Short Tandem Repeats

by Georgina Cornwall, PhD

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    00:01 short tandem repeats. Short tandem repeats are exactly that. They are short tandem, two letters, repeats.

    00:07 And short tandem repeats are the newer way of doing DNA fingerprinting and we currently use about 13 different well known short tandem repeats that are found throughout the human genome. In the US federal profiling database, which is called CODIS is the 13 that are used in all the court cases and the CODIS means combined DNA indexing system. We can then put in anyone who is DNA fingerprinted, goes into this database and we compare that DNA to all DNA and this is one of the systems in which we are able to release many people that have been properly incarcerated or convict people in crimes where their DNA was found at the scene. Let us look at short tandem repeats. Again these are very similar to RFLPs.

    01:02 They are restriction enzymes that cut outside of the short tandem repeats, but rather than being longer repeats they are like a GTGT or ATAT, GCGC whatever. They are just two letters repeated over and over and over. And we have definite polymorphisms found throughout the human genomes. We use restriction enzymes to cut aorund those short tandem repeats, run it through a gel electrophoresis and you will see that we come out with a certain banding pattern. Over in lane one, you can see the reference piece perhaps the DNA that was found out in crime scene and in the other lanes you can see DNA that we are comparing to that reference peaks. You will notice that there is a region on the Y chromosome of course in the female lane. You were not going to see any of the STRs that are found on the white chromosome, but she doesn't have the white chromosome. We can very easily discern male from female, but in addition to that, using 13 other sites, some of which are on chromosome number 12, we can see that there are different polymorphisms for each segment of short tandem repeats so there will be multiple throughout a genome and when we look at 13 different sites, we have one in several hundred million chance or something of them being similar. You can see clearly by comparing the lane one material to the four-lane material, then lane seven that these DNA short tandem repeat sections match up and so we could implicate person number 7 in the crime or the crime scene where the DNA in lane one was found. That is how DNA fingerprinting works. It is pretty cool technology, but now that we have actually sequenced the human genome probably we are going to move more to actual DNA sequencing because as we'll learn in future lectures, it has become really pretty easy to sequence a whole genome and in probably ten years, it will be in a fact that we will just go with the DNA sequence rather than moving into using the STR's because we can get the specific nuclear type sequence relatively easily, so great stuff coming up in the future of DNA technologies.

    03:46 So now that you understand all about DNA fingerprinting, let us look at some more applications of recombinant DNA. We will now look at how recombinant DNA can be used to establish particular gene function.

    04:04 Recombinant DNA can also be used to create differences in organisms in order to establish a gene's function. In essence, this is sort of reverse genetics. Knockout mice are a great example for this. When we create knockout mice, we are looking to knock out a gene and see what its function is, so we can get the gene from a gene library of the mouse genome and establish what that piece of DNA does. By seeing what happens when we knock it out or interrupt it, so we can take the gene from a library interrupted get it into our mouse and establish the function. For example, here with our lovely mice, you can see that we have a knockout mouse who is no longer producing the gene for leptin. Now he was bred not to produce the gene from leptin. They introduce the gene as an embryo and then we have a normal mouse who has a normal weight. Now the mice that have been knocked out leptin genes, they are going to gain weight throughout their life, which tells us that leptin has something to do with obesity. In knock out technology we're knocking out genes to establish what their function is. Again sort of in a reverse order because that is the nature of how we have to do things when we were looking at larger eukaryotic animals like mammals.

    About the Lecture

    The lecture Short Tandem Repeats by Georgina Cornwall, PhD is from the course Biotechnology.

    Included Quiz Questions

    1. STR's
    2. Gel Electrophoresis
    3. restriction enzymes
    4. RFLP's
    1. …microsatelitte composed of a unit of two nucleotides repeated hundreds of times in a row on the DNA.
    2. …microsatelitte composed of a unit of two hundred nucleotides repeated hundreds of times in a row on the DNA.
    3. …microsatelitte composed of a unit of two hundred twenty-two nucleotides repeated hundreds of times in a row on the DNA.
    4. …microsatelitte composed of a unit of twenty-two nucleotides repeated hundreds of times in a row on the DNA.
    5. …microsatelitte composed of a unit of twenty nucleotides repeated hundreds of times in a row on the DNA.
    1. The normal mouse exhibits an obesity model as compared to the knockout mouse under the laboratory conditions.
    2. Reverse genetics helps to understand the function of a gene by analyzing the phenotypic effects of specifically mutated or silenced gene sequences.
    3. The gene silencing (RNAi) falls under the category of gene knockdown as its effects are temporary, whereas gene knockout effects are permanent.
    4. In reverse genetics, the genes are deleted by gene targeting or gene knockout to determine their phenotypic function.
    5. Reverse genetics works in the reverse direction to that of the forward genetics.

    Author of lecture Short Tandem Repeats

     Georgina Cornwall, PhD

    Georgina Cornwall, PhD

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