading dye.. How much ladder should i mix with dye before denaturing??

This depends on your detection method. If you are using SYBR-gold, then you only need ~200 ng. (See the protocol for SYBR-gold at for instance, http://probes.invitrogen.com/media/pis/mp11494.pdf ) For radioactive labels, it will depend on the specific activity of the label, the efficiency of the labeling reaction and the sensitivity of your film or other detection method. You might also want to adjust the amount so that your sample and the marker can be visualized under the same conditions--for example, you don't want the marker bands to be "overexposed" if your sample requires a long exposure to detect.

I am doing silver staining.. My research work is genetic evaluation using microsatellite markers.. While finding genotypes will this 50 bp ladder helps me?? My products are within 100 and 250..is there any method to overcome the difficulties while comparing with the ladder??

If you need to know the exact sizes of alleles when you genotype unknown samples , then the best thing to do is to use reference samples that you run together with your unknown samples. These reference samples are individuals for which you know the exact allele size(s) for the particular marker that you are testing. You may only need one or two of these reference samples on each gel--instead of one for every possible allele size-- because microsatellites tend to generate a ladder pattern of products during PCR. If the repeat is two or three nucleotides, the bands in the ladder will be two or three nucleotides different in size and you can use that to determine the exact size of most alleles that you see in your samples. In that case, the 50 bp ladder is only useful for indicating the approximate location on the gel where you expect to see your alleles and as a technical control for your staining procedure.