Fosmid
Encyclopedia
Fosmids are similar to cosmid
s but are based on the bacterial F-plasmid. The cloning vector is limited, as a host (usually E. coli) can only contain one fosmid molecule. Fosmids are 40 kb of random genomic DNA. Fosmid library is prepared from a genome of the target organism and cloned into a fosmid vector .
Low copy number offers higher stability than comparable high copy number cosmids. Fosmid system may be useful for constructing stable libraries from complex genome
s. Fosmids have high structural stability and have been found to maintain human DNA effectively even after 100 generations of growth. Fosmid clones were used to help assess the accuracy of the Public Human Genome Sequence.
and codes for the formation of sex pilus to aid in bacterial conjugation. Conjugation involves using the sex pilus to form a bridge between two bacteria cells and to transfer a copy of the plasmid so that both cells contain identical DNA. It later was discovered that the F factor was the first episome and can exist as an independent plasmid making it a very stable vector for cloning. Conjugation aids in the formation of bacterial clone libraries by insuring all cells contain the desired fosmid.
Fosmids are plasmids that use the F-plasmid origin of replication and partitioning mechanisms to allow cloning of large DNA fragments. A library that provides 20–70-fold redundant coverage of the genome can easily be prepared.
Fosmids contain several functional elements:
An example of a mapped fosmid can be found here http://what-when-how.com/molecular-biology/f-plasmid-molecular-biology/
The methods of cutting and inserting DNA into fosmid vectors have been perfected. There are now many companies that can create a fosmid library from any sample of DNA in a very short period of time at a relatively low cost. This has been vital in allowing researchers to sequence numerous genomes for study. More than 180 organisms genomes have been fully sequenced since 1995.
The fosmid system is excellent for rapidly creating chromosome-specific mini-BAC libraries from flow-sorted chromosomal DNA. The major advantage of Fosmids over other cosmid systems lies in its capability of stably propagating human DNA fragments. Highly repetitive in nature, human DNA is well known for its extreme instability in multicopy vector systems. It has been found that the stability increases dramatically when the human DNA inserts are present in single copies in recombination deficient E. coli cells. Therefore, Fosmids serve as reliable substrates for large scale genomic DNA sequencing.
Useful tools such as http://www.ncbi.nlm.nih.gov/nuccore/?term=fosmid allow researchers to search for other fosmid libraries to compare for homologous DNA sequences between species.
Cosmid
A cosmid, first described by Collins and Hohn in 1978, is a type of hybrid plasmid that contains cos sequences, DNA sequences originally from the Lambda phage. Cosmids can be used to build genomic libraries....
s but are based on the bacterial F-plasmid. The cloning vector is limited, as a host (usually E. coli) can only contain one fosmid molecule. Fosmids are 40 kb of random genomic DNA. Fosmid library is prepared from a genome of the target organism and cloned into a fosmid vector .
Low copy number offers higher stability than comparable high copy number cosmids. Fosmid system may be useful for constructing stable libraries from complex genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s. Fosmids have high structural stability and have been found to maintain human DNA effectively even after 100 generations of growth. Fosmid clones were used to help assess the accuracy of the Public Human Genome Sequence.
Discovery
The fertility plasmid or F-plasmid was discovered by Esther LederbergEsther Lederberg
Esther Miriam Zimmer Lederberg was an American microbiologist and immunologist and pioneer of bacterial genetics...
and codes for the formation of sex pilus to aid in bacterial conjugation. Conjugation involves using the sex pilus to form a bridge between two bacteria cells and to transfer a copy of the plasmid so that both cells contain identical DNA. It later was discovered that the F factor was the first episome and can exist as an independent plasmid making it a very stable vector for cloning. Conjugation aids in the formation of bacterial clone libraries by insuring all cells contain the desired fosmid.
Fosmids are plasmids that use the F-plasmid origin of replication and partitioning mechanisms to allow cloning of large DNA fragments. A library that provides 20–70-fold redundant coverage of the genome can easily be prepared.
DNA Libraries
The first step in sequencing entire genomes is cloning the genome into manageable units of some 50-200 kilobases in length. It is ideal to use a fosmid library because of it's stability and limitation of one plasmid per cell. By limiting the number of plasmids in the cells the potential for recombination is decreased, thus preserving the genome insert.Fosmids contain several functional elements:
- OriT (Origin of Transfer): The sequence which marks the starting point of conjugative transfer.
- OriV (Origin of Replication): The sequence starting with which the plasmid-DNA will be replicated in the recipient cell.
- tra-region (transfer genes): Genes coding the F-Pilus and DNA transfer process.
- IS (Insertion Elements): so-called "selfish genes" (sequence fragments which can integrate copies of themselves at different locations).
An example of a mapped fosmid can be found here http://what-when-how.com/molecular-biology/f-plasmid-molecular-biology/
The methods of cutting and inserting DNA into fosmid vectors have been perfected. There are now many companies that can create a fosmid library from any sample of DNA in a very short period of time at a relatively low cost. This has been vital in allowing researchers to sequence numerous genomes for study. More than 180 organisms genomes have been fully sequenced since 1995.
Uses
Sometimes it is difficult to accurately distinguish individual chromosomes based on chromosome length, arm ratio, and C-banding pattern. Fosmids can be used as reliable cytological markers for individual chromosome identification and fluorescent in situ hybridization based metaphase chromosome karyotypes can be used to show whether the positions of these fosmids were successfully constructed.The fosmid system is excellent for rapidly creating chromosome-specific mini-BAC libraries from flow-sorted chromosomal DNA. The major advantage of Fosmids over other cosmid systems lies in its capability of stably propagating human DNA fragments. Highly repetitive in nature, human DNA is well known for its extreme instability in multicopy vector systems. It has been found that the stability increases dramatically when the human DNA inserts are present in single copies in recombination deficient E. coli cells. Therefore, Fosmids serve as reliable substrates for large scale genomic DNA sequencing.
Useful tools such as http://www.ncbi.nlm.nih.gov/nuccore/?term=fosmid allow researchers to search for other fosmid libraries to compare for homologous DNA sequences between species.