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Team:Stanford/Notebook/Lab Work/Week 8
From 2010.igem.org
(→Karina's Notebook=) |
(→8/16 Monday) |
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== 8/16 Monday == | == 8/16 Monday == | ||
| + | ===Francisco's Notebook=== | ||
| + | GFP, RFP - terminator ligations | ||
| + | |||
| + | Promoter - RSID, sRNA ligations | ||
| + | *Redesigned oligos (contains entire sequence, has restriction enzyme sticky ends) | ||
===Karina's Notebook=== | ===Karina's Notebook=== | ||
Need to redesign oligos! It seems that there is a sequence of 16 bp of the "rev-comp scar + scar" that is forming homodimers and selfdimers. 16 bp is significant since our annealing region for the primers is ~20 bp, thus a lot of unwanted byproduct is forming in the PCR stitching reaction. Instead of stitching our parts, we will design our oligos so that they are each the full length of the strand and anneal the two strands together. We will also design our oligos so that they anneal with the XbaI and PstI overhangs, enabling us to skip the restriction digest step. | Need to redesign oligos! It seems that there is a sequence of 16 bp of the "rev-comp scar + scar" that is forming homodimers and selfdimers. 16 bp is significant since our annealing region for the primers is ~20 bp, thus a lot of unwanted byproduct is forming in the PCR stitching reaction. Instead of stitching our parts, we will design our oligos so that they are each the full length of the strand and anneal the two strands together. We will also design our oligos so that they anneal with the XbaI and PstI overhangs, enabling us to skip the restriction digest step. | ||
Revision as of 03:34, 25 October 2010
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|
8/16 Monday
Francisco's Notebook
GFP, RFP - terminator ligations
Promoter - RSID, sRNA ligations
- Redesigned oligos (contains entire sequence, has restriction enzyme sticky ends)
Karina's Notebook
Need to redesign oligos! It seems that there is a sequence of 16 bp of the "rev-comp scar + scar" that is forming homodimers and selfdimers. 16 bp is significant since our annealing region for the primers is ~20 bp, thus a lot of unwanted byproduct is forming in the PCR stitching reaction. Instead of stitching our parts, we will design our oligos so that they are each the full length of the strand and anneal the two strands together. We will also design our oligos so that they anneal with the XbaI and PstI overhangs, enabling us to skip the restriction digest step.
To redesign!
8/17 Tuesday
8/18 Wednesday
Karina's Notebook
Our order for the redesigned oligos came back because of a series of poly-G runs found in the sRNA 2 Reverse and sRNA 2C Reverse. More than 4 G's in a row forms what is called a "guanine tetracomplex" that is highly unstable knot. The poly-G runs are editable and we'll have to edit our designs and resubmit.
