Introduction to DNA Manipulation
Instructor: Marina Ayrapetov, PhD, URI, and Janet Atoyan, MS, URI
Location: URI
Session 1: June 10 – June 12 ( Lab: Room 405 / Lecture Room: Avedisian Rm 403)
Session 2: June 24 – June 26 ( Lab: Room 405 / Lecture Room: Avedisian Rm 403)
Course Overview
This WDT Module is designed to immerse students in the practical aspects of synthetic biology. It will introduce various techniques based on DNA manipulation and analysis methods through a combination of lectures and hands-on laboratory experience. Students will learn about DNA extraction methods and PCR in the classroom, and then apply this knowledge in the lab by preparing genomic and plasmid DNA, performing PCR, cloning, and subsequent analysis. This module is ideal for students new to DNA manipulation and analysis, as it provides a solid foundation for further training in these and related research areas. The module will be completed over 2.5 days and participants who complete the module will receive an RI-INBRE Certificate of completion.
Learning Outcomes
- Learn the background of various DNA manipulation methods to understand how to clone genes
- Prepare genomic DNA, transfer genes between organisms, and confirm the success of the transfer
- Learn the background of DNA sequencing and analyze sequencing data
Lab Report
Students will be expected to maintain detailed laboratory notes to include:
- DNA sample preparation protocols
- Data analysis protocols (e.g., workflows, software used, etc.)
- Quality control metrics for sequencing and data analysis
- Results of bioinformatics analysis
Resources Used in this Module:
- Standard Operating Procedure – DNA extraction methods, PCR, restriction digest, ligation
- SnapGene software
- Slide Decks for Lectures
Timeline
| Day 1 | Day 2 | Day 3 | |
|---|---|---|---|
| 9:00 AM-10:00 AM | Intro to DNA and PCR (lecture) | How to confirm successful cloning (lecture) | |
| 10:00 AM-11:00 AM | Genomic DNA extraction, quantification and PCR set up (hands-on) | Colony PCR Method (hands-on) | Analyzing sequencing data |
| 11:00 AM-12:00 PM | Plasmid extraction and quantification (hands-on) Setting up restriction enzyme reaction (hands-on) | Plasmid extraction and RE digest Method | Open discussion and Q&A session |
| 12:00 - 1:00 PM | Break | Break | WDT Survey and Certificate Distribution |
| 1:00 PM-2:00 PM | Gel extraction and PCR/RE clean up (hands-on) | Analysis of Colony PCR/RE methods | |
| 2:00 PM-3:00 PM | Setting up ligation reaction (hands-on) | Sanger Sequencing Method (lecture) | |
| 3:00 PM-4:00 PM | Transformation | Sending Samples for sequencing (hands-on) |