Editing Tn5 Transposase (section)

== DNA binding tests  ==

*Use constant 200 ng of DNA (dilute from 1 ug/ul stock)<br> * Use serial dilutions of protein starting at 8 ug/ul<br> o 2x dilutions 0, 2, 1, 500, 250, 125, 62.5, 31.25, 15.6, 0 into 20ul TEGX + 200 ng/ul transposon DNA <br> * Incubate 30 minutes at 37<br> * Run on 0.8% E-Gel<br> * DNA mixture 10*200 ng = 2 ug DNA = 2 ul DNA into 200 ul TEGX

<br> Tests 

<br> o 2 ul 116 ng/ul ME0 PCR DNA<br> o 500 ng, 250, 125, 62.5, 31 ng Tpase in 20 ul final volume of storage buffer<br> o incubate 1 hour 37C<br> o overnight at 4C 

Gel images<br> 

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*Fig 1, 1.8 Kb transposon reacted at 2.5 ng/ul (total 1 ug) with Tn5 transposase at 10 ng/ul (total 4 ug) in 400 ul final volume, 1 hour at 37C<br> o this is about 1 pmol of DNA and 72 pmol transposase, or a 72x molar excess of transposase<br> o Concentrated to 20 ul and run on a 1.2% gel <br> * 3.7 Kb transposon reacted at 50 ng/ul (2 ug total) with Tn5 transposase at 10 ng/ul (400 ng total) in 40 ul volume, 1 hour at 37C<br> o this is 1 pmol DNA and 7.2 pmol transposase, for a 3x molar excess

DNA binding and cutting tests 

*0 to 3.8 pmol (nominal 2 ul of transposase, or 200 ng) of Tn5 transposase added to 0.26 pmol (nominal 1 ug of 5700 bp plasmid) plasmid in 20 ul volume<br> o done with a buffer of 100 mM potassium glutamate, 25 mM Tris-acetate pH 7.5, 10 mM Mg-acetate, 50 ug/ml BSA, 0.5 mM b-mercaptoethanol, 2 mM spermidine, 10 ug/ml tRNA<br> o incubated 1 hour at 20C, diluted 2-3x and incubated a further 4 hours at 37C (nominally to dilute CHAPS in transposase storage buffer)<br> o results: near linear increase of cut out fragments with transposase molar excess of 0-9x

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Standard Epicentre reaction 

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*1 ul DNA (100 ng/ul) in TE<br> * 2 ul transposase<br> * 1 ul glycerol<br> * This is:<br> o about 100 fmol or less transposon DNA<br> o at 100 ng/ul, this is 3.8 pmol transposase or 38x molar excess<br> o 25 ng/ul final, so expect 1e4 or so transformants

To Do 

*Prep new Tn5 protein (on hold, unnecessary)<br> * quantitate existing stock with BSA dilution and gel (done, spec readings approximately correct)<br> * Make storage buffer, dilute existing stock into storage buffer (done)<br> * run&nbsp; style test of transposome formation (to do; initial gel unconvincing)<br> * Run&nbsp; style test of transposon cutting (to do)<br> * Try transforming E. coli cells (done, this is what counts, compared to Epicentre enzyme is OK)

<br>pWH1891 Sequence information 

*T7 and Intein-R primers, ATG start at 45<br> * Truncates aa's 1-4 from canonical sequence<br> * Mutations<br> o E54K -- improve binding to OE<br> o M56A -- eliminate start for C-terminal inhibitory protein<br> o L372P -- hyperactive mutation

&gt;pWH1891<br>CCCTCTAGAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGATAACTTCTGCTCTTCATCGTGCGGCCGACTGGGCTAAATCTGTGTTCTCTTC<br>GGCGGCGCTGGGTGATCCTCGCCGTACTGCCCGCTTGGTTAACGTCGCCGCCCAATTGGCAAAATATTCTGGTAAATCAATAACCATCTCATCAGAGGGT <br>AGTAAAGCCGCCCAGGAAGGCGCTTACCGATTTATCCGCAATCCCAACGTTTCTGCCGAGGCGATCAGAAAGGCTGGCGCCATGCAAACAGTCAAGTTGG <br>CTCAGGAGTTTCCCGAACTGCTGGCCATTGAGGACACCACCTCTTTGAGTTATCGCCACCAGGTCGCCGAAGAGCTTGGCAAGCTGGGCTCTATTCAGGA <br>TAAATCCCGCGGATGGTGGGTTCACTCCGTTCTCTTGCTCGAGGCCACCACATTCCGCACCGTAGGATTACTGCATCAGGAGTGGTGGATGCGCCCGGAT <br>GACCCTGCCGATGCGGATGAAAAGGAGAGTGGCAAATGGCTGGCAGCGGCCGCAACTAGCCGGTTACGCATGGGCAGCATGATGAGCAACGTGATTGCGG <br>TCTGTGACCGCGAAGCCGATATTCATGCTTATCTGCAGGACAAACTGGCGCATAACGAGCGCTTCGTGGTGCGCTCCAAGCACCCACGCAAGGACGTAGA <br>GTCTGGGTTGTATCTGTACGACCATCTGAAGAACCAACCGGAGTTGGGTGGCTATCAGATCAGCATTCCGCAAAAGGGCGTGGTGGATAAACGCGGTAAA <br>CGTAAAAATCGACCAGCCCGCAAGGCGAGCTTGAGCCTGCGCAGTGGGCGCATCACGCTAAAACAGGGGAATATCACGCTCAACGCGGTGCTGGCCGAGG <br>AGATTAACCCGCCCAAGGGTGAGACCCCGTTGAAATGGTTGTTGCTGACCAGCGAACCGGTCGAGTCGCTAGCCCAAGCCTTGCGCGTCATCGACATTTA <br>TACCCATCGCTGGCGGATCGAGGAGTTCCATAAGGCATGGAAAACCGGAGCAGGAGCCGAGAGGCAACGCATGGAGGAGCCGGATAATCTGGAGCGGATG <br>GTCTCGATCCTCTCGTTTGTTGCGGTCAGGCTGTTACAGCTCAGAGAAAGCTTCACGCCGCCGCAAGCACTCAGGGCGCAAGGGCTGCTAAAGGAAGCGG <br>AACACGTAGAAAGCCAGTCCGCAGAAACGGTGCTGACCCCGGATGAATGTCAGCTACTGGGCTATCTGGACAAGGGAAAACGCAAGCGCAAAGAGAAAGC <br>AGGTAGCTTGCAGTGGGCTTACATGGCGATAGCTAGACTGGGCGGTTTTATGGACAGCAAGCGAACCGGAATTGCCAGCTGGGGCGCCCTCTGGGAAGGT <br>TGGGAAGCCCTGCAAAGTAAACTGGATGGCTTTCTTGCCGCCAAGGATCTGATGGCGCAGGGGATCAAGATCGGGTGCTTTGCCAAGGGTACCAATGTTT<br>TAATGGCGGATGGGTCTATGA 

<br> Testing the transposase 

*Transform 50 μl of E. coli Top10 electrocompetent cells with:<br> o Tn5 transposons (1 μl); plate out on Tet plates, count colonies<br> o pUC19 positive control 10 pg/μl; plate out on amp plates<br> o Electroporation at 2.5 KV in 2 mm gap cuvette<br> o pUC19 colonies visible in six hours under the microscope<br> o Tet resistant colonies are not visible at that time

<br>Notes 

*uses 100 mM hydroxylamine as a cleavage reagent instead of DTT

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[[Category:Protocols]]