What are recognition sites? (A level Biology Help)

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mia.mgeorge
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Could someone explain to me what recognition sites are? Are they STRs or are they the base sequences next to the STRs? Also, are blunt and sticky ends produced by restriction enzymes cutting DNA made because the enzymes are cutting in the middle of the STR or are they cutting through a base sequence after the STR?
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Felynalanine
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(Original post by mia.mgeorge)
Could someone explain to me what recognition sites are? Are they STRs or are they the base sequences next to the STRs? Also, are blunt and sticky ends produced by restriction enzymes cutting DNA made because the enzymes are cutting in the middle of the STR or are they cutting through a base sequence after the STR?
Short tandem repeats =/= recognition site. They are totally separate ideas.

Restriction enzymes are mostly used in the cloning of genes into plasmids/viral vectors. Each restriction enzyme has its own recognition sequence and the enzyme can either cut the DNA in the recognition sequence or near the recognition sequence, depending on the domain organisation of the specific enzyme.

Blunt ends are made when the enzyme cuts at the exact same point on the DNA, which can be within the recognition site or outside it. Sticky ends are made when it cuts at one point on one strand and at a different point on the other strand.

The recognition site is simply a site that the enzyme can 'recognise' and bind to. It does not necessarily cut within that site, although often it does. For example, type IIA endonucleases cut at a sequence outside the recognition sequence. They can bind to the recognition site with the DNA binding domain and once bound, the endonuclease domain of the enzyme cuts either a blunt end or a sticky end at another (defined) sequence in the DNA. However, if the initial recognition sequence is not found on the DNA, the enzyme cannot bind so it does not cut the DNA.

Take a look at any of these enzymes (click on the enzyme name) and you will see there is a great variety https://international.neb.com/tools-...-specificities.
For example, this one cuts outside its recognition site: https://international.neb.com/produc...%20Information

I don't think you will be asked to explain how sticky ends/blunt ends are made though.

Short tandem repeats are not found in plasmids. They are long sections of non coding DNA in the human genome used in forensic analysis because every person has a different number of repeats (at least I think that's the idea). This analysis does not use restriction enzymes. They are amplifying the sample via PCR, where the primer they use has the same sequence as (part of) the short tandem repeat.
Bacteria and viruses don't contain short tandem repeats because the bacterial genome has to be short/concise to enable fast replication, whereas mammals and invertebrates do contain repeated DNA.
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mia.mgeorge
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(Original post by FelineImplant)
Short tandem repeats =/= recognition site. They are totally separate ideas.

Restriction enzymes are mostly used in the cloning of genes into plasmids/viral vectors. Each restriction enzyme has its own recognition sequence and the enzyme can either cut the DNA in the recognition sequence or near the recognition sequence, depending on the domain organisation of the specific enzyme.

Blunt ends are made when the enzyme cuts at the exact same point on the DNA, which can be within the recognition site or outside it. Sticky ends are made when it cuts at one point on one strand and at a different point on the other strand.

The recognition site is simply a site that the enzyme can 'recognise' and bind to. It does not necessarily cut within that site, although often it does. For example, type IIA endonucleases cut at a sequence outside the recognition sequence. They can bind to the recognition site with the DNA binding domain and once bound, the endonuclease domain of the enzyme cuts either a blunt end or a sticky end at another (defined) sequence in the DNA. However, if the initial recognition sequence is not found on the DNA, the enzyme cannot bind so it does not cut the DNA.

Take a look at any of these enzymes (click on the enzyme name) and you will see there is a great variety https://international.neb.com/tools-...-specificities.
For example, this one cuts outside its recognition site: https://international.neb.com/produc...%20Information

I don't think you will be asked to explain how sticky ends/blunt ends are made though.

Short tandem repeats are not found in plasmids. They are long sections of non coding DNA in the human genome used in forensic analysis because every person has a different number of repeats (at least I think that's the idea). This analysis does not use restriction enzymes. They are amplifying the sample via PCR, where the primer they use has the same sequence as (part of) the short tandem repeat.
Bacteria and viruses don't contain short tandem repeats because the bacterial genome has to be short/concise to enable fast replication, whereas mammals and invertebrates do contain repeated DNA.
Wow you've explained everything really well, thank you
Just to clarify, are restriction endonucleases used to cut DNA fragments (made of STRs) for DNA profiling?
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Felynalanine
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(Original post by mia.mgeorge)
Wow you've explained everything really well, thank you
Just to clarify, are restriction endonucleases used to cut DNA fragments (made of STRs) for DNA profiling?
I am not an expert in DNA profiling so someone correct me if I am wrong.. Restriction enzymes can be used in some methods and were used in RFLP, which I think you need to know about.

Modern STR analysis uses PCR since the repeats are conserved, so primers can be designed that allow the amplification of the DNA between the repeated sequences. Gel electrophoresis then shows all the fragments that were generated.

PCR can be thought of as similar to a restriction digest, except that it also increases the amount of DNA. The section of DNA between the upstream primer and downstream primer is amplified, similar to if you had a double digest where two (different) restriction enzymes cut at two points in the DNA.
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