Proteins are the molecules that are responsible for the majority of functions inside the cell. Thus scientists are usually most interested in which proteins and how much of each protein are present in a cell following a particular experimental manipulation. Unfortunately, it is difficult to study global protein expression, since proteins cannot be replicated easily in the lab. Also, proteins do not have complementary sequences like DNA or RNA that can be used as probes. For this reason, many scientists rely on gene expression analysis to give clues as to how a protein is being regulated. However, new technologies that…

(August 2003) The separation of DNA/RNA fragments or a protein sample based on size can be useful in many applications, but visualizing samples on a gel does not give any information about the identity of the sample (i.e. which gene fragment, mRNA or protein you are looking at). So how can you pick out the band you’re interested in? E.M. Southern answered this question when he developed a method that was subsequently named after him, the Southern Blot. Figure 1. The layout for a Southern Blot. The Southern Blot takes advantage of the fact that DNA fragments will stick to…

(August 2003) The Polymerase Chain Reaction (PCR) is an important tool for many applications. For example, it can be used to amplify a sample of DNA when there isn’t enough to analyze (e.g. a sample of DNA from a crime scene, archeological samples), as a method of identifying a gene of interest, or to test for disease. The method uses specifically designed primers that are complementary to the sequence to be amplified. The primers provide a starting point for the extension of the DNA by a DNA polymerase (usually Taq or Pfu polymerase). Amplification is carried out in cycles. First,…

(August 2003) Messenger RNA (mRNA) is a single stranded molecule that is used as the template for protein translation. It is possible for RNA to form duplexes, similar to DNA, with a second sequence of RNA complementary to the first strand. This second sequence is called antisense RNA (Figure 1). The formation of double stranded RNA can inhibit gene expression in many different organisms including plants, flies, worms and fungi. Figure 1 Formation of antisense RNA blocks translation. Co-Suppression The first discovery of this inhibition in plants was more than a decade ago and occurred in petunias. Researchers were trying…

(August, 2003) Although the structure of DNA is the same throughout all species of plants, animals and microorganisms, each individual organism looks different. This is due to the order in which DNA base pairs are sequenced. Not only does this order make you a human rather than a dog or a daffodil, it also makes each person unique. Sequences of DNA differ from person to person, but every cell within the same person contains the same sequence of DNA. So, your hair, blood, skin and all of the other cells in your body are exactly the same at the molecular…