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Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

j5 DNA assembly design automation software.

Nathan J Hillson1, Rafael D Rosengarten, Jay D Keasling

  • 1Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA. njhillson@lbl.gov

ACS Synthetic Biology
|May 9, 2013
PubMed
Summary
This summary is machine-generated.

j5 is a new web tool that automates DNA assembly design for synthetic biology. This software streamlines complex DNA construction, saving researchers time and reducing errors in biotechnological research.

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Area of Science:

  • Synthetic Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Synthetic biology relies on DNA assembly but designing scar-less multipart DNA constructs is complex and error-prone.
  • Current methods for designing DNA assembly protocols are often manual, time-consuming, and lead to frequent user errors.

Purpose of the Study:

  • To develop and deploy j5, a web-based software tool for automating the design of scar-less multipart DNA assembly protocols.
  • To improve the efficiency, accuracy, and scalability of DNA construction for various biotechnological applications.

Main Methods:

  • Developed j5, a web-based software tool automating DNA assembly design for methods like SLIC, Gibson, CPEC, and Golden Gate.
  • Incorporated cost optimization, design rule enforcement, hierarchical assembly strategies, and combinatorial library design features.
  • Validated j5 designs using a GFP expression testbed for various DNA assembly methods and applications.

Main Results:

  • Demonstrated successful execution of j5 designs with SLIC, Gibson, and CPEC assembly methods.
  • Showcased the utility of j5 for constructing combinatorial DNA libraries using Golden Gate assembly.
  • Applied j5 designs to create linear gene deletion cassettes for E. coli.

Conclusions:

  • j5 significantly reduces researcher time and effort in DNA assembly design.
  • The software minimizes user design errors and off-target assembly products, decreasing research costs.
  • j5 enables scalable scar-less multipart and combinatorial DNA construction, advancing synthetic biology research.