Techniques commonly used to visualize DNA include:
Nucleic acid probing involves using DNA probes to detect specific DNA sequences. Probes are designed to be complementary to the target sequence and labeled with tags like radioactive atoms or fluorescent dyes. By hybridizing with the target DNA, probes allow for the identification of organisms or genes of interest.
Gel electrophoresis separates DNA fragments based on size and biochemical traits. In agarose gel electrophoresis, DNA samples are loaded into wells and drawn through a gel matrix by an electric field. Smaller DNA fragments travel farther through the gel than larger ones. DNA fragment sizes are estimated by comparison to known size markers. Pulsed-field gel electrophoresis (PFGE) can separate very large DNA fragments by alternating the electric field orientation. Detection of DNA fragments in the gel is commonly done using stains like ethidium bromide, though safer alternatives are now available. In PAGE, a fine polyacrylamide gel matrix is used instead of agarose, typically in a vertical setup. PAGE separates proteins based on their size and charge. Proteins can be separated by charge alone or by size after denaturation with SDS. Proteins are visualized after electrophoresis using stains like Coomassie blue or silver stain.
Restriction fragment length polymorphism (RFLP) analysis compares DNA banding patterns after restriction enzyme digestion, revealing differences in DNA sequences among individuals. It has applications in epidemiology for tracking microorganisms in outbreaks and in genetics for studying inheritance patterns of variant genes.
Southern blots DNA fragments from a sample are separated by gel electrophoresis and then transferred to a membrane. The membrane-bound DNA fragments are then exposed to a labeled DNA probe, allowing specific sequences to be detected. Southern blots are useful for identifying specific DNA sequences in a sample, and once visualized, the target DNA fragments can be recovered by cutting out the corresponding portion of the membrane.
Microarray analysis is a technique used to compare gene expression patterns between different cell types. In this method, DNA or cDNA samples from experimental sources are applied onto a glass slide alongside known DNA sequences, allowing for the simultaneous analysis of thousands of DNA fragments. These samples are labeled with fluorescent dyes, hybridized to the microarray, and the resulting fluorescence intensity at specific spots on the array indicates the level of hybridization. Differences in hybridization between samples are observed as differences in color intensity.