View source for Genomics Wonwoo Jeong

<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 38pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l0 level1 lfo1"><span lang="EN-US" style="mso-fareast-font-family: &quot;맑은 고딕&quot;; mso-fareast-theme-font: minor-latin; mso-bidi-font-family: &quot;맑은 고딕&quot;; mso-bidi-theme-font: minor-latin"><span style="mso-list: Ignore"><font size="2" face="맑은 고딕">1.</font><span style="font: 7pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><span style="font-size: small"><span lang="EN-US"><font face="맑은 고딕">Genomics</font></span></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 38pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l0 level1 lfo1"><span style="font-size: small"><span lang="EN-US" style="mso-fareast-font-family: &quot;맑은 고딕&quot;; mso-fareast-theme-font: minor-latin; mso-bidi-font-family: &quot;맑은 고딕&quot;; mso-bidi-theme-font: minor-latin"><span style="mso-list: Ignore"><font face="맑은 고딕">1)</font><span style="font: 7pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><span lang="EN-US"><font face="맑은 고딕">Definition</font></span></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 38pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l0 level1 lfo1"><span style="font-size: small"><span lang="EN-US"><font face="맑은 고딕">Analyzing function and structure of genomes discipline. Using DNA sequencing.<span style="mso-spacerun: yes">&nbsp; </span>Gilbert and Sanger method is used to verify DNA sequence that cleavage DNA strand using ddNTPs and dNTPs.</font></span></span><span lang="EN-US"><font face="맑은 고딕"><font size="2"><o:p></o:p></font></font></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><span lang="EN-US" style="mso-fareast-font-family: &quot;맑은 고딕&quot;; mso-fareast-theme-font: minor-latin; mso-bidi-font-family: &quot;맑은 고딕&quot;; mso-bidi-theme-font: minor-latin"><span style="mso-list: Ignore"><font face="맑은 고딕">2)</font><span style="font: 7pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><span lang="EN-US"><font face="맑은 고딕">Application</font></span></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><span lang="EN-US"><font face="맑은 고딕">Human Genome Project is the most famous application of genomics. The project is clarifying sequence of chemical base pairs. Not only human but also any other animals can be subjected to this project. By mapping organism&rsquo;s genome in a row, it is possible to figure out taxonomical relationship as well. Relationship between primates and humankind, between Siberia tiger and Bengal tiger and between any other co-existent codes.</font></span></span><span lang="EN-US"><font size="2"><font face="맑은 고딕"><o:p></o:p></font></font></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><span lang="EN-US" style="mso-fareast-font-family: &quot;맑은 고딕&quot;; mso-fareast-theme-font: minor-latin; mso-bidi-font-family: &quot;맑은 고딕&quot;; mso-bidi-theme-font: minor-latin"><span style="mso-list: Ignore"><font face="맑은 고딕">3)</font><span style="font: 7pt &quot;Times New Roman&quot;">&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><span lang="EN-US"><font face="맑은 고딕">Sanger method</font></span></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><span lang="EN-US"><font face="맑은 고딕">(</font></span></span><span lang="EN-US"><span style="font-size: small"><a href="http://en.wikipedia.org/wiki/Sanger_sequencing"><span style="text-decoration: none; color: windowtext; text-underline: none"><font face="맑은 고딕">http://en.wikipedia.org/wiki/Sanger_sequencing</font></span></a><font face="맑은 고딕">)</font></span><font size="2"><font face="맑은 고딕"><o:p></o:p></font></font></span></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><font face="맑은 고딕"><span lang="EN" style="mso-ansi-language: EN">The classical chain-termination method requires a single-stranded DNA template, a DNA </span></font></span><font face="맑은 고딕"><span style="font-size: small"><span lang="EN-US"><a title="Primer (molecular biology)" href="http://en.wikipedia.org/wiki/Primer_(molecular_biology)"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">primer</span></a></span><span lang="EN" style="mso-ansi-language: EN">, a </span></span><span style="font-size: small"><span lang="EN-US"><a title="DNA polymerase" href="http://en.wikipedia.org/wiki/DNA_polymerase"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">DNA polymerase</span></a></span><span lang="EN" style="mso-ansi-language: EN">, normal deoxynucleotidetriphosphates (dNTPs), and modified di-deoxynucleotidetriphosphates (ddNTPs), the latter of which terminate DNA strand elongation. These chain-terminating nucleotides lack a 3'-</span></span><span style="font-size: small"><span lang="EN-US"><a title="Hydroxyl" href="http://en.wikipedia.org/wiki/Hydroxyl"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">OH</span></a></span><span lang="EN" style="mso-ansi-language: EN"> group required for the formation of a </span></span><span style="font-size: small"><span lang="EN-US"><a title="Phosphodiester bond" href="http://en.wikipedia.org/wiki/Phosphodiester_bond"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">phosphodiester bond</span></a></span><span lang="EN" style="mso-ansi-language: EN"> between two nucleotides, causing DNA polymerase to cease extension of DNA when a modified ddNTP is incorporated. The ddNTPs may be radioactively or </span></span><span style="font-size: small"><span lang="EN-US"><a title="Fluorescence" href="http://en.wikipedia.org/wiki/Fluorescence"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">fluorescently</span></a></span><span lang="EN" style="mso-ansi-language: EN"> labeled for detection in automated sequencing machines.</span></span><span lang="EN" style="mso-ansi-language: EN"><font size="2"><o:p></o:p></font></span></font></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 56pt; text-indent: -18pt; mso-para-margin-left: 0gd; mso-list: l1 level1 lfo2"><span style="font-size: small"><font face="맑은 고딕"><span lang="EN" style="mso-ansi-language: EN">The DNA sample is divided into four separate sequencing reactions, containing all four of the standard </span></font></span><font face="맑은 고딕"><span style="font-size: small"><span lang="EN-US"><a title="Deoxynucleotides" href="http://en.wikipedia.org/wiki/Deoxynucleotides"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">deoxynucleotides</span></a></span><span lang="EN" style="mso-ansi-language: EN"> (dATP, dGTP, dCTP and dTTP) and the DNA polymerase. To each reaction is added only one of the four </span></span><span style="font-size: small"><span lang="EN-US"><a title="Dideoxynucleotides" href="http://en.wikipedia.org/wiki/Dideoxynucleotides"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">dideoxynucleotides</span></a></span><span lang="EN" style="mso-ansi-language: EN"> (ddATP, ddGTP, ddCTP, or ddTTP), while the four other nucleotides are ordinary ones. The dideoxynucleotide is added in approximately 100-fold excess of the corresponding deoxynucleotide(e.g. 0.5mM ddATP&nbsp;: 0.005mM dATP) allowing for enough fragments to be produced while still transcribing the complete sequence.</span></span><span style="font-size: small"><span lang="EN-US"><a href="http://en.wikipedia.org/wiki/Sanger_sequencing#cite_note-Sanger1977-2"><sup><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">[2]</span></sup></a></span><span lang="EN" style="mso-ansi-language: EN"> Putting it in a more sensible order, four separate reactions are needed in this process to test all four ddNTPs. Following rounds of template DNA extension from the bound primer, the resulting DNA fragments are heat </span></span><span style="font-size: small"><span lang="EN-US"><a title="DNA denaturation" href="http://en.wikipedia.org/wiki/DNA_denaturation"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">denatured</span></a></span><span lang="EN" style="mso-ansi-language: EN"> and separated by size using </span></span><span style="font-size: small"><span lang="EN-US"><a title="Gel electrophoresis" href="http://en.wikipedia.org/wiki/Gel_electrophoresis"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">gel electrophoresis</span></a></span><span lang="EN" style="mso-ansi-language: EN">. In the original publication of 1977,</span></span><span style="font-size: small"><span lang="EN" style="mso-ansi-language: EN"><sup><a href="http://en.wikipedia.org/wiki/Sanger_sequencing#cite_note-Sanger1977-2"><span style="text-decoration: none; color: windowtext; text-underline: none">[2]</span></a></sup> the formation of base-paired loops of ssDNA was a cause of serious difficulty in resolving bands at some locations. This is frequently performed using a denaturing </span></span><span style="font-size: small"><span lang="EN-US"><a title="Polyacrylamide gel" href="http://en.wikipedia.org/wiki/Polyacrylamide_gel"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">polyacrylamide</span></a></span><span lang="EN" style="mso-ansi-language: EN">-urea gel with each of the four reactions run in one of four individual lanes (lanes A, T, G, C). The DNA bands may then be visualized by </span></span><span style="font-size: small"><span lang="EN-US"><a title="Autoradiography" href="http://en.wikipedia.org/wiki/Autoradiography"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">autoradiography</span></a></span><span lang="EN" style="mso-ansi-language: EN"> or UV light and the DNA sequence can be directly read off the </span></span><span style="font-size: small"><span lang="EN-US"><a title="Radiography" href="http://en.wikipedia.org/wiki/Radiography"><span lang="EN" style="text-decoration: none; color: windowtext; text-underline: none; mso-ansi-language: EN">X-ray film</span></a></span><span lang="EN" style="mso-ansi-language: EN"> or gel image. (</span></span><span style="font-size: small"><span lang="EN-US"><a href="http://en.wikipedia.org/wiki/Sanger_sequencing"><span lang="EN" style="mso-ansi-language: EN"><font color="#0563c1">http://en.wikipedia.org/wiki/Sanger_sequencing</font></span></a></span><span lang="EN" style="mso-ansi-language: EN">)</span></span><span lang="EN" style="mso-ansi-language: EN"><font size="2"><o:p></o:p></font></span></font></p>
<p class="MsoListParagraph" style="margin: 0cm 0cm 8pt 40pt"><span style="font-size: small"><span lang="EN" style="mso-ansi-language: EN"><o:p><font face="맑은 고딕">&nbsp;</font></o:p></span></span><span lang="EN" style="mso-ansi-language: EN"><o:p></o:p></span></p>
<p>&nbsp;</p>