GEL Electrophoresis Techniques

A set of vocabulary flashcards based on the lecture by Dr. Maati. M. El-Ghuol regarding nucleic acid electrophoresis techniques, automated analysis, and Pulsed Field Gel Electrophoresis.

Electrophoresis of nucleic acids

The most usual way to separate DNA/RNA molecules according to size using agarose or polyacrylamide gels.

Pulsed field gel electrophoresis (PFGE)

A modification of electrophoresis used to separate large fragments of DNA such as chromosomes, with a size range from $10\,kb$ to $1\,mb$.

Ethidium bromide (EtBr)

A dye that binds to DNA by intercalation and exhibits a strong orange/red fluorescence when illuminated with ultraviolet (UV) light.

Intercalation

The process by which ethidium bromide binds to DNA by insertion between set base pairs.

Agarose gels

Gels typically used to separate DNA molecules larger than about $100\,bp$; they are usually run in a horizontal format.

Polyacrylamide gels

The preferred gel method for higher resolution or for the effective separation of shorter DNA molecules.

Agarase

An enzyme used to digest agarose to recover a DNA fragment from the gel.

Electroelution

A recovery method where a piece of gel is closed in dialysis tubing containing buffer and placed between two electrodes to allow DNA to migrate out of the gel.

Agilent’s Lab-on-a-Chip

An automated technology developed to avoid the need for electrophoretic gel preparation by using computer-controlled electrophoresis through micro-channels.

DNA charge and migration

DNA is negatively charged and moves towards the positive pole; small molecules migrate rapidly because they experience little frictional drag.

Conventional electrophoresis capacity

This method only separates small size DNA ranging from a smallest size of $50-100\,bp$ and a larger size of $12\,kb-15\,kb$.

PFGE field parameters

In this technique, the electric field alternates $120^\circ$ every $90$ seconds for $18$ to $24$ hours at $14^\circ C$.

PFGE bacterial subtyping

A laboratory technique used to produce a DNA fingerprint for a bacterial isolate, serving as a universal generic subtyping method.

Restriction enzyme in PFGE

An enzyme used to digest large genomic DNA molecules into smaller fragments before separation by alternating field directions.