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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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Generating functional plasmid origins with OriGen.

Jamie Irvine1, Jonathan N V Martinson1, Jigyasa Arora1

  • 1Innovative Genomics Institute, University of California, Berkeley, CA 94720, United States.

Nucleic Acids Research
|December 1, 2025
PubMed
Summary
This summary is machine-generated.

A new AI model, OriGen, designs novel plasmid origins of replication that are functional in Escherichia coli. This breakthrough enables the creation of custom DNA vectors with desired properties for biological research.

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Area of Science:

  • Synthetic Biology
  • Computational Biology
  • Genomics

Background:

  • Generative artificial intelligence (AI) shows potential for biological design.
  • No computational system has yet created replicable biological sequences.
  • Plasmids serve as minimal replicating systems for studying DNA replication.

Purpose of the Study:

  • To develop a computational system, OriGen, capable of generating novel and functional plasmid origins of replication.
  • To experimentally validate the AI-generated origins of replication.
  • To demonstrate the model's ability to design origins with specific desirable properties, such as avoiding restriction sites.

Main Methods:

  • Development of OriGen, a language model focused on generating plasmid origins of replication.
  • Maintaining essential functional elements within the generated sequences.
  • Experimental validation of OriGen-generated origins in Escherichia coli.
  • Directing OriGen to design origins that avoid specific restriction sites.

Main Results:

  • OriGen successfully generated novel plasmid origins of replication.
  • Experimental validation confirmed the activity of these origins in Escherichia coli.
  • The generated origins diverged from existing wild-type sequences.
  • OriGen produced functional origins that avoid common restriction sites, demonstrating controllable design.

Conclusions:

  • OriGen represents a significant advancement in computational biological design.
  • The model can capture complex replication mechanisms and generate functional, novel DNA sequences.
  • OriGen has the potential for automated, controllable design of DNA vectors with specific properties for various applications.