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Plasmids

Plasmids

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...

Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

Genome Copying Errors

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.

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Related Experiment Video

Updated: Sep 15, 2025

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

Deciphering plasmid replication dynamics: a computational approach to predict ColE1-like plasmid copy number.

Rinat Saban^1,2, Ofri Tfilin³, David Haggiag^1,2

¹Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.

Journal of the Royal Society, Interface

|July 15, 2025

Summary

This summary is machine-generated.

Researchers developed a new machine learning model to predict plasmid copy number from DNA sequence. This tool aids synthetic biology by simplifying plasmid design for better protein production and reduced cellular burden.

Keywords:

ColE1-like plasmids gene expression machine learning plasmid copy number plasmid replication

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Last Updated: Sep 15, 2025

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Area of Science:

Synthetic Biology
Molecular Biology
Bioinformatics

Background:

Plasmids are essential tools in synthetic biology for research and industry.
Plasmid copy number is critical for protein production and host cell metabolism.
No existing models can computationally predict plasmid copy number from its origin of replication (ORI) sequence.

Purpose of the Study:

To develop a novel computational model for predicting plasmid copy number.
To create a software solution for simplifying plasmid copy number design.
To advance plasmid engineering workflows in synthetic biology.

Main Methods:

Developed a machine learning model using features extracted from the ORI sequence.
Incorporated promoter strength and RNA folding dynamics of regulatory elements into the model.
Established a protocol for manipulating plasmid ORIs to validate model predictions.

Main Results:

The machine learning model accurately predicts plasmid copy number based on ORI sequence.
The developed software simplifies the design process for plasmid copy number.
Experimental validation confirmed the model's predictive power.

Conclusions:

The novel computational model and software represent a paradigm shift in plasmid engineering.
This innovation offers unprecedented avenues for advancing synthetic biology research and applications.
The software is publicly available to facilitate plasmid design and optimization.