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9

This is a great question as I just made my own "homebrew" chemically competent cells. There are a vast variety of E. coli strains that are commonly used for cloning. They may be transformed chemically by heat shock method, or electrically by electroporation (a brief summary may be found here). These can be made in the lab manually, or purchased commercially ...


7

For the impatient, I'm going to say that probably if you only have a regular home freezer, its unlikely that you will be able to do this. If you have access to a -80C or liquid nitrogen storage its possible, but also less likely. Cloning an animal typically starts with the transplantation of a nucleus into an egg cell whose nucleus has been removed. So ...


7

Yes, you must fragment the genome in order to insert it into a vector for cloning; you can't "insert" the whole 5 Mbp genome of E. coli into a vector. It's difficult to transform cells with huge plasmids, 2-20 kbp is an optimal range. In any case, if you want a clone of the whole genome, wait 30 minutes and the cell will happily oblige you. Most ...


6

During the generation of gametes (sperm, eggs), chromosomes can cross-over - this swaps paternal and maternally-derived genetic material. So none of the descendant's chromosomes would be a direct copy of Einstein's, and furthermore, each offspring receives half of its genetic complement from each parent. This means that if you pool the DNA data from small ...


6

I have heard that Epi300 electrocompetent cells (1) from Epicentre are very efficient: > 1 x 1010 cfu/µg of pUC19. Dan Gibson used them in his paper for the synthesis of the mitochondrial genome (2). We were also thinking of using them for our assemblies, but they are pretty expensive. 1. TransforMax™ EPI300™ Electrocompetent E. coli 2. Chemical synthesis ...


5

Did you identify structural domains in the protein using Pfam or some other domain detecting peptide search? It's pretty useful to cut your constructs at the boundaries of structurally independent domins in the protein if you know where they are. Hydrophobicity plots might lead you to cut right in the middle of a protein fold, only exascerbating inclusion ...


5

I have lots of experience with the TOPO TA kit which is very similar to the kit your using. Here's a link to the TOPO Directional cloning product page which shows a schematic of the enzymatic ligation. From your comments, you said you have doubly-digested the PCR product. This is likely your point of failure unless you are absolutely confident that your ...


5

Try dissolving at 50C. In the Qiagen gel extraction kit, it says to dissolve at 50C or until completely dissolved. The size of the gel is important too. Make sure it is 1.5% or less, and the size of the gel needs to be less than 400 mg. Also, pay attention to the first step. If the liquid is not the same color as the color of the first QG buffer then ...


5

When I optimized gel extraction in my hands, two factors turned out to be critical in maximizing gel extraction yield: The pH of the eluting solution. I used to elute the final product with DEPC-treated water initially, but the yield would vary a lot as the pH of the water changed. Using buffer EB is better, since it maintains a stable pH 8. Most ...


5

I think the best way is option #2: Suppose that your gene of interest is AAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGG and you want to insert EcoRI restriction site GAATCC Then your Fwd primer will be GAATCC AAAAAAAAAAAAAAAA and your Rev primer will be GGATTC CCCCCCCCCCCCCCCC But in general, it shouldn't matter which option you choose, as long as you ...


4

As can be inferred from the Shanks et al. paper linked in the question: In molecular biology, "suicide plasmid" is a term that refers to a plasmid which is replication incompetent.* Plasmids normally bear a sequence called "origin of replication" Ori which marks the plasmid for replication by the host cell. Plasmids that lack this Ori will not be replicated ...


3

Not any time soon. By far the greatest challenge is getting the DNA sequence from the computer into a form that could be implanted into an embryo. Craig Venter's team was able to build a bacterial genome from scratch, but that was incredibly painstaking work, requiring the assembly of many small fragments of DNA into a single circular chromosome. With ...


3

Just in case you are having difficulty visualising what happens in the answer from @Chris, here are the steps with the linker shown in lower case ...NNNNNGAATTCNNNNN... ds DNA ...NNNNNCTTAAGNNNNN... | V ...NNNNG AATTCNNNNN... after EcoRI digestion ...NNNNCTTAA GNNNNN... | V ...NNNNG ...


3

The recognition site for EcoRI is GAATTC, and the enzyme cuts after the first base. See this picture from NEB: The overhang is: AATT, which is supplied by your oligo and fits into the overhang. If the next nucleotide whould be a C than the site would be recreated, since its a G its not. The new sequence of the old EcoRI site is GGATTG which is not ...


3

The prototypes for these proteins are: the bacteriophage λ proteins Int and Xis, required for, respectively the integration and excision of prophages. They are, as mentioned by @WYSIWYG, recombinases. Genetic map of bacteriophage λ (source of image) the original Ihf (integrative/integration host factor) was identified as an E. coli ...


3

In my own personal lab experience, I got some unexpected results using Phusion polymerase. However, I have not seen deletions, only insertions (ranging from single bases to 3 tandem copies of a primer sequence). This is not an answer to your deletion question, but it does suggest unusual things might happen. I have seen deletions with T4 DNA polymerase ...


3

Making maps of plasmids Annotating plasmids with common features Plasmapper works through commandline Finding restriction sites Simple regex searches can do that Mapping Sanger sequencing reads BLAST will do it. Showing sequence, reverse complement of the sequence, translations in different frames EMBOSS has a collection of tools ...


2

The option #2 is most common. Do not forget to add 3 or more additional terminal base pairs for optimal restriction enzyme cutting (source: BioTechniques 1998, 24:582-584)


2

Here is a good overview of primer design considerations when using Gibson assembly. http://j5.jbei.org/j5manual/pages/22.html


2

Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two ...


2

I assume that we are talking about eukaryotic genomes which are split into introns and exons. Depending on what you want to do with your cloned gene, you need different strategies. The method is based on the assumption that the gene sequence has only very little differences to the known sequences of other organisms. If you want to express your gene from a ...


2

The buffer conditions used in the reaction also mitigate against the endonuclease reaction, so it should not be a problem if you stick to the protocols exactly. I've worked on this enzyme since 1988 and was the original "cloner' of the overproducer see http://www.sayers.staff.shef.ac.uk/fen/ for more information on these enzymes Jon Sayers, University of ...


1

Cloning of animals typically involves: Taking nucleus from healthy adult cell of animal to clone Taking a healthy egg and replace the egg's nucleus with nucleus from source animal. Implanting egg in female, stimulating the pregnancy process. This same process should work on humans BUT: "Is it really possible to create humans in lab?" No. Animal cloning ...


1

To learn about the process of how cloning works, you need to appreciate the underlying principles. A general bio textbook should suffice (most popular one is Alberts, where you should focus on chapter 21, but maybe read other chapters for background) Nature Scitable is also a good source. I'd discourage reading research papers at this stage, primary ...


1

I've never actually done a Gibson assembly, but looking over the protocols at the New England Biolabs website, I think the answer must be that the ssDNA exposed by the T5 exonuclease is quickly protected from the ssDNA-endonuclease activity because it (the exposed DNA) anneals with the complementary sequence on the other component of the assembly reaction. ...


1

The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform E. coli, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in ...


1

After cloning, the recipient cell is converted into embryonic stem cell. When it is a stem cell, it can produce enzyme telomerase itself which a naturally occurring enzyme that maintains telomeres and prevents them from shortening during cell division in cells. So i think there are no problem on shortening of telomeres.


1

Yes, it is. Dolly died of cancer in early years. Length of the telomeres depends on the donor tissue: "In Dolly's study, the animal produced from fetal tissue appeared to have telomere lengths non-distinguishable from normal controls, while the other two, including Dolly, which originated from adult cells, were found to have shorter telomeres." (Xu & ...


1

Elute from the column with Elution Buffer that has been preheated to 50-60 degrees. I stick mine in the incubator for the duration of the extraction so it is warm when I come to elute. It seems to help yield.


1

The neurological basis of behavior is still unclear, and the genetic basis of behavior is even less clear. What can be said is that genetics may predispose you to certain behaviors, but what the predisposing factors are, and how much they determine your behavior (and how much is due to environmental factors), is unclear. And this varies for different ...



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