Column chromatography is a method used in many areas of science to isolate a single compound from a mixture. The basic principle of column chromatography is the adsorption of target to the column by designing a column with specific affinity to the target. The target compound adsorbs to the column resin while the remaining mixture easily flow through the column and out the other end. A similar method is used to purify protein and nucleic acids, and it is generally referred to as affinity chromatography. Affinity chromatography requires a solid support (typically a magnetic bead or a resin column) on which to covalently attach a capture molecule which has affinity to the target protein or nucleic acid.
Cell lysis is the act of breaking the cell membrane to enable the study of specific proteins, nucleic acids, and other molecules inside of cells. When cell lysis is successful, the undamaged contents of the cell escape through the damaged cell membrane. These contents are then separated out of the mixed sample and used for further study. The methods used for separation of the lysed cell contents are dependent on the goal of the study. Careful investigation of these inner workings can reveal disease patterns, improve our understanding of normal cellular function, and elucidate biochemical pathways and therapeutic targets. Protein isolation is different from nucleic acid separation, and the reagents used vary drastically. There are a few ways to lyse the cell membrane; these include mechanical disruption, liquid homogenization, freeze/thaw cycles, manual griding, and the use of detergents. Sonication cell lysis is an example of mechanical disruption used for releasing the contents of cells.
An antigen is a molecule that is part of an object that is foreign to the body. The body uses antibodies to recognize the foreign object by its antigens and stimulates an immune response, activating white blood cells to produce more antibodies and other immune pathways. Antigens can be proteins or sugars that are located on the outer surfaces of pathogenic cells. All cells have antigens including the ones inside the body, bacteria, and even viruses. The antibodies produced by the immune system are custom-fitted to the antigen that initially stimulated the immune response. The antibodies have an antigen recognition site (paratope) that is highly specific affinity for a region on the antigen called the epitope.
An isolation kit helps you isolate a material of interest. When we talk about an isolation kit, we are likely talking about a kit that helps you isolate nucleic acid (RNA or DNA) or protein. These kits often contain all the buffers and hardware you need for your isolation. Let’s do a review of the types of isolation kits and how they work, then we’ll give you a general protocol to understand how the process works!
Introduction to dNTP’s
dNTP stands for deoxynulceoside triphosphate. dNTP’s are what make up one of the four macromolecules of life, nucleic acids. A nucleoside is a molecule that consists of a ribose (sugar) bound to a nitrogenous base. On dNTP’s the ribose is actually a deoxyribose because it lacks an oxygen atom on the second carbon position. There are four dominant types of nitrogenous bases that define the type of dNTP it is, they are A,T,C,G. The triphosphate is the three phosphate groups that bind the ribose as well. Our DNA is made up of these dNTPS, A binding favorably to T and C binding favorably to G. In addition to their role in the genetics of nature, dNTP’s are also used as a tool for polymerase chain reactions (PCR). Let’s discuss how PCR works and how dTNP’s are used for it.
Overview of antibodies
Antibodies are part of the adaptive immune response of the body. After an initial defense against a pathogen from immune cells such as neutrophils, our body launches B and T cells to create antibodies to fight a pathogen. The structure of an antibody looks like the letter Y of the latin alphabet. The central part, which goes from the stalk up to the arms of the antibody, is called the “heavy chain”. A “light chain” is attached to the upper arms of the heavy chain. The stalk is also called the “Fc” region and the arms on top are called the “Fab” region. The Fab region contains the part of the antibody that binds pathogens. This region that binds pathogens is called the paratope, and it binds an epitope on a pathogen. This interaction is specific and is based on the tertiary structure and amino acid sequence. There is one epitope per paratope.
The main reason for changing from latex to magnetic latex particles is the need for a change from an homogeneous to an heterogeneous immunoassay. Latex beads are micrometer sized polystyrene beads. They are made of polymer chains that form a sphere with a hydrophobic exterior that can participate in hydrophobic interaction. The beads bind proteins through passive adsorption or can be functionalized with chemical groups which better bind amine groups on proteins to bind them. Magnetic latex particles have an easy protocol that allows you to do washing steps quickly and efficiently, which helps to improve analytical sensitivity and to reduce interference from sample components. The main consideration in shifting from a process that utilizes latex beads to one that uses magnetic latex beads will be the physical separation process itself. Applications that utilize latex beads traditionally make use of a centrifuge or, alternatively, tangential filtration. In contrast, processes that use magnetic latex beads are carried out in a biomagnetic separator. As such, it is necessary to acquire an adequate separator for the process. Ideally, this would be a homogeneous separator.
HRP stands for horseradish peroxidase, an enzyme derived from horseradish. Streptavidin is a protein derived from a species of bacteria in the genus streptomyces. Streptavidin has a high affinity for the molecule biotin. Streptavidin HRP is a streptavidin protein conjugated to HRP. HRP is used for detection/read out signals in an assay such as ELISA. Depending on which substrate you give the HRP, the enzyme will produce a different signal that you can read out with whatever hardware/technology you have in your laboratory. Let’s discuss the general protocol for using streptavidin HRP and the various substrates you can use to get an output.