From Genes to Genomes: Concepts and Applications of DNA Technology

“…clearly written and well-structured throughout…attractively sized…unlikely to be left gathering dust on the shelf…” — Human Genomics, Vol 1(3), Mar 2004

“…when compared to some of the more overbearing, super-dense books that typically litter the lab…it is a welcome change…” — BSDB Newsletter, Winter 2003

Introduction

This book is about the study and manipulation of nucleic acids, and how this can be used to answer biological questions. Although we hear a lot about the commercial applications, in particular (at the moment) the genetic modification of plants, the real revolution lies in the incredible advances in our understanding of how cells work. Until about 30 years ago, genetics was a patient and laborious process of selecting variants (whether of viruses, bacteria, plants or animals), and designing breeding experiments that would provide data on how the genes concerned were inherited. The study of human genetics proceeded even more slowly, because of course you could only study the consequences of what happened naturally. Then, in the 1970s, techniques were discovered that enabled us to cut DNA precisely into specific fragments, and join them together again in different combinations. For the first time it was possible to isolate and study specific genes. Since this applied equally to human genes, the impact on human genetics was particularly marked. In parallel with this, hybridization techniques were developed that enabled the identification of specific DNA sequences, and (somewhat later) methods were introduced for determining the sequence of these bits of DNA. Combining those advances with automated techniques and the concurrent advance in computer power has led to the determination of the full sequence of the human genome.

This revolution does not end with understanding how genes work and how the information is inherited. Genetics, and especially modern molecular genetics, underpins all the biological sciences. By studying, and manipulating, specific genes, we develop our understanding of the way in which the products of those genes interact to give rise to the properties of the organism itself. This could range from, for example, the mechanism of motility in bacteria to the causes of human genetic diseases and the processes that cause a cell to grow uncontrollably giving rise to a tumour. In many cases, we can identify precisely the cause of a specific property. We can say that a change in one single base in the genome of a bacterium will make it resistant to a certain antibiotic, or that a change in one base in human DNA could cause debilitating disease. This only scratches the surface of the power of these techniques, and indeed this book can only provide an introduction to them. Nevertheless, we hope that by the time you have studied it, you will have some appreciation of what can be (and indeed has been) achieved.

Genetic manipulation is traditionally divided into in vitro and in vivo work. Traditionally, investigators will first work in vitro, using enzymes derived from various organisms to create a recombinant DNA molecule in which the DNA they want to study is joined to a vector. This recombinant vector molecule is then processed in vivo inside a host organism, more often than not a strain of the Escherichia coli (E. coli) bacterium. A clone of the host carrying the foreign DNA is grown, producing a great many identical copies of the DNA, and sometimes its products as well. Today, in many cases the in vivo stage is bypassed altogether by the use of PCR (polymerase chain reaction), a method which allows us to produce many copies of our DNA in vitro without the help of a host organism.

In the early days, E. coli strains carrying recombinant DNA molecules were treated with extreme caution. E. coli is a bacterium which lives in its billions within our digestive system, and those of other mammals, and which will survive quite easily in our environment, for instance in our food and on our beaches. So there was a lot of concern that the introduction of foreign DNA into E. coli would generate bacteria with dangerous properties. Fortunately, this is one fear that has been shown to be unfounded. Some natural E. coli strains are pathogenic -in particular the 0157:H7 strain which can cause severe disease or death. By contrast, the strains used for genetic manipulation are harmless disabled laboratory strains that will not even survive in the gut. Working with genetically modified E. coli can therefore be done very safely (although work with any bacterium has to follow some basic safety rules). However, the most commonly used type of vector, plasmids, are shared readily between bacteria; the transmission of plasmids between bacteria is behind much of the natural spread of antibiotic resistance. What if our recombinant plasmids were transmitted to other bacterial strains that do survive on their own? This, too, has turned out not to be a worry in the majority of cases. The plasmids themselves have been manipulated so that they cannot be readily transferred to other bacteria. Furthermore, carrying a gene such as that coding for, say, dogfish insulin, or an artificial chromosome carrying 100000 bases of human genomic DNA is a great burden to an E. coli cell, and carries no reward whatsoever. In fact, in order to make them accept it, we have to create conditions that will kill all bacterial cells not carrying the foreign gene. If you fail to do so when you start your culture in the evening, you can be sure that your bacteria will have dropped the foreign gene the next morning. Evolution in progress!

Whilst nobody today worries about genetically modified E. coli, and indeed diabetics have been injecting genetically modified insulin produced by E. coli for decades, the issue of genetic engineering is back on the public agenda, this time pertaining to higher organisms. It is important to distinguish the genetic modification of plants and animals from cloning plants and animals. The latter simply involves the production of genetically identical individuals; it does not involve any genetic