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Ampicillin is one of the most extensively used antibiotics as a selection marker in molecular biology and bacteriology. Ampicillin is available as Ampicillin anhydrous, Ampicillin trihydrate and Ampicillin sodium salt. Ampicillin sodium salt is often used to prepare stock solution as it has better solubility in water (>50 mg/ml in water). A 50 mg/ml stock solution of ampicillin can be prepared by dissolving 500 mg ampicillin sodium salt in water to a final volume of 10 ml.

The 2 x YT medium, also known as a 2 x TY medium, is a rich medium. It is recommended for the growth and propagation of E. coli infected with the single strand filamentous bacteriophage M13. It can be prepared by dissolving 16 g tryptone, 10 g yeast extract, and 5 g Sodium chloride (NaCl) in water to a final volume of 1000 ml.

To isolate plasmid from the host bacteria, cells are first lysed that lead to the release of plasmid and in subsequent steps, the plasmid is purified from the lysate. Purification of plasmid from the lysed cells are mostly dependent on the type of lysis method used to release plasmid in solution. For example, alkaline lysis which completely disrupts the bacterial cells leading to the release of cell components including both plasmid DNA and genomic DNA in denatured state relies on selective renaturation of only plasmid DNA in a perfect manner at the purification step. On the other hand, boiling lysis selectively releases only plasmid DNA from the bacterial cells. The purified plasmid can be further purified by a number of methods to obtain high quality plasmids. These methods are centrifugation in gradients of CsCl – ethidium bromide (EtBr), selective precipitation in high salt SDS, extraction with Phenol-chloroform, and hydroxylapatite and ion-exchange chromatography.

Amplification of plasmid is desirable for many applications including gene cloning, DNA sequencing, transfection, and probe preparation. The fastest and routinely used method to amplify plasmid is to introduce plasmid in an appropriate strain of E. coli e.g., DH5α (the process is called transformation), grow them to a suitable culture volume, and finally, extract plasmid from them (the process called plasmid isolation).

Both TAE (Tris-Acetate EDTA) and TBE (Tris-Borate EDTA) are common electrophoresis buffers for DNA agarose gel electrophoresis. However, they are quite different in nature, have some useful features and also some disadvantages. You can maximize your results by choosing an electrophoresis buffer depending on your application. The following table lists their properties, and advantages and disadvantages, and also provides explanation for their peculiar behaviour.

Agarose gel can be used for the separation of nucleic acids (DNA and RNA) and high molecular weight proteins or protein complexes.

Agarose is a useful matrix for a number of analytical and preparative techniques including gel electrophoresis, chromatography, and support matrix to immobilize enzymes and cells. Agarose is available in a variety of forms, which differ in physical properties. The two most common agarose are standard agarose and low melting agarose. Standard agarose is most commonly used for analysis of DNA and RNA. Low melting agarose is often used for preparative purposes such as elution of DNA fragments and complexes.