Difference between revisions of "Team:HK SKHLPSS/Description"

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<h1>Project Description</h1>
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<p>
+
  <h1>Background </h1>
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The biodiversity of organism is originated from the information carried on DNA that it is only constructed by the fundamental Watson-Crick base pairing rules governing two basic combination of base pairs. The programmability of DNA allows the use of it as LEGO bricks to build different objects in both two-dimensional and three-dimensional manner.
+
 
−
</p>
+
  <p>
−
<p>
+
    <!-- (There are different type of Influenza, why H3N2 so popular?)  -->
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In addition to showing the possibility of programming DNA into different shapes, the field of DNA nanotechnology was developed to use it for medical purposes. Under the presence of target nucleic acids, conformational change of a molecular beacon that is also consisted of DNA will occur through a simple strand displacement process. Apart from nucleic acids target, presence of metal ions is also detectable by DNA molecular beacon as it affects the stability of DNA. To detect metal ion, G-quadruplex as a four-stranded nucleic acid structure is well known that the formation of it is highly depending on cation. The formation of quadruplex is able to stabilize the molecular structure of hemin and enhance its’ peroxidase activity that leads to the result of quantitative fluorescence or colorimetric signal.
+
    According to Hong Kong department of Health, the H3N2 flu outbreak in Hong Kong has been a cause for concern. 307 people died from this disease, which is even more than that in SARS outbreak in 2003. This influenza also can be a serious illness to the weak and frail or elderly, and may be complicated by bronchitis, chest infection or even death.
−
</p>
+
    <!-- (Currenty used testing method for H3N2 ? What is the disadvantage?) -->
−
<p>
+
  </p>
−
This year, the ultimate goal of our iGEM team is trying to establish a metal ion responsive molecular beacon in E. coli as a general platform for detecting environmental contamination using bacteria. In order to achieve this progressively, we will first perform the experiment in vitro using molecular beacon that consists of short oligos as a prove of concept. Then we will try to express the system in E. coli and conduct the same experiment using laboratory prepared sample and on-site collected sample for the detection of contamination.
+
 
−
</p>
+
  <p>   
 +
    In our previous project, we made a nano-tweezer to detect nucleic acids target in E. coil. This 2D structure made use of the Guanine rich sequence to bind with E. coli target strand to form a G-quadruplex. The G-quadruplex will enhance the peroxidase activity of hemin and lead to the peroxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) giving a colorimetric signal. The degree of peroxidase activity indicates the concentration of E.coli.
 +
    <!-- (Use of the Watson & Crick's principle.) -->
 +
  </p>
 +
 
 +
  <p>
 +
    Inspired by this technology, we want to make a 3 dimensional nanostructure to detect H3N2 virus. Hence, we want to use this as an example to demonstrate the possibility in using DNA Nanotechnology for diagnosis.
 +
    <!-- (What is the advantages of this method?
 +
    How can the project be designed?) -->
 +
    <!--
 +
      http://www.scmp.com/news/hong-kong/health-environment/article/2103673/mutation-may-be-behind-surge-flu-cases-summer-hong
 +
 
 +
      http://www.scmp.com/news/hong-kong/health-environment/article/2103878/how-worried-should-you-be-about-hong-kongs-unusual
 +
      Our aim is to provide a faster ; cheaper ; more specific / precise and simple to use detection method to check for H3N2 virus. 

 +
    -->
 +
  </p>
 +
 
 +
  <h1>Hypothesis</h1>
 +
  <p> 
 +
  <!-- Hypothesis can be divided into two parts. -->
 +
    First, we hypothesize that those eight DNA strands, which are designed by us and DNA strands are held by Watson-Crick base pairing, will self-assemble to form a cube, with the help of a thermal cycler.
 +
    Second, we hypothesis our nano-cube can bind with H3N2 virus to form G-quadruplex and can show its peroxidase activity in the presence of hemin.
 +
  </p>
 +
 
 +
  <h1>Graph</h1>
 +
 
 +
  <h1>Objectives </h1>
 +
  <ol>
 +
      <li>We hope the DNA strands we designed can be self-assemble to form a cube.</li>
 +
      <li>The cube can bind with the target strand</li>
 +
      <li>The higher the concentration of H3N2 virus, the higher the colour intensity is.</li>
 +
      <li>The result can be shown in-vivo.</li>
 +
  </ol>
 +
  <!--
 +
    (1.  DNA nano cube is designed with the use of the target DNA of the disease/virus.
 +
    2.  The eight oligos can self-assembled to form a nano cube with the use of thermal cylcer.
 +
    3.  The chemical test result is reliable. The concentration of the target DNA is proportional to the intensity of the ABTS color change.
 +
    4.  DNA plasmids can be used to produce the single strain of the nano DNA cube.)
 +
  -->
 +
 
 +
 
 +
  <!--
 +
    <h1>Project Description</h1>
 +
    <p>
 +
      The biodiversity of organism is originated from the information carried on DNA that it is only constructed by the fundamental Watson-Crick base pairing rules governing two basic combination of base pairs. The programmability of DNA allows the use of it as LEGO bricks to build different objects in both two-dimensional and three-dimensional manner.
 +
    </p>
 +
    <p>
 +
      In addition to showing the possibility of programming DNA into different shapes, the field of DNA nanotechnology was developed to use it for medical purposes. Under the presence of target nucleic acids, conformational change of a molecular beacon that is also consisted of DNA will occur through a simple strand displacement process. Apart from nucleic acids target, presence of metal ions is also detectable by DNA molecular beacon as it affects the stability of DNA. To detect metal ion, G-quadruplex as a four-stranded nucleic acid structure is well known that the formation of it is highly depending on cation. The formation of quadruplex is able to stabilize the molecular structure of hemin and enhance its’ peroxidase activity that leads to the result of quantitative fluorescence or colorimetric signal.
 +
    </p>
 +
    <p>
 +
      This year, the ultimate goal of our iGEM team is trying to establish a metal ion responsive molecular beacon in E. coli as a general platform for detecting environmental contamination using bacteria. In order to achieve this progressively, we will first perform the experiment in vitro using molecular beacon that consists of short oligos as a prove of concept. Then we will try to express the system in E. coli and conduct the same experiment using laboratory prepared sample and on-site collected sample for the detection of contamination.
 +
    </p>
 +
  -->
 
</div>
 
</div>
  

Revision as of 06:51, 4 October 2017

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Background

According to Hong Kong department of Health, the H3N2 flu outbreak in Hong Kong has been a cause for concern. 307 people died from this disease, which is even more than that in SARS outbreak in 2003. This influenza also can be a serious illness to the weak and frail or elderly, and may be complicated by bronchitis, chest infection or even death.

In our previous project, we made a nano-tweezer to detect nucleic acids target in E. coil. This 2D structure made use of the Guanine rich sequence to bind with E. coli target strand to form a G-quadruplex. The G-quadruplex will enhance the peroxidase activity of hemin and lead to the peroxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) giving a colorimetric signal. The degree of peroxidase activity indicates the concentration of E.coli.

Inspired by this technology, we want to make a 3 dimensional nanostructure to detect H3N2 virus. Hence, we want to use this as an example to demonstrate the possibility in using DNA Nanotechnology for diagnosis.

Hypothesis

First, we hypothesize that those eight DNA strands, which are designed by us and DNA strands are held by Watson-Crick base pairing, will self-assemble to form a cube, with the help of a thermal cycler. Second, we hypothesis our nano-cube can bind with H3N2 virus to form G-quadruplex and can show its peroxidase activity in the presence of hemin.

Graph

Objectives

  1. We hope the DNA strands we designed can be self-assemble to form a cube.
  2. The cube can bind with the target strand
  3. The higher the concentration of H3N2 virus, the higher the colour intensity is.
  4. The result can be shown in-vivo.