Science Buddies: "Ask an Expert"

My project is "What makes a DNA fingerprinting unique?"and on Procedures the 6 says that when you cut the DNA that was already make by the Random DNA Generator it says to cut it and paste it in a REBsites from New England's Biolab but I would click the link and it would tell me that the sit is unavailable is there another site where I can make the fingerprint? Please respond I have a 1 month and a half to complete my science fair project. On October 30, 2015

Hi,

Sorry you had a problem with the website. The program REBsites must be down for some reason.

I found another program that works and it is also on the New England Biolabs website: http://nc2.neb.com/NEBcutter2/

Just paste your random DNA sequence into the box, leave the settings the way they are and click SUBMIT. What you will see now will be the result for ALL the restriction enzymes that cut your DNA. According to the Scibuddies project, the only cutters that you should use are:

BamHI
EcoRI
HindIII
SmaI
XbaI
XhoI

Look at the screen of the DNA cut with all the enzymes and below and to the left you will see a menu entitled MAIN OPTIONS. Select 'Custom Digest'. Now you will see a list of the names of all the restriction enzymes (REs) that cut your DNA sequence. Scroll down through the list looking for the names of the above enzymes. You won't find all of them because your DNA only has sequences that are recognized by a few of them--maybe only one. Tick the boxes of the enzymes that are on your list then click DIGEST.

Now you will see a representation of your DNA with the enzyme cut sites indicated. Below on the left is another menu that says MAIN OPTIONS. Click on VIEW GEL and you will get a picture of what the cut DNA would look like if it were run on an agarose gel by electrophoresis. This is a simple technique for separating DNAs according to size. If you are curious about how this is done, here's a video--https://www.youtube.com/watch?v=QEG8dz7cbnY

Let us know when you try this so we know if it works. Someone else may have the same problem with the REBsites being down. Also, don't hesitate to ask a bunch of questions because that's what we are here for!

Good luck,

Sybee

Thanks you and it does help but I have another question on the project's procedure it says on the last step about what fingerprints are different or which are the same? How do you find out how they are similar or different? What do you compare? Thank You

You generated several random DNA sequences using the software tool. These each have a unique 'fingerprint' that results from the types of restriction enzyme cut sites that they have. When these DNAs are digested (virtually in your case)and run on a gel, you see a specific pattern of bands. These are the DNA fragments from the digest and the gel patterns are the 'fingerprints' that you compare. You can also compare the sequences but this requires a different program.

Let us know if need more help.

Good luck!

Sybee

How long does the electrohoresis gel last, please let me know (asap)

Hi isacm,

It is easier for the experts to follow one person's questions if they are not mixed up with another persons. So, please, if you have a question start a NEW thread so it is separate from one that belongs to another person's science project.

In answer to your question, I am not sure what you mean by 'last'. Did you run DNA on a gel already and want to know how long the band will remain visible? If you keep it in the fridge at 4C the bands will diffuse more slowly. Small DNAs, 20-50 nucleotides will diffuse faster than large fragments.

If you are planning to pour several gels and store them for later then you can keep them a month in the fridge wrapped in plastic wrap.

Let us know more details about your project and we can help you better.

Sybee