Difference between revisions of "Team:Jilin China/Construction"

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     <div>
 
       <h2>Type IIs Restriction Endonuclease</h2>
 
       <h2>Type IIs Restriction Endonuclease</h2>
−
<p>Restriction enzymes can be divided into four categories according to their different enzyme digestion methods, named Type I, Type II, Type III and Type IV. Our commonly used restriction endonucleases, such as EcoRI, belong to type II restriction endonucleases, which recognize specific 4 to 8 nucleotide sequences . The recognized sequence is inverted repeats and the cleavage site is located in the recognition site. After enzymatic cleavage and the cleavage end or blunt end is produced. The cutting diagram is as follows:</p>
+
<p>Restriction enzymes can be divided into four categories according to their different enzyme digestion methods, named Type I, Type II, Type III and Type IV. Our commonly used restriction endonucleases, such as EcoRI, belong to type II restriction endonucleases, which recognize specific 4 to 8 nucleotide sequences . The recognized sequence is inverted repeats and the cleavage site is located in the recognition site. After enzymatic cleavage and the sticky end or blunt end is produced. The cleavage diagram is as follows:</p>
  
 
<!--高能预警[Warning:Long Pieces of Codes!]-->
 
<!--高能预警[Warning:Long Pieces of Codes!]-->
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−
<p>However, compared with the common Type II restriction enzymes the Type IIS restriction endonuclease is a relatively specific enzyme that cleaves DNA downstream of the recognition site, from the three-dimensional structure analysis of the enzyme. This is due to the fact that the recognition and catalytic regions of the Type IIS restriction enzyme are separated by a polypeptide linker.</p>
+
<p>Type IIS restriction enzymes differ from other Type II restriction enzymes in several ways.These enzymes recognize sequences comprise two distinct domains, one for DNA binding, the other for DNA cleavage. Type IIS restriction endonucleases cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites, creating 4-base overhangs.</p>
−
<p> The advantage of the TypeII S restriction enzyme is that it has no requirement to a cleavage sequence. The cutting position can be any sequence, and multiple DNA fragments can be assembled through complementary ends. This assembly method is also called GoldenGate Assembly.</p>
+
<p>Type IIS cleavage domains have no inherent sequence-specificity, so the sequence of the overhang they generate varies from one recognition site to another. Fragments produced by Type IIS-digestion of natural DNA molecules generally have different overhangs, therefore, and will not anneal to one another. </p>
 +
<p>However, if the sequence of the overhang is predetermined, by designing it into a PCR primer, for example, then it can be made to complement another and to be directional. This feature is used to great advantage in 'Golden Gate' assembly where multiple fragments can be stitched together in the correct order and orientation in a single ligation. The advantage of using Type IIS enzymes for assembly is that the recognition sequence can be placed in the primer on either side of cleavage site. If placed inside, 3' to the cleaved end, it will be retained in the construct and can be re-used subsequently. If placed outside, 5' to the cleaved end, it will be lost, leading to a ‘scar-less’ assembly. This characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning</p>
 
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     <div>
 
     <div>
 
       <h2>Goldengate Assembly</h2>
 
       <h2>Goldengate Assembly</h2>
−
<p>The goldengate assembly relies on the type IIS restriction enzyme. By adding the recognition site of type IIS enzyme on the plasmid, it will be digest by enzyme and will not appear at the end constructs. The fragment gene of interest contains complementary sticky ends can ultimately be assembled by ligation. </p>
+
<p>Golden Gate Assembly is a one-tube efficient cloning method based on Type IIS restriction enzymes that cleave outside their recognition sites and leave 4-base overhangs. By adding the recognition site of type IIS enzyme on the plasmid, it will be digested by enzyme and will not appear at the end constructs. The fragment gene of interest contains complementary sticky ends can ultimately be assembled by ligation. </p>
 
<p>Commonly used IIS type restriction enzymes are as follows:</p>
 
<p>Commonly used IIS type restriction enzymes are as follows:</p>
 
<table width="200" border="1">
 
<table width="200" border="1">
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<p>The procedure of construction is annealed DNA oligos, phosphorylation and goldengate assembly:</p>
 
<p>The procedure of construction is annealed DNA oligos, phosphorylation and goldengate assembly:</p>
 
<h3>1. Annealed DNA oligos</h3>
 
<h3>1. Annealed DNA oligos</h3>
−
<p>Oligos annealing can be use to add any short stretch of DNA to a plasmid. Most of the thermosensors we designed are 40~80bp, so we can design a top oligo with the sequence of thermosensor and with the bottom oligo being the reverse compliment so that they anneal. We also need to make sure to include the cohesive end bases to complement the overhangs generated when digesting the plasmid. The cohesive end bases can be a part of thermosensor, because we use the goldengate assembly, which is a no-scar assembly.</p>
+
<p>Oligos annealing can be use to add any short stretch of DNA to a plasmid. Most of the thermosensors we designed are 40~80bp, so we can design a forward oligo with the sequence of thermosensor and with the reverse oligo being the reverse compliment so that they could anneal. We also need to make sure our annealing products contain the cohesive end bases to complement the overhangs on the plasmid. The cohesive end bases could be a part of thermosensor, because we use the goldengate assembly, which has no-scar products.</p>
 
<h3>2. Phosphorylation</h3>
 
<h3>2. Phosphorylation</h3>
 
<p>After annealing, we do the 5' phosphorylation of DNA for subsequent ligation. The T4 polynucleotide kinase can catalyze the transfer and exchange of P from the γ position fo ATP to the 5'-hydroxyl terminus of polynucleotides and 3'-monophosphates.</p>
 
<p>After annealing, we do the 5' phosphorylation of DNA for subsequent ligation. The T4 polynucleotide kinase can catalyze the transfer and exchange of P from the γ position fo ATP to the 5'-hydroxyl terminus of polynucleotides and 3'-monophosphates.</p>
 
<h3>3.Goldengate assembly</h3>
 
<h3>3.Goldengate assembly</h3>
−
<p>We use Type IIS restriction enzyme to digest the plasmid and use T4 DNA ligase to assemble DNA fragments we have annealed before.</p>
+
<p>We use Type IIS restriction enzyme to digest the plasmid and use T4 DNA ligase to assemble DNA fragments we have phosphorylated before.</p>
 
<p>We have recorded the detailed protocol of the goldengate assembly on the protocol page. Other users can refer to our protocol to design their own experiments (the amount of each added reagent in the protocol has been reduced to a minimum, it is not recommended to continue to reduce the amount. At the same time, when selecting other types of Type IIs restriction endonucleases, you should test whether the enzyme can work normally in T4 buffer. We have tested T4 ligase and T4 buffer from NEB and Takara, others did not tested yet.) .</p>
 
<p>We have recorded the detailed protocol of the goldengate assembly on the protocol page. Other users can refer to our protocol to design their own experiments (the amount of each added reagent in the protocol has been reduced to a minimum, it is not recommended to continue to reduce the amount. At the same time, when selecting other types of Type IIs restriction endonucleases, you should test whether the enzyme can work normally in T4 buffer. We have tested T4 ligase and T4 buffer from NEB and Takara, others did not tested yet.) .</p>
 
</div>
 
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<div>
 
<div>
 
<h2>Construction Device</h2>
 
<h2>Construction Device</h2>
−
<p>Since we need to build more than 400 components, if we use the traditional assembly method, this will bring a huge amount of work. Due to the low efficiency of traditional assembly, it will seriously delay our experimental process. And Gibson assembly can't guarantee the success rate, and it is not suitable for our large amount of work. Therefore, after the discussion, we finally decide to use GoldenGate Assembly. However, the selection of the correct construct is also a problem, so we designed the following Construction Device to select the correct constructs by visible color changes of the colonies.</p>
+
<p>Since we need to build more than 400 components, if we use the traditional assembly method, it will be a huge amount of work. Due to the low efficiency and success rate of traditional assembly, which will seriously delay our experimental process. We finally decide to use GoldenGate Assembly after discussion. However, the selection of the correct construct is also a problem, hence we designed the following Construction Device to select the correct constructs by visible color changes of the colonies.</p>
−
<p>The Construction Device includes a promoter J23104, a pigment protein tspurple, a pigment protein cjblue, a BbsI site, and a BsaI site. J23104+cjblue can be replaced with other promoter sequences by using BbsI restriction enzymes, and tspurple can be replaced with RNA thermosensor sequences using BsaI restriction enzymes. When not replaced, the colonies appear blue due to the expression of cjblue. After the first replacement, the colonies of the correct constructs appeared purple. After the second replacement, the colonies of the correct constructs exhibited their own milky white color. Color changes can refer to the following table:</p>
+
<p>The Construction Device includes a promoter J23104, a pigment protein tsPurple, a pigment protein cjBlue, a BbsI site, and a BsaI site. J23104+cjblue can be replaced with other promoter sequences by using BbsI restriction enzymes, and tsPurple can be replaced with RNA thermosensor sequences using BsaI restriction enzymes. When not replaced, the colonies appear blue due to the expression of cjBlue. After the first replacement of the promotor, the colonies of the correct constructs appeared purple. After the second replacement, the colonies of the correct constructs show their own milky white color. Color changes can refer to the following table:</p>
 
<div align="center">
 
<div align="center">
 
<img src="https://static.igem.org/mediawiki/2018/2/25/T--Jilin_China--Parts--Composite_Part--color_table.png" align="center"/>
 
<img src="https://static.igem.org/mediawiki/2018/2/25/T--Jilin_China--Parts--Composite_Part--color_table.png" align="center"/>
  
 
</div>
 
</div>
−
<p>We can successfully construct more than <b>200 plasmids</b> in one day, and the sequencing success rate is <b>over 95%</b>, which is a very exciting result.</p>
+
<p>We can successfully construct more than <b>200 plasmids</b> in one day. And the assembly success rate is <b>over 95%</b>, which is a very exciting result.</p>
 
     </div>
 
     </div>
 
     </li>
 
     </li>

Revision as of 09:38, 14 October 2018

CONSTRUCTION


Construction

  • Type IIs Restriction Endonuclease

    Restriction enzymes can be divided into four categories according to their different enzyme digestion methods, named Type I, Type II, Type III and Type IV. Our commonly used restriction endonucleases, such as EcoRI, belong to type II restriction endonucleases, which recognize specific 4 to 8 nucleotide sequences . The recognized sequence is inverted repeats and the cleavage site is located in the recognition site. After enzymatic cleavage and the sticky end or blunt end is produced. The cleavage diagram is as follows:

    R II

    R IIs

    R IIs

    Type IIS restriction enzymes differ from other Type II restriction enzymes in several ways.These enzymes recognize sequences comprise two distinct domains, one for DNA binding, the other for DNA cleavage. Type IIS restriction endonucleases cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites, creating 4-base overhangs.

    Type IIS cleavage domains have no inherent sequence-specificity, so the sequence of the overhang they generate varies from one recognition site to another. Fragments produced by Type IIS-digestion of natural DNA molecules generally have different overhangs, therefore, and will not anneal to one another.

    However, if the sequence of the overhang is predetermined, by designing it into a PCR primer, for example, then it can be made to complement another and to be directional. This feature is used to great advantage in 'Golden Gate' assembly where multiple fragments can be stitched together in the correct order and orientation in a single ligation. The advantage of using Type IIS enzymes for assembly is that the recognition sequence can be placed in the primer on either side of cleavage site. If placed inside, 3' to the cleaved end, it will be retained in the construct and can be re-used subsequently. If placed outside, 5' to the cleaved end, it will be lost, leading to a ‘scar-less’ assembly. This characteristic is widely used to perform in-vitro cloning techniques such as Golden Gate cloning

  • Goldengate Assembly

    Golden Gate Assembly is a one-tube efficient cloning method based on Type IIS restriction enzymes that cleave outside their recognition sites and leave 4-base overhangs. By adding the recognition site of type IIS enzyme on the plasmid, it will be digested by enzyme and will not appear at the end constructs. The fragment gene of interest contains complementary sticky ends can ultimately be assembled by ligation.

    Commonly used IIS type restriction enzymes are as follows:

    Enzyme Recognition Sequence
    BbsI GAAGAC (2/6)
    BsaI GGTCTC (1/5)
    BtgZI CGTCTC (1/5)
    BsmBI GCGATG (10/14)
    Esp3I CGTCTC (1/5)
    SapI GCTCTTC (1/4)

    We chose BbsI and BsaI type IIS restriction enzymes this year.

    The procedure of construction is annealed DNA oligos, phosphorylation and goldengate assembly:

    1. Annealed DNA oligos

    Oligos annealing can be use to add any short stretch of DNA to a plasmid. Most of the thermosensors we designed are 40~80bp, so we can design a forward oligo with the sequence of thermosensor and with the reverse oligo being the reverse compliment so that they could anneal. We also need to make sure our annealing products contain the cohesive end bases to complement the overhangs on the plasmid. The cohesive end bases could be a part of thermosensor, because we use the goldengate assembly, which has no-scar products.

    2. Phosphorylation

    After annealing, we do the 5' phosphorylation of DNA for subsequent ligation. The T4 polynucleotide kinase can catalyze the transfer and exchange of P from the γ position fo ATP to the 5'-hydroxyl terminus of polynucleotides and 3'-monophosphates.

    3.Goldengate assembly

    We use Type IIS restriction enzyme to digest the plasmid and use T4 DNA ligase to assemble DNA fragments we have phosphorylated before.

    We have recorded the detailed protocol of the goldengate assembly on the protocol page. Other users can refer to our protocol to design their own experiments (the amount of each added reagent in the protocol has been reduced to a minimum, it is not recommended to continue to reduce the amount. At the same time, when selecting other types of Type IIs restriction endonucleases, you should test whether the enzyme can work normally in T4 buffer. We have tested T4 ligase and T4 buffer from NEB and Takara, others did not tested yet.) .

  • Construction Device

    Since we need to build more than 400 components, if we use the traditional assembly method, it will be a huge amount of work. Due to the low efficiency and success rate of traditional assembly, which will seriously delay our experimental process. We finally decide to use GoldenGate Assembly after discussion. However, the selection of the correct construct is also a problem, hence we designed the following Construction Device to select the correct constructs by visible color changes of the colonies.

    The Construction Device includes a promoter J23104, a pigment protein tsPurple, a pigment protein cjBlue, a BbsI site, and a BsaI site. J23104+cjblue can be replaced with other promoter sequences by using BbsI restriction enzymes, and tsPurple can be replaced with RNA thermosensor sequences using BsaI restriction enzymes. When not replaced, the colonies appear blue due to the expression of cjBlue. After the first replacement of the promotor, the colonies of the correct constructs appeared purple. After the second replacement, the colonies of the correct constructs show their own milky white color. Color changes can refer to the following table:

    We can successfully construct more than 200 plasmids in one day. And the assembly success rate is over 95%, which is a very exciting result.

  • References

    • Dai H, Wang Y, Lu X, et al. Chimeric antigen receptors modified T-cells for cancer therapy[J]. JNCI: Journal of the National Cancer Institute, 2016, 108(7).
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