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Team:EPF-Lausanne/Our Project/TetR mutants/MITOMI data
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Revision as of 22:34, 21 September 2011
MITOMI data
In vitro Main | Why TetR? | Mutant TetRs | MITOMI Data | In-vivo & In-vitro outlineAbout MITOMI technique.
The raw data from the successful experiments can be found here.
Contents |
wtTetR
muTetRs
V36F
In vitro characterization
Using the MITOMI technique we determined the DNA binding landscape of the TetR V36F mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM).
WebLogo we obtained for the V36F mutant:
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005 Jul 1;33:W389-92.
Position Weight Matrix
| PO | A | T | C | G |
| 1 | 0.164072 | 0.519334 | 0 | 0.22966 |
| 2 | 0.642569 | 0.164072 | 0.188965 | 0.943314 |
| 3 | 1.04481 | 0.558693 | 0.164072 | 0.848264 |
| 4 | 0.959646 | 0.164072 | 2.17536 | 0.718959 |
| 5 | 0.164072 | 1.19894 | 1.79469 | 1.56685 |
| 6 | 1.46463 | 0.164072 | 1.74384 | 1.54845 |
| 7 | 0.966397 | 1.07557 | 0.164072 | 1.72883 |
| 8 | 0.164072 | 0.504312 | 0.755195 | 0.148902 |
| 9 | 0.0876645 | 0.164072 | 0 | 0.0156484 |
| 10 | 0.289722 | 0.164072 | 0.00707563 | 0.843474 |
| 11 | 1.77568 | 1.3447 | 2.34804 | 0.164072 |
| 12 | 0.164072 | 1.72354 | 1.62782 | 1.49176 |
| 13 | 0.877518 | 0.164072 | 1.30879 | 1.9052 |
| 14 | 0.164072 | 0.544642 | 0.3387 | 1.7537 |
| 15 | 0.540091 | 0.8821 | 1.0861 | 0.164072 |
| 16 | 0 | 0.280358 | 0.442769 | 0.164072 |
| 17 | 0.31238 | 0 | 0.164072 | 0 |
Each row represents the changes in binding energy, ΔΔG (kcal/mol), compared to the reference sequence upon the substitution to the indicated nucleotide at certain position within the target DNA element. Values are indicated in kcal/mol.
We compared the measured DNA binding affinities of the V36F mutant to the affinities obtained for the wt-TetR and found that V36F mutant interacts with the tetO as strong as the wild-type variant.
V36FW43S
V36FW43ST141A
P39K
Y42F
Y42F K108E
P39QY42M
P39Q Y42M L197S
P39Q Y42M L52P
E37A P39K
EA37PQ39YF42
