---+ _Acinetobacter baylyi ADP1_ Golden Transformation ---++ Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double-stranded DNA fragments that template sequence replacements and/or deletions in the ADP1 genome. Addition of the flanking sequence homology needed for efficient transformation is based on Golden Gate Assembly and is much simpler and less time consuming to perform. Fundamentally, [[http://www.ncbi.nlm.nih.gov/pubmed/25871405][Golden Gate Assembly/cloning]] involves the use of plasmids which contain defined parts, called “part plasmids”, that when cut with BsaI enzymes and re-ligated (using the Golden Gate Reaction reagents and thermocycler protocol), allow the assembly of multiple parts in the desired order into a new plasmid. All of this is achieved in a single reaction tube, and then the unpurified reaction mix can be used to transform competent cells. Here we use Golden Gate assembly to simply add flanking homology to the pos/neg selection cassette (tdk/kan) we routinely use for ADP1 transformations. Thus, this reaction requires only three DNA parts: <br />A- pYTK001-tdkkan-camR plasmid <br />B- Purified PCR product of 5’-flank homology (~1kb) <br />C- Purified PCR product of 3’-flank homology (~1kb) * The 3 reaction components <br /> <img width="200" alt="Figure_GoldenGateTransformation.JPG" src="%ATTACHURLPATH%/Figure_GoldenGateTransformation.JPG" height="250" /> Note: pYTK001-tdkkan-camR plasmid (ColE1 origin) doesn't replicate on ADP1, thus can be used as an additional negative control during transformations. ---++ Primer design The [[http://openwetware.org/wiki/User:Gabriel_A._Suarez/Notebook/ADP1_Baylyi_reference][tdk/kan cassette]] in the pYTK001 plasmid has *BsaI* sites at both ends of its sequence such that when cut by a BsaI enzyme – which cuts outside its recognition sequence - will leave the standard 4bp Golden Gate *type2/type4* sticky ends. In this procedure, a *BsaI* site is added to each flanking homology which is designed to provide the complementary *type2* and *type4* sticky ends, thereby allowing the correct assembly of the three parts as follows: * Transformation cassette generated by the Golden Extension reaction <br /> <img width="478.4" alt="Image_Type2Type4.JPG" src="%ATTACHURLPATH%/Image_Type2Type4.JPG" height="56.8" /> Each of the target’s flanks needs to be amplified in independent PCR reactions, so only two sets of primers are required. *Primer Set 1*: 5’FW + GoldenRV5’ [5-ATGCGGTCTCACGTTCGTCTCAGACC (N)<sub>20</sub> -3’] <br />N = ~20bp Reverse complement terminal sequence of 5'flanking homology *Primer Set 2*: GoldenFW3’ [5-GCATGGTCTCAGCTGCGTCTCAGGTC (N)<sub>20</sub> -3’] + 3’Rv <br />N = ~20bp Fw terminal sequence of 3'flanking homology Each set contains one *“Golden Primer”* (GoldenFW3’ or GoldenRV5’) which contains ~20bp (denoted as a sequence of Ns) overlapping/targeting the flank to be amplified, plus BsaI and BsmBI sites. BsmBI sites will be used for construction of “rescue” cassette used to remove tdk/kan at the final stage of this protocol. See figure below for details. <br/> <img width="718.3'" alt="Figure_rescue.JPG" src="%ATTACHURLPATH%/Figure_rescue.JPG" height="226.05" /> The annealing temperatures for the “Golden Primer” are determined by the sequence of N’s chosen (the overlapping sequence). It is critical that the primers on each set have about the same annealing temperature (aim 60C for Phusion pol). The Barrick Lab routinely uses the NEB Tm Calculator (http://tmcalculator.neb.com/#!/) to determine primer annealing temperatures and IDT’s OligoAnalyzer Tool (https://www.idtdna.com/calc/analyzer) to check for hairpins or self-dimers, thus avoiding most common problems in primer design. %X% Additional BsaI or BsmBI sites on the 3'-flank or 5'-flank chosen should not be a problem (so far has never been observed to be an issue), since these would generate unique sticky ends which would re-ligate during the Golden Extension Reaction. If you want to be extra careful, you can select flanks with fewer or none of these present in them. <br /> %X% GoldenFW and GoldenRV primers should not overlap, even if the intention is to generate an insertion and not a deletion. Overlapping GoldenFw and GoldenRv primers leads to failed transformations. ---++ Golden Extension Reaction and Transformation for Tdk-kan cassette insertion/replacement 1. Use *set1* and *set2* primers to run PCR reactions to amplify both flanking regions of the target deletion/replacement site. <br />2. Run a gel electrophoresis to verify that the correct PCR product size was amplified. <br />3. Purify the PCR products using PCR purification columns and measure the DNA concentrations. <br />4. In a PCR tube, setup the BsaI Golden Extension Reaction with the following: - Reaction components - <br />2 μL of 10X T4 DNA ligase buffer (NEB: M0202S) <br />1 μL BsaI (NEB: R3535S) <br />1 μL of T7 DNA ligase (NEB: M0318S)** <br />250ng pYTK001-tdkkan-CamR plasmid <br />150 ng 5’flank homology (for ~1000bp)* <br />150 ng 3’flank homology (for ~1000bp)* <br />dH2O to 20µL rxn total volume *Depending on the length of each flank homology, fragment (flanks) to plasmid ratio can be adjusted to achieve the optimal 1:1:1 for each part, considering that the tdk/kan cassette is only 1.7kb and about half the size of the pYTK001-tdkkan-CamR plasmid (3.3kb). Click [[http://cels.uri.edu/gsc/cndna.html][here for a simple DNA molecule copy-number calculator]]. Also, the [[http://www.promega.com/a/apps/biomath/index.html?calc=ugpmols][Promega ug to pmol calculator]], the [[http://www.endmemo.com/bio/dnacopynum.php][DNA copy number calculator]] and the [[http://www.molbiol.edu.ru/eng/scripts/01_07.html][DNA mole conversion calculator]] are useful for balancing out quantities. For more Golden Gate rxn details, see the [[Trash.ProtocolsGoldenGateAssembly][Golden Gate Assembly Protocol]] <br />**T4 ligase (NEB: M0202) may be used instead, but T7 ligase is preferred because it rarely generates any blunt ligation products and thus yields minimal off-target ligation. T7 ligase buffer is avoided because it contains PEG which is known to inhibit electroporation, although its effects on natural competence are unknown. 5. Run thermocycler with the following setting: <br />1) 37°C, 5:00 <br />2) 16°C, 5:00 <br />3) Goto 1, 30X <br />4) 55°C, 5:00 <br />5) 80°C, 5:00 <br />6) 12°C, ∞ *Transformation steps:* <br />6. Prepare two tubes with 500 µL LB media + 35 µL overnight culture. Label one “NoDNA control” and the other “DNA+”. <br />7. Add all 20 µL of the Golden Gate rxn to the tube labeled “DNA+”. <br />8. Incubate overnight (or at least 6hrs) at 30C, 200 rpm. <br />9. Plate 100 µL of the transformation mix into an LB-Kan plate and incubate overnight. Plate also 100µL of the “NoDNA” negative control on another LB-Kan plate ([[https://advanced.bact.wisc.edu/instr/book/displayarticle/103][Click here for cell count and dilution basics]]). <br />10. Select 2-3 colonies to grow in liquid LB-Kan and proceed to confirm deletion/replacement in each by PCR. Note: This procedure is yet to be tested using different size flanking homologies and varying amounts of DNA, two critical factors that affect transformation efficiencies. Under the specified conditions, the transformation efficiency observed is roughly 1.25 x 10<sup>–5</sup>, thus plating 100 µL will yield ~1000 colonies (ADP1-ISx strain) and why it's recomended to also plate 100x dilutions to make it easier to later pick out single colonies. It may be possible to obtain a good amount of transformants using lower DNA concentrations, which would be useful if you have lower quantities of any of the parts previous to the assembly or if you need to do multiple transformations with the 20 µL Golden Gate rxn product (e.g., use only 10 µL per transformation mix). ---++ Tdk/kan cassette “rescue” (Removal of tdk/kan marker with minimal 4bp scar) 1. Ligate 3’-flank to 5’-flank (using same PCR products step#3 above) by BsmBI Golden Gate assembly. <br /> <br />- Reaction components - <br />2 μL of 10X T4 DNA ligase buffer (NEB: M0202S) <br />1 μL BsmBI (NEB: R0580S) <br />1 μL of T7 DNA ligase (NEB: M0318S) <br />100 ng 5’flank homology <br />100 ng 3’flank homology <br />dH2O to 20µL rxn total volume Tips and general Golden Gate Assembly protocol: http://barricklab.org/twiki/bin/view/Trash/ProtocolsGoldenGateAssembly) 2. Run thermocycler with the following setting (or as described before with shorter one-minute incubation times). <br />1) 37°C, 5:00 <br />2) 16°C, 5:00 <br />3) Goto 1, 30X <br />4) 55°C, 5:00 <br />5) 80°C, 5:00 <br />6) 12°C, ∞ 3. Repeat transformation steps above, but this time plate on LB-AZT (include a 100X dilution to make sure you can pick out single colony isolates)*. Once colonies are visible, select 3-5 to grow in liquid LB and confirm tdk/kan removal by PCR using the 5'-flank FW primer with the 3'-flank RV primer (e.g., a positive result will produce an approximately 2kb band). Successful confirmation (strongly recommended) can be additionally supported by confirming their lack of growth on LB-kan (negative control), see [[ProtocolsAntibioticRemovalVerification][Quick 3hr Antibiotic Rescue Verification]]. *You may want to determine your rate of "rescue", equal to the transformation rate minus the mutation rate. For this, you will plate 100uL of 100x dilution of your 500uL overnight culture, grown without DNA, on LB and on LB-AZT. If successful, you will see many colonies on LB (transformation+mutation), and few or no colonies on LB-AZT (mutation). If you do not obtain these results, you will want to run through the following troubleshooting steps:<br />1. Verify that you are plating an adequate dilution of your overnight culture _e.g._ 100x. If you have a high concentration of cells _e.g._ >10^10 and if your mutation rate is high, plating 100uL of overnight culture directly onto LB-AZT can result in a lawn.<br />2. Check that you are using the correct AZT working concentration (200ug/mL). That is, 400uL of AZT (stock = 10mg/mL) in 20mL of agar.<br />3. Regrow your overnight culture in LB-Kan to ensure the removal of possible contaminants.<br />4. Check the date of your AZT and remake your liquid stock if necessary. For 30mL of 10mg/mL AZT, add 0.3g of powder AZT to 30mL DIW. Filter sterilize solution by pushing it through a 50 mL syringe fitted with a 0.22 µm filter. Label and store at -20°C. ---++ Tdk/kan cassette “rescue” with allele replacement (removal of tdk/kan to introduce mutations) If the aim is to introduce point mutations or you want to introduce genes, promoters or other genetic elements into ADP1's chromosome, first perform the tdk-kan replacement step and then generate the desired genetic sequence with >500bp flanking homologies (ordered as a gBlock, assembled via extension PCR or PCRed from a mutant variant) and use it to perform the "rescue" step ( step#3) described above.
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Topic revision: r30 - 2020-02-20 - IsaacGifford