User:Vlau: Difference between revisions
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==Contact Info.== | |||
vlau@fas.harvard.edu/vhtlau@gmail.com | |||
==Week 1== | ==Week 1== | ||
==='''06.12.06: Mon.'''=== | ==='''06.12.06: Mon.'''=== | ||
====Folding DNA | ====''Folding DNA Nanostructure''s==== | ||
1. Working Stocks | 1. Working Stocks | ||
44 nM scaffold (20 microL) | 44 nM scaffold (20 microL) | ||
Line 22: | Line 26: | ||
37 dC, 30' | 37 dC, 30' | ||
- neg. controls: 1 replacing oligos w/ water, 1 replacing scaffold w/ water | - neg. controls: 1 replacing oligos w/ water, 1 replacing scaffold w/ water | ||
====Transformation==== | ====''Transformation''==== | ||
1. Plasmids | 1. Plasmids | ||
R0010: lac operon promoter | R0010: lac operon promoter | ||
Line 39: | Line 43: | ||
==='''06.13.06: Tues.'''=== | ==='''06.13.06: Tues.'''=== | ||
====Gel Electrophoresis w/ 2% Gel==== | ====''Gel Electrophoresis w/ 2% Gel''==== | ||
1. Protocol | 1. Protocol | ||
- mixed 2 g Ultrapure agarose w/ 100 mL 1X TBE in plastic flask | - mixed 2 g Ultrapure agarose w/ 100 mL 1X TBE in plastic flask | ||
Line 59: | Line 63: | ||
3. Image | 3. Image | ||
[[Image:Pic 1.jpg]] | [[Image:Pic 1.jpg]] | ||
====Transformation P. 2==== | ====''Transformation P. 2''==== | ||
1. Protocol | 1. Protocol | ||
- prepared 2 liquid cultures for each transformation | - prepared 2 liquid cultures for each transformation | ||
Line 66: | Line 70: | ||
==='''06.14.06: Wed.'''=== | ==='''06.14.06: Wed.'''=== | ||
====Miniprep==== | ====''Miniprep''==== | ||
1. Plasmids (2 samples each) | 1. Plasmids (2 samples each) | ||
R0010: lac operon promoter | R0010: lac operon promoter | ||
Line 90: | Line 94: | ||
- centrifuged for 1 min | - centrifuged for 1 min | ||
- nanodropped | - nanodropped | ||
====Digestion==== | ====''Digestion''==== | ||
1. Materials | 1. Materials | ||
8 microL DNA (R0010, E0241) | 8 microL DNA (R0010, E0241) | ||
Line 104: | Line 108: | ||
- added 0.1 microL (1 unit) of 10,000 units/mL CIP to vector DNA (R0010) | - added 0.1 microL (1 unit) of 10,000 units/mL CIP to vector DNA (R0010) | ||
- incubated vector DNA @ 37 dC for 1 hr | - incubated vector DNA @ 37 dC for 1 hr | ||
====Gel Electrophoresis and Purification==== | ====''Gel Electrophoresis and Purification''==== | ||
1. 1.0% Agarose Gel | 1. 1.0% Agarose Gel | ||
L. 1: 1 kb Ladder | L. 1: 1 kb Ladder | ||
Line 115: | Line 119: | ||
==='''06.15.06: Thurs.'''=== | ==='''06.15.06: Thurs.'''=== | ||
====Ligation==== | ====''Ligation''==== | ||
====Transformation==== | ====''Transformation''==== |
Revision as of 22:03, 15 June 2006
Contact Info.
vlau@fas.harvard.edu/vhtlau@gmail.com
Week 1
06.12.06: Mon.
Folding DNA Nanostructures
1. Working Stocks
44 nM scaffold (20 microL) 0.99 microM of each oligo
2. Protocol
- goal: 10 nM scaffold w/ 100 nM each oligo, total rxn vol of 20 microL - calculations: scaffold = (10 nM)/(44 nM) * 20 microL = 4.5 microL oligos = (100 nM)/(990 nM) * 20 microL = 2 microL - reaction mixture: 4.5 microL p7308 scaffold 2 microL oligos 2 microL 10x folding buffer (500 mM HEPES ph 7.5, 500 mM NaCl, 100 mM MgCl2) 11.5 microL dH2O - annealing times: 90 dC, 5' 65 dC, 20' 55 dC, 20' 45 dC, 20' 37 dC, 30' - neg. controls: 1 replacing oligos w/ water, 1 replacing scaffold w/ water
Transformation
1. Plasmids
R0010: lac operon promoter E7104: T7 promoter + GFP E0241: GFP
2. Protocol
- let chemically competent OneShot Top10 cells thaw on ice - added appropriate DNA to cells and tapped gently to mix - let sit on ice for 20 min - heat shocked @ 42 dC for 30" - let cool on ice for 2 min - added 200 microL SOC media - shook @ 37 dC for 1 hr - pipetted and spread onto agar plates treated w/ ? - incubated @ 37 dC overnight agar side-up
06.13.06: Tues.
Gel Electrophoresis w/ 2% Gel
1. Protocol
- mixed 2 g Ultrapure agarose w/ 100 mL 1X TBE in plastic flask - heated for 1.5 min in microwave w/ top loosely screwed on - added 3 microL EtBr - poured into gel frame and let set for 20 min - placed into running box and submerged w/ TBE - wells loaded - ran gel @ 130 V, 45 min
2. Samples
L. 1: 1 kB ladder L. 2 and 3: DNA nanostructure L. 4 and 5: neg control w/ no oligonucleotides L. 6 and 7: neg control w/ no scaffold L. 8: 1 kB ladder loading dye: BTB dye 50% glycerol + 10X TBE ladder: 10 microL + 1 microL dye samples: 10 microL + 1 microL dye
3. Image
Transformation P. 2
1. Protocol
- prepared 2 liquid cultures for each transformation - added 50 microL of 5 mg/mL amp to 5 mL LB per culture - shook @ 180 rpm, 37 dC overnight
06.14.06: Wed.
Miniprep
1. Plasmids (2 samples each)
R0010: lac operon promoter E7104: T7 promoter + GFP E0241: GFP
2. Protocol
- w/ 5 mL samples, 1 mL saved for glycerol stock - rest of samples transferred to 1.5 eppendorfs and centrifuged to form pellet - supernatant removed and pellet resuspended in 250 microL Buffer P1 - 250 microL Buffer P2 added and tube inverted 4-6 times for mixing (no vortexing to prevent shearing of genomic DNA; let sit for no longer than 5 min) - 350 microL Buffer N3 added and tube inverted 4-6 times for mixing - centrifuged @ 13,000 rpm for 10 min (formation of white pellet) - supernatant transferred to QIAprep spin column and centrifuged for 1 min - 0.5 mL Buffer PB added and centrifuged for 1 min (optional) - added 0.75 mL Buffer PE for washing and centrifuged for 1 min - flowthrough discarded and centrifuged for 1 min to remove residual buffer - QIAprep column transferred to 1.5 eppendorfs - 50 microL water added to center of column (let column stand for 1 min) - centrifuged for 1 min - nanodropped
Digestion
1. Materials
8 microL DNA (R0010, E0241) 2.5 microL 10x BSA 2.5 microL 10x Buffer (Buffer 2) 11 microL dH2O 0.5 microL enzyme 1 and 2 (SpeI and PstI, XbaI and PstI) total vol = 25 microL
2. Protocol
- checked www.neb.com to determine correct Buffer - digested @ 37 dC for 1 hr - heat shocked @ 97 dc for 15 min to inactivate restriction enzymes - added 0.1 microL (1 unit) of 10,000 units/mL CIP to vector DNA (R0010) - incubated vector DNA @ 37 dC for 1 hr
Gel Electrophoresis and Purification
1. 1.0% Agarose Gel
L. 1: 1 kb Ladder L. 2: R0010 Sample 1 L. 3: R0010 Sample 2 L. 4: E0241 Sample 1 L. 5: E0241 Sample 2
2. Image