Library (biology)

In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated). DNA library technology is a mainstay of current molecular biology, and the applications of these libraries depends on the source of the original DNA fragments. There are differences in the cloning vectors and techniques used in library preparation, but in general each DNA fragment is uniquely inserted into a cloning vector and the pool of recombinant DNA molecules is then transferred into a population of bacteria or yeast such that each organism contains on average one construct (vector + insert). As the population of organisms is grown in culture, the DNA molecules contained within them are copied and propagated (thus, "cloned").

Terminology

The term "library" can refer to a population of organisms, each of which carries a DNA molecule inserted into a cloning vector, or alternatively to the collection of all of the cloned vector molecules.

cDNA libraries

main article: cDNA library

A cDNA library represents a sample of the mRNA purified from a particular source (either a collection of cells, a particular tissue, or an entire organism), which has been converted back to a DNA template by the use of the enzyme reverse transcriptase. It thus represents the genes that were being actively transcribed in that particular source under the physiological, developmental, or environmental conditions that existed when the mRNA was purified. cDNA libraries can be generated using techniques that promote "full-length" clones or under conditions that generate shorter fragments used for the identification of "expressed sequence tags".

cDNA libraries are useful in reverse genetics, but they only represent a very small (less than 1%) portion of the overall genome in a given organism.

Applications of cDNA libraries include:

• Discovery of novel genes
• Cloning of full-length cDNA molecules for in vitro study of gene function
• Study of the repertoire of mRNAs expressed in different cells or tissues
• Study of alternative splicing in different cells or tissues

Genomic libraries

A genomic library is a set of clones that together represents the entire genome of a given organism. The number of clones that constitute a genomic library depends on (1) the size of the genome in question and (2) the insert size tolerated by the particular cloning vector system. For most practical purposes, the tissue source of the genomic DNA is unimportant because each cell of the body contains virtually identical DNA (with some exceptions).

Applications of genomic libraries include:

• Determining the complete genome sequence of a given organism (see genome project)
• Serving as a source of genomic sequence for generation of transgenic animals through genetic engineering
• Study of the function of regulatory sequences in vitro
• Study of genetic mutations in cancer tissues

Randomized mutant libraries

In contrast to the library types described above, a randomized mutant library is created by de novo synthesis of a gene^[1]. During synthesis, alternative nucleotides or codons are incorporated into the DNA sequence at specific positions. This results in a mixture of double stranded DNA molecules which represent variants of the original gene. These variants can then be ligated into an expression vector, individual clones can be created, and the encoded protein variants can be expressed.

The expressed proteins can then be screened for variants which exhibit favourable properties. Typically the properties that are to be improved by screening a randomized mutant library are the binding affinity of antibodies or other protein-protein interactions, the activity of enzymes, or the stability of a protein. Multiple cycles of creating gene variants and screening the expression products are typically involved in directed evolution experiments.

Overview of library preparation techniques

Vectors

The nucleotide sequences of interest are preserved as inserts to a plasmid or the genome of a bacteriophage that has been used to infect bacterial cells.

References

1. ^ [1]Tian-Wen Wang, Hu Zhu, Xing-Yuan Ma, Ting Zhang, Yu-Shu Ma and Dong-Zhi Wei, Molecular Biotechnology Volume 34, Number 1, 55-68: Mutant library construction in directed molecular evolution

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