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Lab Tools

Automatic DNA Sequencer
Automatic DNA sequencers are basically elaborate gel electrophoresis machines mated to fluorescent marker detectors. Earlier models used flat traditional gels with the sample replicated into four different lanes. That way, each lane could be dedicated to detecting one specific fluorescent marker (corresponding to one nucleotide species). More modern machines can read all four different markers in the same lane. The model we use in the lab is even more advanced, using a capillary tube instead of a flat gel to run the electrophoresis; thus, the quantity of required sample is smaller.

Digestion Buffer
Readily available in kits, this is a generalized buffered solution of proteolytic enzymes designed to eat the bacterial cell wall and release the cellular content into the solution. Other proteins are also digested.

Microconcentrator Column
This small piece of equipment essentially acts as a sophisticated microfilter. Microconcentrator columns separate macromolecules based on size. The model used in this lab retains large DNA molecules while smaller molecules such as nucleotides, primers, and DNA polymerases pass through. The trapped DNA molecules can be released by centrifuging the column upside down.

PCR Machine
Automatic PCR machines have become sophisticated, easy to use, and widely available. It can be argued that this is one piece of equipment that has revolutionized the study of genetics in recent years. Standard predescribed settings can give perfectly good results (as we do in this lab), but the researchers can always customize the cycling program (i.e., number, temperature, duration, etc.) in case of difficulties.

PCR Master Mix
The "brew" that contains everything necessary to carry out the polymerase chain reaction to amplify the 16S rRNA gene. Consists of water; a buffer to keep the mix at the correct pH for the PCR reaction; large quantities of the four nucleotides adenine, cytosine, guanine, and thymine; large quantities of oligonucleotide DNA primers that bind the 16S rDNA region to initiate the replication process; and a heat-stable DNA polymerase that extends the copy DNA strand.

Strip Tube
These are conveniently joined and color-coded microcentrifuge tubes. Each tube is designed to contain a different primer, and the different colors correspond to forward or reverse replication direction. (See part 4 for details.)

Standard micropipette that has become the workhorse of modern biology labs.