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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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Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

Published on: November 25, 2015

PlasmID: a centralized repository for plasmid clone information and distribution.

Dongmei Zuo¹, Stephanie E Mohr, Yanhui Hu

¹Harvard Institute of Proteomics, Harvard Medical School, 320 Charles Street, Cambridge, MA 02141, USA.

Nucleic Acids Research

|November 30, 2006

Summary

The Plasmid Information Database (PlasmID) offers a searchable online repository for over 46,000 plasmid clones. This resource facilitates easy access to diverse plasmids for scientific research and clone sharing.

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

The Dana-Farber/Harvard Cancer Center (DF/HCC) DNA Resource Core maintains a large collection of plasmid clones.
A centralized, accessible system was needed to manage and distribute these valuable research resources.

Purpose of the Study:

To establish the Plasmid Information Database (PlasmID) as a community-based resource portal.
To facilitate the searching and requesting of plasmid clones from the DF/HCC DNA Resource Core.
To provide researchers with online access to detailed plasmid information and downloadable data.

Main Methods:

Developed PlasmID as a central data repository with online search capabilities.
Integrated common gene names, identifiers, keywords, vector features, author names, and PubMed IDs for searching.
Stored over 46,000 plasmids in 98 vectors, including cDNA and genomic fragments from 26 species.
Utilized an automated -80°C freezer storage system for glycerol stocks.
Automated clone replication and distribution processes.

Main Results:

As of October 2006, PlasmID contained over 46,000 plasmids across 98 vector types.
The collection includes diverse clones for routine and advanced techniques, human cDNA sets, and genome-scale collections for multiple microbial species.
Plasmids are fully annotated to a high standard.
Downloadable vector maps and sequence data are freely available online.

Conclusions:

PlasmID serves as a comprehensive and accessible resource for plasmid information and distribution.
The database enhances research efficiency by simplifying the search and acquisition of plasmid clones.
The platform encourages community participation through sharing of plasmid resources.