Synthetic Biology & iGEM Terms

Lab Note #7
Jul 15, 2016

Are some of the procedures we discuss unfamiliar? Wish you knew more about synthetic biology and iGEM? Look no further than this document, which includes some commonly used terms for easy reference.

Competent cells take in foreign DNA more easily than their incompetent friends; this image depicts many bacteria accepting the double helix strands of DNA while Hans, an incompetent bacterium is left out

Assay: Another name for “experiment,” but an experiment designed to qualitatively or quantitatively measure the characteristics of a specific target

Autoclave: A machine that uses both steam and pressure to sterilize laboratory fluids and equipment

BioBrick: A standardized, interchangeable biological part (small sequence of DNA) that can be used in genetic constructs with a specific restriction enzyme assembly method

Characterization: Typically a term applied to protein analysis, characterization occurs through a series of assays to determine the properties of specific proteins produced by a genetic construct

Chassis: A chassis is the host organism for designed genetic constructs; a chassis may be a microbe, plant, or animal

Competent cells: Competent cells are more likely to uptake foreign DNA (a desirable quality in synthetic biology) than their wild counterparts

Digestion: The use of restriction enzymes to modify DNA segments by cleaving or cutting at specific points to have compatible ends for ligation, the next step in DNA cloning

DNA: Deoxyribonucleic acid, DNA, is a molecule that is used to encode information about growth, development, function, and reproduction; it’s what makes us who we are--unique individuals.

Enzyme: A biological molecule that serves as a catalyst, accelerating complex chemical reactions

Expression: The process by which the instructions written in DNA are used to create a functional protein product; hence, a gene is “expressed”

Gel electrophoresis: A method to separate DNA fragments from other particles in which electricity is run through an agarose gel, resulting in differently-sized fragments being pulled through the gel different distances

Gel extraction: After gel electrophoresis, the process in which desired fragments are cut from a gel and the gel is cleaned from them, leaving only appropriate DNA

Genetic construct: A complete modified genetic sequence that is inserted into a chassis

GFP: Green fluorescent protein, a common gene included with an inserted DNA sequence to check for expression, as the GFP will be visible, whereas the desired protein may not

Giant Jamboree: International iGEM competition that is held annually in Boston; the weekend is at the end of October, and this year 302 teams will participate

"Growth on a plate": Typically, an indication that a transformation was successful; cells are grown on antibiotic plates and can only survive if they have uptaken the plasmid with the genetic construct on it; growth is typically apparent in either a cloudy appearance to the plate or small, round colonies dotted across its surface

Human Practices (HP): An emphasis of iGEM and competition requirement, HP involves that which is “beyond the bench” including ethics, sustainability, safety, security, and intellectual property issues

Ligation: After digestion, the next step in assembly in which digested DNA pieces are joined together

Miniprep: A process for isolating small amounts of DNA from bacteria by splitting open (lysing) the cells and purifying the plasmid DNA within them

Part: A BioBrick, or part of a genetic construct

PCR amplification: A process by which copies of a single DNA fragment are synthesized using DNA polymerase, an enzyme that creates DNA by assembling its small particles

Pipette: An instrument by which small amounts of liquids are precisely measured

Plasmid: A small, typically circular piece of DNA found in cells that can replicate independently from chromosomal DNA

PPE: Personal protective equipment, safety measures such as lab coats, gloves, long pants, and closed-toe shoes that must be worn at all times in the laboratory

Restriction enzyme: An enzyme that recognizes a particular sequence of bases in DNA, and then cuts the DNA's backbone at that point

RFP: Red fluorescent protein, a common gene included with an inserted DNA sequence to check for expression, as the RFP will be visible, whereas the desired protein may not

"Running a gel": The process by which gel electrophoresis is completed in which electricity is actively flowing through a gel

Transformation: The process by which a competent cell uptakes a plasmid with desired genetic constructs in it

Vector: A vehicle to insert genetic material into a cell; a plasmid is a vector

Wiki: The most comprehensive report of an iGEM project; every team is required to create and maintain a wiki, which serves as their project’s permanent record

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