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9

The techniques used to do this are ChIP-seq and ChIP-chip. Basically, you let the pathogen bind to the (highly replicated) DNA cut up the DNA into little random pieces by sonication enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen sequence the thus enriched DNA map the sequenced fragments back to ...


7

I found article in Nature: A helper phage to improve single-chain antibody presentation in phage display Experimental protocol Standard cloning procedures, determination of colony-forming units and plaque-forming units, and immunoblot after PAGE were carried out according to Sambrook et al. Construction of the packaging cell line. ...


5

This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation. Salting out The solubility of proteins is affected by the ionic strength of the ...


5

See here. Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.) ...


5

This is the figure the question is about. On the right is the control experiment with GTP-γS, on the left without it: The bands that are visible in both experiments are unspecific binding. If GTP-γS doesn't affect their presence, the mechanism by which they bind to the column can't be specific to the GTPase functionality. The proteins the authors were ...


4

I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within one polypeptide. (Wikipedia agrees.)


4

ChIP-exo does seem to be the "ChIP-seq killer." I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed. One thing I'd do if I were of the "experimental bent" would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the "peaks" in ChIP-exo seem to be quite ...


3

Telomerases are tightly controlled on all level: Expression, post-translational modifications and by external factors. I think for this the external factors, a protein class called telomeric proteins. They bind to the end of the telomere and regulate the telomerase. The figure is from this paper, which looks into the topic quite extensively: Regulation ...


2

Like any other protein, antibodies will aspecifically bind nitrocellulose or PVDF membranes, but any other protein present in your antibody preparation will also do. Depending on the antibody class, more specific binding can be obtained with protein A or protein G, that recognize the Fc domain. It's usual to have protein A/G immobilized on a stationary ...


2

In prokaryotes the glucose transporter is always present in the cell membrane; in cells whose glucose uptake is insulin-regulated the transporter is only present in the plama membrane when hormone levels are high. GLUT4 is the isulin-regulated glucose transporter found in muscle and adipose tissue. When insulin levels are low the GLUT4 protein is in the ...


2

Background binding in this case would be the extent to which two proteins associate together by chance. A hypothetical example: you may have a mitochondrial protein import complex. Usually cases there is a specific peptide sequence the import complex binds to , but proteins without an import peptide sequence will occasionally be bound to the import ...


2

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/ In this work they find that formaldehyde crosslinking happens by formation of a methylol adduct (due to nucleophilic attack by N or S in case of proteins) in protein which then attacks the DNA or vice-versa. The final crosslink is by a methylene bridge Formaldehyde can react to amino groups in ...


2

I've always just gone with the name hetereodimer but there isn't any technical reason why it isn't a quaternary structure. As for an example, I work with antibody fragments or FAbs and cys-diabodies which are exactly that, two distinct polypeptides that are connected by a disulfide bond linkage. These do have a significant amount of non-covalent ...


2

A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in this short paper. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix). Now that the ...


2

The following paper answers your question in detail: http://www.ncbi.nlm.nih.gov/pubmed/18568020 It seems like the following aa are responsible for the binding, but please refer to the paper for more details: Val152,Tyr156,Asn157,Ser422,(Asp79)


2

Take a look at the paper by Ojasoo et al. [1] It reports the relative binding affinity for a wide variety of steroids for the AR, PR and GR. Nandrolone (19-nor testosterone) does not have any affinity for the GR, but is a potent activator of the AR. However, it does have some affinity for the progesterone receptor (does this matter for your research?). ...


2

A second telomerase is not necessary, as the lagging strand is filled in by the DNA-Polymerase, see this figure:


1

This is speculation, as I haven't done or read of the required experiment. However, I imagine that this would not be a problem. You're right that the RNA template (TERC) would not hybridize with a poly-G sequence, and so the telomerase would not be able to add more telomere repeats. You can imagine that the poly-G sequence is a cap, preventing telomerase ...


1

P-values reflect how well the data fits some background model. This background model should reflect some assumptions you make about the data. What assumptions do you think would be reasonable in this case? For example, do you assume high values are more likely to be incorrect? Throwing away outliers like kmm suggested is probably not a good idea, because it ...


1

Apparently poly(ethylene oxide) is a biologically interesting polymer, with minimal protein interactions. The apparently means that I haven't tried it myself, but my polymer teacher told us so. http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=20204110 http://en.wikipedia.org/wiki/Polyethylene_glycol Nomenclature ...



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