Deoxyribonucleic acid (DNA) is the molecule which carries the genetic instructions for almost every living thing. Its unique chemistry not only allows this information to be copied and passed on to an organism’s descendents, it also allows scientists opportunities to investigate and manipulate an organism at a molecular level. As a result, molecular biology techniques are at the forefront of most cutting edge scientific research. In this project you will investigate a number of commonly used molecular biology techniques involving DNA.

What is molecular biology?

Molecular biology is the study of living things at the level of the molecules which control them and make them up. While traditional biology concentrated on studying whole living organisms and how they interact within populations (a “top down” approach), molecular biology strives to understand living things by examining the components that make them up (a “bottom up” approach). Both approaches to biology are equally valid, although improvements to technology have permitted scientists to concentrate more on the molecules of life in recent years.

Molecular biology is a specialised branch of biochemistry, the study of the chemistry of molecules which are specifically connected to living processes. Of particular importance to molecular biology are the nucleic acids (DNA and RNA) and the proteins which are constructed using the genetic instructions encoded in those molecules. Other biomolecules, such as carbohydrates and lipids may also be studied for the interactions they have with nucleic acids and proteins. Molecular biology is often separated from the field of cell biology, which concentrates on cellular structures (organelles and the like), molecular pathways within cells and cell life cycles.

The molecules which form the basis of life provide scientists with a more predictable and mechanistic tool for scientists to study. Working with whole organisms (or even just whole cells) can be unpredictable, with the outcome of experiments relying on the interaction of thousands of molecular pathways and external factors. Molecular biology provides scientists with a toolkit with which they may “tinker” with the way life works. They may use them to determine the function of single genes or proteins, and find out what would happen if that gene or protein was absent or faulty. Molecular biology is used to examine when and why certain genes are switched “on” or “off”. An understanding of each of the factors has granted scientists a deeper understanding of how living things work, and used this knowledge to develop treatments for when living things don’t work so well.

Common molecular biology techniques

The following list covers some of the more commonly used molecular biology techniques – it is by no means exhaustive.

  • Electrophoresis – a process which separates molecules such as DNA or proteins out according to their size, electrophoresis is a mainstay of molecular biology laboratories. While knowing the size of a molecule might not seem like all that much information, it can be used to identify molecules or fragments of molecules and as a check to make sure that we have the correct molecule present.
  • Polymerase Chain Reaction (PCR) – a process used to amplify very small amounts of DNA to amounts which can be used in further experiments. It is used as a basic tool in molecular biology to ensure that we have sufficient DNA to carry out further techniques such as genetic modification, however it has wider practical uses such as in forensics (identification using DNA profiling) and disease diagnosis. PCR can also be used to introduce small point mutations into a gene in a process called site-directed mutagenesis.
  • Restriction Digest – the process of cutting DNA up into smaller fragments using enzymes which only act at a particular genetic sequence.
  • Ligation – the process of joining two pieces of DNA together. Ligation is useful when introducing a new piece of DNA into another genome.
  • Blotting – a technique used to specifically identify biomolecules following electrophoresis. The molecule of interest is indicated using either a labeled probe (a complementary strand of nucleic acid) or a labeled antibody raised against a specific protein.
  • Cloning – the technique of introducing a new gene into a cell or organism. This can be used to see what effect the expression of that gene has on the organism, to turn the organism into a factory which will produce large quantities of the gene or the protein it codes for, or (within the inclusion of a label) to indicate where the products of that gene are expressed in the organism. Insertion of genetic material into a bacterium is called transformation, while insertion into a eukaryotic cell is called transfection. If a virus is used to introduce this material, the process is called transduction.

Each of these techniques is used in conjunction with other techniques to help scientists solve a particular research question. For example, following using PCR to create large quantities of a particular gene a scientist may ligate a gene for a particular protein into a plasmid vector (a short circular strand of DNA which acts as a carrier), perform a quick restriction digest and electrophoresis to ensure that the gene has been inserted properly, and then use that plasmid to transform a bacterial cell which is used to produce large quantities of the vector. After purification of the vector from the bacteria, it is then used to transfect a mammalian cell in culture. The scientist then uses protein electrophoresis and western blotting to demonstrate the expression of the gene product.