IGEM:MIT/2005/Monday, June 6th
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MIT iGEM 2005 Laboratory "bootcamp" (run by Natalie Kuldell and Kate Bacon Schneider)
I. Tour of 68-074
II. Pipetman use
- Background Information/Demonstration (asked students what they knew):
- settings on different Pipetman
- different sizes of tips used (blue for P1000, yellow or white for P20, P200)
- first stop to pull up liquid/push through to second stop to release liquid
- releasing tips with ejector button-->dispose of in SHARPS
- change tips frequently!
- Exercise (each student):
- pipette minimum and maximum from each Pipetman (1 µl and 20µl for P20; 20 µL and 200 µL for P200; 200 µL and 1000 µL for P1000) using Xylene Cyanol dye
- allowed students to see how consistent pipetmen were, get a feel for what a certain volume looks like in an Eppendorf tubes
III. Sterile technique, serial dilutions, plating bacteria
- Background Information/Demonstration (asked students to help explain):
- keep sterile things sterile by not touching them with nonsterile things (fingers, benchtop, etc.)-->work CLEANLY!
- flaming tubes after uncapping, after adding/removing liquid from tubes
- dilutions: a 1:10 dilution is 1 part concentrated solution + 9 parts dilution (10 parts total)
- serial dilutions:
- dilutions "in series"-->make 1:10 dilution, take 1 volume of 1:10 into 9 parts diluent to create 1:100 dilution, etc.
- More accuracy/less error than pipetting small volumes (e.g. 1 µL in 100 µL total)
- plating cells:
- label plates on media side with initials, date, strain name, dilution, etc.
- add liquid to be plated to center of plate (keep lid face down on bench top while adding, then cover)
- sterilize glass spreader by dipping in EtOH and passing through flame (don't bake spreader!)
- touch spreader to plate away from cells (to avoid killing them!)
- move spreader back and forth while spinning plate (about 45 seconds to "dryness"-->notice change in resistance as you spread)
- Exercise:
- Students made 1:10 and 1:100 serial dilutions of log phase bacteria and plated 50 µl of each (plus undiluted) on LB plates, then grew overnight at 37˚C
IV. Streaking bacteria for single colonies
- Background Information/Demonstration:
- the fabulous Beckwith lab 3 toothpick method for obtaining single colonies
- remember: it's a serial dilution on a plate!
- the fabulous Beckwith lab 3 toothpick method for obtaining single colonies
- Exercise:
- had students streak out 1 AmpR and 1 AmpS strain on an LB Amp plate, then grew plates overnight at 37˚C
V. Making media with antibiotic and inoculating liquid cultures
- Background Information/Demonstration:
- How to make LB Amp media from LB and Ampicillin stock solution (1000X working concentration)
- how to inoculate O/N culture
- use "stick" (dowel) and touch colony (gets ~106 cells on stick)
- open tube (sterile technique) and touch stick to liquid media
- flame tube and cap tube quickly
- don't use small pick (have to drop toothpick in media, part of stick that touched your fingers is not sterile and will contaminate culture!)
- Exercise:
- had each group of 2 students make 25 mL of LB Amp media
- each student inoculated 3, 3 mL cultures: one "media alone," one AmpR strain, one AmpS strain
- grew cells O/N @ 37˚C
VI. Polymerase Chain Reaction (PCR)
- Background Information:
- Basics of DNA, DNA synthesis and PCR cycle
- DNA
- DNA is double stranded in E. coli cells
- Two strands of DNA are held together by basepairing (A and T, G and C)
- DNA has a 5' and 3' end (numbers= those of carbons of the sugar of the nucleotide...here deoxyribose)
- DNA sequences written 5'->3' left to right
- DNA synthesis
- requires a primer (provides 3'OH for nucleotide addition)
- proceeds in the 5'-->3' direction
- PCR cycle:
- Denaturation: separation of template strands (95˚C)
- Annealing: primers bind via basepairing to template (50-65˚C, based on primer sequence and length)
- Extension: DNA strand is "extended" from primers using the rules of basepairing (e.g. if template says A, add T onto primer) (72˚C, optimal temperature for thermostable polymerase)
- DNA
- Components of a PCR reaction
- template (genomic DNA, plasmid)
- primers (short DNA molecules, give specificity to amplification, usually ~1000X excess of template)
- dNTPs
- DNA polymerase (thermostable, like Taq, so don't have to add enzyme after each denaturation cycle)
- pH buffer and salts
- Mg+2 (required for DNA polymerase function, concentration can be altered in PCR reaction)
- Basics of DNA, DNA synthesis and PCR cycle
- Exercise:
- students set up PCR with template and primers from Natalie's lab
- standard PCR master mix—ran cycle O/N.