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The Colors that Do Magic

How Fluorescence Enabled Automation in Nucleic Acid Sequencing

By Ghizlane Bendriss, Ali Chaari, Kuei-Chiu Chen

The Colors that Do Magic


 

Abstract

This directed case study with a lab component tells the story of “Sara,” a college sophomore majoring in biological science. Sara has been awarded an internship in a lab focusing on sequencing gene markers for species identification. On her first day, she learns that the sequencing machine is temporarily out of service, so she is asked to prepare the reaction tube for sequencing the following day using the traditional Sanger method. Sara experiences experimental errors that lead to unexpected results, but her good lab notes allow her to pinpoint the cause. When she runs her prepared reaction tube the following day through the repaired automated sequencing machine she realizes that the invention of Professor Leroy Hood at Caltech and the team of DuPont Research Station has paved the way for second, third, and next generation sequencing (NGS). Central to the case is an activity in which students simulate the synthesizing of new strands of DNA by playing the role of DNA polymerase using the labeled dideoxynucleotide sequencing method.  Originally designed for a first-year medical college general biology class, this case can also be used in high school and college-level biology or biochemistry courses.

   

Date Posted

08/23/2021

Overview

Objectives

  • Describe the principles of Sanger sequencing.
  • Simulate the DNA synthesis process
  • Describe the reactants needed for sequencing and their function
  • Visualize the actions taking place in a sequencing reaction tube.
  • Differentiate the 3´ and 5´ ends of a sequence in a replication process.
  • Determine the sequence of a DNA template from an agarose gel result and from a chromatogram.
  • Describe the advantage of using fluorescent labels on the primer in a sequencing reaction as developed in Caltech.
  • Describe the advantage of using fluorescent labels on ddNTPs in a sequencing reaction as developed by the DuPont group.
  • Troubleshoot sequencing experiments.

Keywords

Sequencing; dideoxyribonucleotide; DNA polymerase; fluorescence; Sanger; chromatogram; DNA synthesis; agarose gel; nucleotides; dNTP; ddNTP

  

Subject Headings

Bioinformatics
Biology (General)
Molecular Biology

EDUCATIONAL LEVEL

High school, Undergraduate lower division, Undergraduate upper division

  

FORMAT

PDF, PowerPoint

   

TOPICAL AREAS

N/A

   

LANGUAGE

English

   

TYPE/METHODS

Directed, Laboratory

 

 

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