Biotechnology research and development projects typically require DNA composition and/or editing at some phase of the project. Companies of diverse nature, spanning virtually all the spectrum of biotech sectors, require editing of DNA as part of their development cycle. These include, among others, companies developing biocatalysts for industry, genetically modified crops, therapeutic proteins and cells engineered for industrial applications.
In this section we do not attempt to provide a comprehensive review of applications requiring composition and editing of DNA, but rather describe in some detail only a few applications. The examples we chose are not a shortlist of our preferred applications, but rather a sample intended to ignite the readers' imagination regarding the applicability of the technology to one's own research and development:
Protein (usually enzyme) engineering - rational and semi rational design
Many DNA coded enzymes catalyze chemical transformations of commercial value. Biotechnology companies design and screen these catalysts to meet commercial and research needs.
Designer plasmid construction
DNA plasmids are arguably the most used tool in molecular biology and biotechnology. Much of biological research and development is centered on preparing plasmids for various applications. Plasmid preparation typically requires together DNA fragments from several sources and gluing them with synthetic fragments with specific functions (e.g. restriction sites).
When a protein, DNA or RNA molecule is claimed by a patent, only the actual sequences deposited are protected. Screening nearby sequences and finding ones with similar functionality could help strengthen the patent.
Industrial Synthetic Biology
An emerging field that aims to develop genetically engineered cells, typically micro-organisms, that can produce a wide range of commercially viable products such as drugs and fuel. Cell engineering typically requires large-scale assembly and modification of DNA from multiple sources.
Genetically modified crops are engineered so that they have superior traits compared to the original wild type crops. Biotechnology companies worldwide are developing these next-generation DNA modified crops and gaining control over the production chain of crops and food.
Homologues recombination libraries and tagged proteins
Generating libraries of tagged proteins is a major research tool both in academic basic research and in the drug discovery industry. Each library member typically consists of several concatenated DNA fragments that originate from different genomes or from different locations within a genome. Such libraries allow the screening of multiple proteins against multiple molecules or conditions in an orderly fashion and therefore provide valuable information for drug discovery and basic research.
Therapeutic antibodies optimization
Antibodies are proteins that bind selectively and with high affinity to specific targets. They have come a long way in medicine and are now the active component of many recent drugs as well as a prime candidate for new drugs. Their rational and semi-rational engineering is a leading emerging method of their research and development. Supporting this engineering method requires the systematic editing of antibodies previously optimized within an animal.
Microbes for Energy Production
Natural microorganisms employ highly efficient energy production processes. Scientists are now trying to genetically modify organisms so that these capabilities are directed towards the production of usable energy for mankind.
The study of major human diseases using DNA synthesis and editing – the Mitochondria Example
A growing number of human diseases, including Alzheimer's, Parkinson's, type II diabetes and other metabolic disorders are implicated with inheriting or acquiring abnormal Mitochondrial DNA. Being able to quickly and cheaply edit the mitochondrial genome according to a scientist's specification could help develop mitochondrial gene replacement and other therapy approaches.
Rational protein surface engineering for x-ray crystallography
Protein X-ray crystallography, used to determinate 3D protein structures with atomic level resolution, enhances our understanding of protein structure and function and is therefore an integral component of the structure-guided drug discovery process. Modification of the target proteins is a key element leading to successful crystallization.