In this exercise, you will learn how to use the features on Benchling, such as annotating and visualizing a plasmid, as well as how to run a virtual plasmid digest.
Learning Objectives
At the end of the activity, you will be able to:
Abilities
Describe the major components of the Benchling platform based on the Navigate Benchling and Navigation tutorials.
Perform the operations on the Benchling platform outlined in the Design and analyze sequences in Molecular Biology tutorial as well as the Importing DNA, Finding Enzymes, Simulating a Digest and Enzyme Lists tutorials
Skills
Using Benchling's software to run a virtual digest of plasmids
Being able to perform operations on the Benchling platform
Running a virtual digest
What is Benchling
Benchling is a modern research platform that connects the entire R&D lifecycle — from project documentation and data acquisition to sequence design, sample management, process management, and reporting.
How to create a Benchling account:
1. Read Part 1: Navigate your Benchling workspace and Part 4: Design and analyze sequences in Molecular Biology in the Benchling Training Kit for Academics.
2. Go to plasmid pSB1-C3
3. Examine the plasmid map and identify everything you see.
4. Open the “Annotations” tab by locating and clicking the image. Take your time to ensure that you can recognize the annotated DNA parts and explain what they do.
5. Complete the tutorials Finding Enzymes and Simulating a Digest
6. Change your enzyme list to BioCurio/GMO Bootcamp
7. Visualize the location of recognition sequences and number of cut sites for the following enzymes: EciI, BseSI, ApaLI and TseI
8. Change your enzyme list to BioCurio/GMO Bootcamp
9. Run a virtual digest using with the following lanes - EcoRI, DpnI, PstI, XbaI, NotI, EcoRI + PstI, PstI + SpeI and NotI + PstI. Pay special attention to size of fragments, number of cuts and suggested buffers.
Tutorial on Navigating Benchling and how to use the different features on the Notebook.
Circular DNA sequence on Benchling. The left hand side is the DNA sequence, and the right hand side is a visual of the circular plasmid with the cut sites labelled.
Simulation of a digest using Not1. The left hand side shows the DNA ladder, and the right hand side shows the digest of pSB1K3 containing mRFP1-Not1.
Extra Resources
- https://help.benchling.com/en/articles/668777-importing-dna-sequences
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