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Related Concept Videos

Plasmids01:28

Plasmids

83
Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
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DNA Agarose Gel Electrophoresis02:35

DNA Agarose Gel Electrophoresis

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Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
In cloning experiments, both the insert and vector DNA...
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Related Experiment Video

Updated: Aug 23, 2025

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion
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ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program.

M Wayne Davis1, Erik M Jorgensen1

  • 1Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, UT, United States.

Frontiers in Bioinformatics
|October 28, 2022
PubMed
Summary
This summary is machine-generated.

A plasmid Editor (ApE) is a free, multi-platform software for DNA sequence visualization and plasmid design. It simulates cloning methods and creates clear plasmid maps for Mac, PC, and Linux users.

Keywords:
DNA visualizationfreely available softwaremolecular biology toolsmolecular techniques simulatorplasmid editor

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Synthetic Biology

Background:

  • Designing and visualizing DNA sequences, particularly plasmids, is crucial for molecular biology research.
  • Existing tools may lack flexibility in annotation or simulation of diverse cloning methods.

Purpose of the Study:

  • To introduce A plasmid Editor (ApE), a versatile software for DNA sequence manipulation.
  • To provide a user-friendly platform for designing and presenting biological constructs.

Main Methods:

  • ApE offers a flexible framework for manual or library-based sequence annotation.
  • It enables *in silico* simulation of various DNA cloning techniques, including PCR, Gibson assembly, restriction-ligation, and Golden Gate assembly.
  • The software facilitates the creation of visually appealing linear and circular plasmid maps.

Main Results:

  • ApE supports multi-platform compatibility (Mac, PC, Linux).
  • It provides robust tools for designing complex DNA constructs through simulated cloning.
  • The application generates clear and customizable plasmid visualizations.

Conclusions:

  • A plasmid Editor (ApE) is a valuable, free resource for researchers involved in DNA sequence design and plasmid construction.
  • Its multi-platform availability and diverse functionalities enhance its utility in molecular biology and synthetic biology workflows.