• For "intramolecular" ligation of a PCR product the 5'-ends are phosphorylated with T4 Polynucleotidekinase (PNK)
• Set up the following reaction:

reagent	volume (in µL)
10x T4 DNA ligase buffer	2.5
T4 PNK	1
PEG 4000 50%	2.5
DNA (100 to 600 ng)	x
water	to 25

• Incubate at 37 °C, 30 min
• Heat inactivate at 65 °C, 20 min
• Add 1 µL T4 DNA ligase after reaction has cooled down to room temperature
• Incubate at room temperature for at least 2 h, overnight also works.
• Next step: Transformation via heat shock

• One Reaction mix contains
• 5µL 5x GoTaq buffer (Promega)
• 1 µL MgCl₂ (25 mM stock)
• 0.5 µL 10 mM dNTPs
• 0.25 µL primer mix (prefix/suffix primers or sequencing primers) 100 mM
• 17.625 µL ddH₂O
• 0.125 µL GoTaq polymerase (Promega)
• 0.5 µL template
• PCR program
• Cell lysis and denaturation: 5 min, 95 °C
• 30 cycles
• Denaturation: 10 s, 95 °C
• Hybridisation: 30 s, annealing temperature
• Elongation: 60 s/kb of product, 72 °C
• Final elongation: 5 min, 72 °C
• Template alternatives
• Pick a colony with sterile tip, elute in 100 µL ddH₂O or buffer, store at 4 °C during PCR, plate if insert is of correct size
• Pick colondy, streak at marked position on a new plate and solute remaining cells on the tip in the PCR tube with reaction mixture, cultivate if insert is of correct size
• Gel electrophoresis for control of fragment size

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• Thaw 50 µl electrocompetent E. coli cells on ice, dilute with icecold 50 µl glycerine (10%) if necessary
• Add 0.5-5 µl plasmid to 50 µl electrocompetent cells
• Store cells on ice for 1 minute
• Electroporate at U = 2.5 kV, C = 25 µF, R = 400 Ω
• Transfer transformation reaction to 450 µl SOC-Medium and incubate 1 h at 37 °C
• Plate on selective LB-Medium
• Incubate over night at 37 °C

• Thaw 100 µl chemo competent E. coli cells on ice
• Add 0.5-5 µl plasmid to 100 µl chemocompetent cells
• Store cells on ice for 10-30 min on ice
• Heat shock for 90 seconds at 42 °C
• Store reaction on ice for 60 seconds
• Optional: Preheat SOC medium to 37 °C
• Transfer reaction to 1 ml SOC medium and incubate at 37 °C for at least 1 hour
• Centrifuge 3 minutes at 12000 rpm and plate on selective LB medium
• Incubate at 37 °C over night

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• According to protocol from Caschera and Noireaux 2015b. Weigh all aminoacids seperatly into microcentrifuge tubes. Add 500 µl of 5 M KOH to each amino acid. Solubilization is achieved via multiple inverting and, if necessary, vortexing. Especially tyrosine takes a while, and is a suspension rather than a solution. Stock solutions are afterwards stored at -20 °C. Note: Caschera and Noireaux say these stock solutions can only be stored a few weeks, however, we did not see a loss in performance after more than 3 months (16 weeks).

	Molecular weight	mass to weigh (in mg) to obtain desired stock-solution	concentration in stock solution in mM
Alanine	89.09	182	4089
Arginine	174.20	202	2314
Asparagine-Monohydrate	150.14	282	3759
Aspartic acid	133.10	250	3752
Cysteine	121.16	149	2465
Glutamic acid	147.13	269	3655
Glutamine	146.15	183	2501
Glycine	75.07	158	4210
Histidine	155.15	255	3281
Isoleucine	131.18	247	3765
Leucine	131.18	167	2549
Lysine	146.19	175	2392
Methionine	149.21	186	2491
Phenylalanine	165.19	142	1716
Proline	115.13	224	3883
Serine	105.90	209	3953
Threonine	119.12	229	3853
Tryptophan	204.23	170	1661
Tyrosine	181.19	217	2396
Valine	117.15	152	2595

• Combine stock solutions to an amino acid mixture like depicted below. Add water to 4 mL and 110 µL of glacial acetic acid to adjust pH to about 6.5. Aliquot (do not forget to mix properly!) and flash-freeze in liquid nitrogen, store at -80 °C.

	Volume (in µL) for mixture	Concentration in mixture (without water and glacial acetic acid added)	concentration in final mixture
Alanine	13.6	146	13.56
Arginine	22.2	135	12.53
Asparagine-Monohydrate	13.6	134	12.44
Aspartic acid	13.6	134	12.44
Cysteine	22.2	143	13.28
Glutamic acid	13.6	130	12.07
Glutamine	22.2	145	13.46
Glycine	13.6	150	13.93
Histidine	13.6	117	10.86
Isoleucine	13.6	134	12.44
Leucine	22.2	148	13.74
Lysine	22.2	139	12.91
Methionine	22.2	145	13.46
Phenylalanine	34	153	14.21
Proline	13.6	138	12.81
Serine	13.6	141	13.09
Threonine	13.6	137	12.72
Tryptophan	34	148	13.74
Tyrosine	22.2	139	12.91
Valine	22.2	151	14.02
sum	381.6	2807	260.62

• Stock solutions needed:
• 2 M HEPES
• 174 mM NAD
• 33.9 mM folinic acid
• 65 mM coenzyme A (CoA)
• 50 mg/mL E. coli tRNA (Roche)
• 200 mM putrescine
• 1.5 M spermidine
• Combine stock solutions to a create cofactor premix that is 20x final reaction concentration, depicted in the following list
• 1 M HEPES
• 6.6 mM NAD
• 1.4 mM folinic acid
• 5.4 mM coenzyme A (CoA)
• 4 mg/mL E. coli tRNA (Roche)
• 20 mM putrescine
• 30 mM spermidine

• The following harvest protocol mainly orientates to the procedures in Sun et al. 2013 and Kwon and Jewett 2015.
• Gather all materials needed: Harvest tubes and falcon tubes, washing buffer, DTT aliquot, liquid nitrogen, and a lot of ice. Start the harvest when E. coli culture reaches mid- to late exponential growth phase. For the E. coli we used in our experiments and cultivations, the mid- to late exponential growth phase was reached at an OD₆₀₀ of 3-4 (see growth curves in notebook section).
• harvest protocol - keep everything on ice between the steps!
1. Transfer culture into prechilled and weighted harvest tubes or falcons
2. Centrifugate: 5000x g, 4 °C, 15 min. While centrifugating, add DTT to S30 buffer to a final concentration of 2 mM
3. Discard supernatant and weigh pellets
4. Add about 10 mL of S30 washing buffer and resuspend cells by vortexing and vigourous shaking. For us, cycles of 15 s vortexing/shaking and 30 s resting on ice worked well.
5. Centrifugate: 5000x g, 4 °C, 12 min
6. Discard supernatant
7. Repeat steps 4 to 6 two times
8. Centrifuge a last time at 5000x g, 4 °C, for 5 min and remove residual washing buffer by pipetting.
9. Flash freeze pellets in liquid nitrogen and store at -80 °C, unless you want to proceed with sonification directly.

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• After every step the reaction tube is centrifuged with 1000 g for 1 minute.
• The supernatant after centrifugation and every wash step (starting from the step when the protein is added to the agarose) is stored for analyzing the samples for protein and DNA amounts.
• As negative controls no protein to the agarose were added.
• Steps:
• 25 µL Ni-NTA agarose is put in a reaction tube. Then the sample is centrifuged.
• The agarose is washed three times with Kpi buffer (Volume: 50 µL).
• 250 pmol protein in 20 µL Kpi buffer is added and incubated for 30 min. Then the sample is centrifuged.
• The agarose is incubated three times in Kpi Buffer (Volume: 50 µL).Then the sample is centrifuged.
• 0.75 pmol plasmid (lacO) is mixed with 20 µL binding buffer (Incubation time: 15 min).
• Unbound DNA is washed away three times with binding buffer (Volume: 50 µL, Incubation time: 15 min). Then the sample is centrifuged.
• 3x elution with analytes in binding buffer (Volume: 50 µL, Incubation time: 15 min)
• Imidazol solution (50 µl) is used to release proteins from the agarose.
• Water (volume: 10 µL) is mixed with agarose.
• The DNA amount of the supernatant after centrifugation is analyzed via gel electrophoresis.

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• Dissolve 10 mg p-Phenylenediisothiocyanate either in 30 ml pure ethanol or in 500 µL dried DMSO and add up to 30 ml with water. (the drying is essential, perform it with 4 Angström molecular sieves at least 24 h)
• Whatman filter paper is activated for 1-2 days by orbital shaking in the PDITC solution.
• Wash paper twice with DMSO or water respectively. Dry it for approximately 5 min
• Generate an aminolabeled DNA fragement
• The optimal concentration required for the immobilization is 20 µM. You can achieve this through hybridization of 2 Primers in 50 mM sodium phosphate buffer, pH 8.5. Boil the primers at 98 °C for a few minutes and afterwrds slowly decrease the temperature.
• Alternatively, you can perform an conventional PCR with one of the primers aminolabeled. We recommend labeling of the other oligo with a fluorescent dye. This enables detection of the immobbilized DNA on Scanners like the Typhoon or Ettan Dige.
• Pipett 1-0.1 µL onto the paper and incubate it over night in an humidification chamber (avoid direct contact of the liquid with the paper)
• Block the paper with 50 °C warm blocking solution (0.1 M Tris, 50 mM ethanolamine, pH 9.0)
• wash the paper three times for 2 min with water and dry it by an airstream. (If you wish to immobilze ssDNA, add an washing step with 50°C 4xSSC buffer, 30 min.)

• You can detect immobilized DNA und your fusion protein by measuring the fluorescence.
• You need Cy3- and amino-labeled DNA with an operator site for immobilization, a repressor fused to a fluorescence protein and cellulose on a black 96-well plate.
• Excitation for Cy3: 545 nm, Emission for Cy3: 590 nm
• For example: Excitation wavelength for sfGFP: 480 nm, Emission wavelength for sfGFP: 515 nm
• The gain needs to be adapted.
• After every step the supernatant is transferred into another 96-well plate for measurement.
• The plate with the cellulose is dried after having taken out the supernatant and measured again.

• Cellulose on the plate is prepared in a black 96-well plate.
• DNA is immobilized on cellulose.
• Protein in Kpi buffer (Concentration: 20 µg/mL, Volume: 25 µL) is added to the wells with immobilized DNA (Incubation time: 15 min).
• The wells are washed with binding buffer (Volume: 200 µL, incubation time: 10 min).
• 100 µl analyte solution (e.g. 0.5 mM IPTG in binding buffer) is put in the well and shaken for 30 min.