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Digestion of Miniprpes with SpeI only for further cloninf, because double digestion with BamHI is not recommed.
PCR of Minipreps of "positive" clones: To check if we have positive clones we make PCR of the Minipreps we made. Inoculation of ONC with Reference_promoter cells (BBa_I20260), Colicin E1 cells, Colicin E9 cells and MG1655 in 10 ml TB media.
Additionally we tried to establish an enzyme assay for our own construct of the glpX (SBPase).
We tried to bring the prkA with RBS behind our construct ptac_Hneap but it was not successful. We tried to prove that the carboxysome we built can form the micro compartiment for the CO2 fixation. I designed and created enzymes consisting of the catalytic domain of Hin-H107Y, a hyperactive mutant DNA invertase, fused via a flexible linker sequence to engineered zinc finger DNA-binding domains. In response to foreign antigens, the body’s immune system concentrates specific white blood cells at the site of infection. There are four subfamilies of chemokines and their respective receptors, distinguished by patterns of cysteine residues (abbreviated “C”) in the former. Chemokine receptor 5, encoded by gene CCR5, plays a central role in cellular infection by the human immunodeficiency virus (HIV). CCR5 is a required co-receptor for HIV-1 infection of macrophages in the first (M-tropic) phase. In studies of disease progression following exposure to HIV-1, a genetic mutation in CCR5 has been linked to resistance to HIV-1 infection (de Silva and Stumpf 2004). Although rare in Africans and Asians, up to 20% of Caucasians are heterozygous ?32 allele carriers.
Although extremely rare, there are 12 documented cases of individuals homozygous for the CCR5-?32 allele who have been successfully infected with HIV-1 (D. Given the promising phenotype of the CCR5-?32 mutation, many researchers have striven to mimic its effects. Using the natural ?32 deletion mutation as a model, I aim to emulate the CCR5-?32 mutation at the DNA level in the genomes of individuals lacking the allele.
Site-specific recombinase enzymes are ideal for genome modification applications due to their ability to recognize precise DNA sequences and remove, replace, or invert the flanked sequence (Gordley et al.
The serine family of recombinase enzymes (named for their active-site serine residues), catalyze excision or inversion depending on the orientation of a two-base pair overhang at the center of the recombination sites. Recombinase-mediated excision or inversion in the serine recombinase family occurs via an enzyme tetramer. The serine recombinase family is attractive for protein engineering applications due to the enzymes’ structural modularity. Because sequence recognition and catalysis functions of a recombinase can be specified by unrelated protein domains, it is possible to replace the enzyme’s native helix-turn-helix DNA-binding motif with a zinc finger DNA-binding motif (Akopian et al.
A zinc finger is a protein domain that binds to DNA via sequence-specific base contacts by an ?-helix in the major groove (Segal et al.
Of all zinc finger classes in the human genome, Cis2His2 zinc fingers, named for pairs of cysteine and histidine residues which interact with the zinc ion, are the most prevalent (Matthews and Sunde 2002). Several researchers have categorized the zinc finger protein sequences needed to recognize specific triplets of DNA base pairs. As mentioned previously, replacement of the helix-turn-helix DNA-binding motif of a serine recombinase with a zinc finger DNA-binding motif changes the specificity of the resulting chimeric enzyme to a site recognized by the zinc finger (Akopian et al. After identifying candidate CCR5 recombination sites and recombinase target sequences (see Supplementary Text), I evaluated each of the candidate recombination sites and chose the two sites yielding the four enzyme target sequences with the most promising designed-zinc finger binding affinities and least competition (ability of other zinc fingers to bind to the sequences) (Segal et al. Hin DNA invertase is a serine recombinase with a similar size and organization as ??-resolvase and Tn3-resolvase (Figures 3 and S3) (Grindley et al. Oligonucleotides (Integrated DNA Technologies, Coralville, IA) encoding the designed zinc fingers were assembled and ligated to generate DNA sequences encoding the respective zinc finger domains. Enzymes were assayed individually using substrate DNA plasmids with target recombination sites containing a total of four identical zinc finger DNA binding sequences.
As enzymes capable of acting upon the plasmid encoding them, recombinases are suitable for substrate-linked protein evolution. I first crafted DNA plasmids containing a gene for a chimeric recombinase X (A, B, C, or D) as well as two recombination sites for recognition by chimeric recombinase Y (a different recombinase).
The selection plasmid for a given recombinase enzyme contained several restriction endonuclease sites flanked by recombinase recognition sites. With these plasmids, I used HindIII and EcoRI restriction enzymes (New England Biolabs, NEB, Ipswich MA) to cleave the zinc finger regions and therefore separate the DNA-binding domain of recombinase X from the backbone containing sites Y. To facilitate backbone gel-purification, I created four new plasmids expressing the comparatively large chloramphenicol resistance gene in place of the short zinc finger region. Restriction digests cleave the zinc finger region, or chloramphenicol resistance gene, from the backbone vector (containing the recombination sites and the Hin-H107Y recombinase catalytic domain). After creating chimeric recombinase enzymes engineered to bind to CCR5, I assayed the enzymes individually in E. As confirmed via sequencing, recombinase-mediated inversion occurred with engineered chimeric enzymes A and B. The activity assays described above support the conclusion that I successfully conferred CCR5 binding specificity to the four chimeric recombinase enzymes. Following purification of insert X zinc finger regions and backbone vector containing X recombination sites, DNA was ligated and transformed into cells. The library of engineered zinc finger-recombinase enzyme mutants appeared to be of substantial size for all four enzyme libraries as determined by sample dilutions (Fig S7). Libraries of engineered zinc finger-recombinase enzyme mutants were generated in order to isolate mutant enzymes with improved activity and specificity via iterative rounds of selection.
Restoring self-preservation in the lodgepole pine trees: Inhibiting blue stain fungal proliferation using class I chitinase activity in transformed E.
To determine whether our transformation was successful, antibiotics were added to our agar plates. Having visualized that plasmid isolation was successful, we used the remaining product of our miniprep to perform a restriction digest of our experimental plasmids.
Modifications of the transformation protocol included suspending cells in CaCl2 on ice for 15 min prior to removing the second supernatant, increasing the spin RPMs in order to collect a greater volume of pellet while making cells competent, increasing the heat shock 45 s, floating on ice for 5 min, increasing the volume of solution taken for growth on plates, addition of more luria broth media before growing colonies on plates and including control plates along with the experimental plates.
Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 80-500nM. Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 60-250nM. Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 60-100nM. Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 40-100nM (10h30-17h30). Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 20-60nM (15h00-22h00). Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 60-20nM (14h00-21h00).
Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 5-40nM (18h30-1h30). Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 40-100nM (15h00-22h00). Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 60-20nM (15h00-22h00).
Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 40-100nM (19h30-2h30).
Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 10-40nM (10h-17h). Measure of the cells' growth and fluorecence on TECAN infiniteM200 with rank of GFP 40-80nM (20h40-3h40). PCR purification of sample 1 and 4 of the Gel 1 were purified with the NucleoSpin kit (Macherey Nagel). Miniprep cultures from the 2cnd of september was purified with the NucleoSpin Plasmid kit (Macherey-Nagel).
Glycerol stock were prepared started from the 16 cultures from the 2cnd of september (750 µl of culture + 750 µL of 10% glycerol) and stored at -80°C. PCR product of first colony of each transformation was loaded on 1% agarose gel and gel run 45 minutes at 110 mV.
3 ml LB culture were started from tested colonies which presented the right PCR product profile. Promoters were resuspended from 2014 distribution kit plates with 10 µl of sterile MiliQ watter and stored at -20°C. A PCR was performed with 8 colonies for BBa_K823012 and for BBa_J23101 following the protocol Table 3 and 4. Transformations of registry parts (BBa_K823012 and J23101) were performed to obtain colonies with plasmid containing parts for future amplifications. Miniprep cultures from the 19th August was purified with the NucleoSpin Plasmid kit (Macherey-Nagel). Therefore we measured the GFP fluorescence signal with the GloMax® Discover Multimode-Reader of Promega. Individually, the engineered enzymes show both activity and substrate specificity with regards to their target sequences on CCR5. Cell migration and activation in this process is mediated by signaling molecules known as chemokines (chemoattractant cytokines) which are secreted early in the immune response (de Silva and Stumpf 2004). For example, the nomenclature “CCR5” refers to the 5th chemokine receptor of the CC subfamily. CCR5 is expressed on the surface of numerous cells of the immune system, including macrophages and CD4+ T cells (Berger et al.


HIV-1 (top) infects a macrophage cell (bottom) via binding of viral protein gp120 to cell-surface molecule CD4 and to co-receptor CCR5, poising gp41 for membrane fusion (BBC 2007).
The corresponding HIV-1 variants are deemed “R5.” Almost all primary HIV-1 isolates are “R5” viruses, as this is the dominant viral phenotype of new infections (Janeway et al. The CCR5-?32 mutation is a naturally-occurring deletion polymorphism in CCR5 that yields a non-functional cellular receptor.
In addition to having fewer functional CCR5 receptors due to ?32 heterozygosity, the truncated protein may reduce wild-type CCR5 and CXCR4 cell-surface expression by forming heterodimers with them, which are retained in the endoplasmic reticulum (de Silva and Stumpf 2004; Agrawal et al. Recently, zinc finger nucleases have been targeted to CCR5 to replace the wild-type allele with the ?32 by homologous recombination (Perez et al. Specifically targeting CCR5 on chromosome three, I will use engineered, genome-editing enzymes capable of safely excising DNA to create a deletion in CCR5 which results in a similarly-truncated receptor. Enzyme dimers recognize the two sites to be recombined, interact to form a catalytic tetramer between crossover sites, and coordinately cleave all four DNA strands with catalytic serine residues, covalently attaching each recombinase monomer to the DNA backbone (Gordley et al. One domain is responsible for DNA binding, while a distinct, catalytic domain mediates all subsequent enzymatic steps (Gordley et al.
Illustration depicting the full-length CCR5 gene (protein-coding sequence marked by the blue arrow) within a segment of genomic DNA (light and dark blue horizontal lines).
Illustration of genomic DNA before and after recombinase-mediated excision of the C-terminal region of gene CCR5.Central dinucleotides (marked by “TT” and “AA” in white and yellow)are in direct repeat. These functionally modular sequences can be combined to make proteins that can bind with nanomolar affinity to DNA sequences up to 18 base pairs in length (Segal et al.
These zinc fingers were cloned into Hin-H107Y hyperactive recombinase mutants, replacing their C-terminal domains, in a manner analogous to that reported by Stark and coworkers using hyperactive mutant Tn3 resolvase. Each enzyme acted a homotetramer to carry out recombinase-mediated DNA inversion or excision. For inversion assays, the second recombination site was the reverse complement of the sequence listed above.
CCR5 coding sequence excerpts of wild-type, ?32 deletion mutant, and recombinase-treated CCR5 versions. Using a selection scheme similar to that demonstrated by Buchholz and coworkers, albeit adapted to zinc finger-recombinase recognition sequences, I constructed recombinase selection plasmids (Buchholz and Stewart 2001).
However, only purification of the zinc finger region, not the backbone, was feasible due to the similar sizes of digested, backbone DNA and undigested vector.
This resulted in plasmids encoding a gene for the chimeric recombinase catalytic domain fused to the chloramphenicol resistance gene. Subsequent ligation reactions pair each recombinase zinc finger region with the catalytic domain on plasmids containing the appropriate recombination sites. To assay for enzyme activity, PCR reactions were performed using primers which bind in the same orientation unless recombinase enzymes can invert the segment containing the one primer’s binding sequence.
Inserts for library generation were first subjected to mutagenic PCR to introduce diversity. Due to time constraints, here I report analyses of the initial libraries only, not those after multiple rounds of directed evolution. Normal and library plasmid samples were analyzed after either four or 21 hours in cells, and with or without restriction endonuclease digestion to cleave substrates that did not recombine.
This beetle burrows into the bark of the lodgepole pine of these Mountains and with the help of a fungus called the Blue Stain Fungus(Grosmannia clavigera), lays its eggs in the tree.
The Mountain Pine Beetle has always been a factor in this ecosystem, but historically, winters have been harsh and cold enough to keep the beetle population in check.
To begin, our specific gene of interest, the chitinase, is not available in the iGEM registry. The experimental plasmids contained antibiotic resistance and therefore only cells that had successfully been transformed with our experimental plasmids grew on the agar plates. To ligase our parts into J04550 and J04500 we added 6.5 uL of each digested chitinase inserts (Pc1-, Pge1-1 and Pge1-2) to 2 uL of either the J04450 plasmid or the J04500 plasmid.
Microwave 30s by 30s until agarose total dissolution Gel was cooling down until to be lukewarm, one BET drop was added.
We took 1 ml of the culture, washed it with 1 ml 1x PBS buffer and resuspend it in 600 µl 1x PBS buffer.
To optimize enzyme activity and specificity individually, I developed and validated a substrate-linked protein evolution selection scheme.
Several ligands bind to each chemokine receptor, and many ligands bind to multiple receptors. Thirty-two nucleotides of the CCR5 coding region are absent in the mutation, resulting in a frameshift and premature stop codon (Janeway et al.
1997), although some studies indicate that heterozygous CCR5-?32 allele carriers may have increased risks of cervical cancer development (Singh et al. The sequence of interest (arrow) between recombinase enzyme recognition sites (boxes) is excised, creating a freed loop of DNA (Akopian et al. If successful, this project will further efforts to confer resistance to HIV-1 infection, or to possibly treat infected individuals by generating a reserve of resistant cells.
Similarly, a sequence can be integrated into a recombination site via the reverse reaction. Catalytic domains in yellow, interdomain linkers in orange, DNA-binding domains in green, and DNA in gray (Akopian et al.
Proteins containing zinc fingers are common in eukaryotes; in humans they comprise approximately two percent of all genetically-encoded proteins.
Thee (32 deletion region (purple bracket), recombinase-mediated deletion region (green bracket), and central dinucleotides of both recombination sites (green arrows and “TT,” “AA”) are indicated.
The two-base pair overhangs base pair with exchange partners during recombinase-mediated excision.
Unlike helix-turn-helix DNA-binding domains, which often dimerize to recognize symmetric DNA sequences, zinc finger DNA-binding domains are modular and can be combined to recognize extended, asymmetric sequences (Segal et al.
Chimeric enzymes of the serine recombinase family have been retargeted to sites precisely specified by Zif268 zinc finger DNA-binding domains (Akopian et al.
The hyperactive Hin mutant H107Y, which is able to catalyze efficient DNA inversions and deletions without the Fis regulatory protein, recombinatorial enhancer sequence, or supercoiled DNA substrate required by the wild-type enzyme, and was selected as the catalytic core (Sanders and Johnson 2004). The flexible peptide sequence linking the catalytic and engineered DNA-binding domain of the most active reported chimeric recombinase was retained (Akopian et al. This strategy allowed determination of the activity of each individual engineered recombinase enzyme, permitting individual optimization prior to testing the four variants together for heterotetramer activity on CCR5. Pairings were as follows: recombinase A with recombination sites C, recombinase B with recombination sites D, recombinase C with recombination sites B, and recombinase D with recombination sites A. Active enzymes excise the region subjected to restriction endonuclease digestion, while inactive library members are cleaved. Right: Agarose gel depicting the presence or absence of PCR products, reflecting enzyme activity on target recombination sites or lack there-of. Like the zinc finger region, the resistance gene was flanked by HindIII and EcoRI restriction sites. PCR product formation was indicative of active recombinase enzymes as no product was expected from non-inverted substrates.
In this activity assay, substrate plasmids were separate from those that encoded the recombinase enzymes. Activity levels cannot be directly compared because PCR amplification bias renders this a non-quantitative assay.
Sixteen random library members were sequenced to determine the mutation rate for each library, which appeared to be fairly low (Table S1). This construct will then be placed in E.coli bacteria so that this bacteria, when subjected to pine tree resins, will secrete the chitinase which will kill the Gc.
The winter then kills the beetle off, but the eggs, which are protected from the cold by the tree, survive the winter and mature to be able to start the cycle all over again. With global warming beginning to produce noticeable increases in winter temperatures, more and more beetles have been able to survive, and the population has reached a level where it is capable of ravaging huge chunks of forest, not only destroying the ecosystem, but rendering the lumber unusable. Secondly, by focussing on the BSF, we are attempting to minimize our disruption of MPB predator populations, such as woodpeckers and other birds. Extensive research has been conducted to determine whether plant chitinases have a role in defense against fungal diseases. This construct as previously mentioned will be placed into lab grade Top 10 and k12 lab strain E.coli bacteria thus allowing these new, genetically altered bacteria to successfully produce and secrete the chitinase enzyme thus showing proof of concept. Kolosova, two researchers at UBC’s Michael Smith Laboratory and members of the TRIA project. Gel was loaded with 10µl per sample previously added with 2 µl of loading dye 6X, and 5 µl for ladders. To recheck the Minipreps we try an additional PCR with our old protocoll (no Phusion MasterMix).
Because the culture in xylose did not grow we only could measure the OD600 of the glucose cultures. Due to this redundancy, a chemokine receptor knockout rarely results in phenotypic changes (Allen et al.
Infection of these cells by HIV-1 is often described in two consecutive stages, the M-tropic and T-tropic phases, corresponding to the target cells: macrophage or T-lymphocyte cells. It is estimated that “R5” viral strains account for 90% of all HIV-1 infections (O’Brien and Moore 2000). As “R5” HIV-1 variants require co-receptor CCR5 for infection, heterozygous carriers of the CCR5-?32 allele experience a delayed onset of AIDS by two to three years if infected with HIV-1.
The viral strains in these individuals appear to use CXCR4 as a co-receptor during infection (Agrawal et al. These genome-editing enzymes introduce a double-stranded DNA break which is corrected via homologous recombination with a provided ?32 template strand. Furthermore, recombinase enzymes are unlikely to suffer the same disadvantages as zinc finger nuclease enzymes because recombinase-mediated DNA excision does not rely on the generation of DNA damage as a means to effect a CCR5-null phenotype.


The dimers then exchange partners by 180° rotation about a flat, hydrophobic interface, preventing dissociation. Many zinc finger-containing proteins are involved in gene regulation, conferring sequence specificity to transcription factors and other DNA-localized proteins (Matthews and Sunde 2002).
Chimeric recombinase enzyme target sequences are marked by their respective zinc finger DNA-binding domain recognition sites (orange, pink, gray, turquoise brackets). Not all triplets can be recognized; while there is nearly complete coverage of 5’-GNN-3’, 5’-ANN-3’, and 5’-CNN-3’ DNA-recognition sequences (Segal et al.
Three of the four chimeric recombinase enzyme target sequences are marked by locations of their respective zinc finger DNA-binding domain recognition sites (orange, pink, and turquoise underlines). Upon recombinase- mediated inversion, primer 2 inverted and could form a PCR product with primer 1.
These plasmids, too, would be unable to recombine due to the recombinase-chloramphenicol fusions and lack of zinc finger DNA-binding domains.
Upon recombinase-mediated inversion one primer binding site was inverted, permitting PCR product formation. Lanes 3 and 5: PCR on plasmid DNA collected from cells transformed with the proper recombination sites plasmid only. Given that the four engineered chimeric recombinases displayed some level of activity, all were suitable candidates for directed evolution.
The Gc spreads its mycelium into the phloem, and then feeds on this essential structure, thus choking off the supply of glucose to the tree.
Thirdly, our objective is to focus specifically on the pathogenic BSF and not destroy the symbiotic relationships of a forest fungal ecosystem. Expression of cloned chitinase genes in transgenic plants has provided further evidence for their role in plant defense.
It is important to note that our engineered bacteria will not be used outside of a controlled lab setting during our for the current project. The following morning, 100?L of cells were grown in 9.9mL of LB broth and grown for 3-4 hours in a shaking incubator.
Their coauthored paper on chitinase and their in depth knowledge of phytochemistry, the mountain pine beetle and the blue stain fungus proved to be a very valuable resource to our team as we set out to test chitinase production in transgenic E.coli4.
During viral infection, a glycoprotein on the surface of the virus, gp120, binds to the immune cell-surface molecule CD4 receptor (Janeway et al.
The resulting truncated protein is not transported to the cell surface and instead accumulates in the cytoplasm (de Silva and Stumpf 2004). Furthermore, the 1% of Caucasians who are homozygous for the allele are nearly fully resistant to infection by the HIV-1 virus (Y. As a therapy, this method requires adoptive transfer of ex vivo-expanded, zinc finger nuclease-modified CD4+ T cells (Perez et al. Given an appropriate delivery mechanism, this therapy should be safe for direct in vivo application, which is a necessity for conditions in the developing world. Subsequently, the four 3’ hydroxyls attack the serine esters, forming new phosphodiester bonds and ligating the strands without DNA loss (W. Although not distinguished in the illustration, the zinc finger domains of chimeric recombinase enzymes A and C bind to the CCR5 coding strand, while those for B and D bind to the non-coding DNA strand.
The resulting protein will lack the proper C-terminal region and will instead contain a segment of amino acids derived from non-coding genomic DNA. For example, three or more zinc fingers together can confer DNA sequence specificity to a protein, allowing it to target a particular gene (Matthews and Sunde 2002). Importantly, such chimeras are capable of recombining their newly-specified target sites in mammalian cells (Gordley et al.
Recombination between the selected sites will excise the entire C-terminal coding sequence of the CCR5—a targeted deletion of 571 base pairs of genomic DNA. After DNA isolation and restriction digest, active library members would remain uncut, while inactive members would be digested. In the event of incomplete digestion, recombined products can be gel-purified before subsequent amplification and diversification steps. Lanes 2-4 and 9-11: PCR templates were plasmids with the correct target recombination sites but different chimeric recombinase zinc finger regions as controls. Chimeric recombinase libraries were created and analyzed as described in the supplementary text. Research also shows the the BSF survives the pine trees defensive resin production, by using the monoterpene chemicals as its food source. The level of protection observed in these plants is variable and may be influenced by the specific activity of the enzyme, its localization and concentration within the cell, the characteristics of the fungal pathogen, and the nature of the host-pathogen interaction.
Cells were then lysed, cellular debris was pelleted and the lysate was passed through a HiBind DNA mini column. Future experiments will use the starting libraries for iterative rounds of directed evolution. Consequently, individuals homozygous for the CCR5-?32 allele do not have detectable CCR5 receptors on lymphoid cell surfaces (Carrington et al. A contrasting example, however, involves a patient infected with HIV-1 who received a stem cell transplant from a homozygous CCR5-?32 allele donor and was effectively cured. Chemokine-receptor functional redundancy has been hypothesized to compensate for the lack of CCR5 in those individuals (Premack and Schall 1996).
Stop codons for the (32 mutant, wild-type, and recombinase-modified CCR5 versions are represented by red brackets. The target sequence for recombinase C is not marked as it is excised during recombinase treatment. The subsequent amplification with PCR primers flanking the excision region and the recombinase gene should positively select for library members active on the desired site.
Lanes 4 and 6: PCR on plasmid DNA collected from cells transformed with both the proper recombination sites plasmid and recombinase plasmid.
The expression of chitinase in combination with one or several different antifungal proteins should have a greater effect on reducing disease development, given the complexities of fungal-plant cell interactions and resistance responses in plants.
Using the HiBind column, DNA was trapped as proteins while eluting proteins, membrane molecules and any other unwanted substrates. After determining efficient recombinase variants individually, I will test the evolved enzymes for recombinase-mediated excision on CCR5, first in E. Gp120 undergoes a conformational change upon CD4 binding, allowing the virus to bind to a chemokine receptor in the cell membrane as a co-receptor. 1997) and heterozygous allele carriers express fewer functional receptors on their cell surfaces (Y.
As a result of transplantation, the patient’s genotype changed from heterozygous to homozygous for the CCR5-?32 allele. Zinc finger nucleases have been shown to induce toxicity as a result of DNA cleavage at non-target sites, resulting in cell death and apoptosis, and so would be ill-suited for in vivo delivery to target cells (D.
The “TAG” stop codon, introduced by the recombinase-mediated excision and resulting frameshift, is followed by another stop codon “TAA” just six base pairs downstream, ensuring that the translated protein will be truncated. In the event of incomplete restriction endonuclease digests, a successfully recombined product would still be distinguishable by size via gel electrophoresis, significantly reducing the background.
Lanes 5-8 and 12-15: PCR templates were plasmids with the correct recombination sites and respective zinc finger regions.
A 375-base pair long product was expected to result from recombinase-mediated inversion and those bands are surrounded by a maroon box. Unrecombined plasmids are 2037 base pairs long, while recombined plasmids are 1017 base pairs long.
Un-recombined plasmids are 2037 base pairs long, while recombined plasmids are 1017 base pairs long. Our plasmids were then added to the microcentrifuge tubes containing the DH5? cells and the tubes were placed in a water bath at 42oC for 60 seconds.
Co-receptor binding allows viral glycoprotein gp41 to fuse the cell membrane and viral envelope together, allowing the HIV-1 genome and proteins to enter the cell (Allen et al. Following the transplant, the patient discontinued highly active antiretroviral therapy (HAART), HIV-1 RNA levels in the patient’s blood and bone marrow became negligible, and CD4+ T cell counts steadily increased. Furthermore, not all characterized sequences exhibit specific binding, and reported success rates of the strict modular assembly methods vary considerably. This heat shock created pores in the cellular membrane thereby allowing the entry of plasmids. These engineered recombinase enzymes have the potential to provide protection from HIV-1 in a manner suitable for delivery in developing nations. At the time of this writing, more than 20 months post-transplant, no detectable replicating, active HIV-1 has been reported in the patient (Hutter et al.
Following this recovery, LB broth was added and the cells were placed in the shaking incubator for 60 minutes at 37 oC. The CCR5-?32 allele appears to not only provide resistance to initial infection, but also potentially to treat current infections. Furthermore, DNA double-strand break repair systems have been linked to human genome instability and cancer (van Gent et al.
After the incubation cells were then plated on agar plates and then incubated for 24 hours incubated.
This represents a major limitation for zinc finger nuclease-mediated gene therapy to become suitable for use in humans.



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