Unraveling the molecular mechanism of DNA binding by Transcription-activator like effectors
Sequence-specific DNA targeting of nucleases, recombinases and transcriptional activators is a powerful tool to manipulate the sequence or regulate the expression of the gene of interest. While Zinc fingers specific to DNA trinucleotides, coupled to different effector domains have been employed for targeted manipulation of the genome with considerable success, we are limited by the off-target toxicity caused by trinucleotide specific zinc fingers. Recently, it has been shown that Xanthomonas secreted virulence factors called transcription-activator like effectors (TALEs), which contain 1.5 to 33.5 tandem repeats bind sequence specifically to the sense strand of the DNA helix. The specificity of this binding is directed by the repeat variable di-residues (RVDs) present on a short loop of every repeat of the TALE. In the Science January 2013 issue, Deng et al. present the structural basis for sequence specific binding of TALEs to the sense strand of the DNA using a crystal structure. They solved the crystal structures of an engineered TALE named dHax3, crystallized both, in its free form and in complex with the DNA at 2.4A resolution. This structure elucidates the molecular mechanism of TALE binding to DNA and provides a foundation for the rational design of DNA-specific TALEs with different effector domains for site-specific manipulations of the genome.
Bacterial TALEs modulate the target gene expression in host cells by acting as transcriptional activators. TALEs are made up of 33 to 35 tandem repeat domains. Each domain consists of 33 to 35 amino acids forming two alpha helices connected by a short loop and recognizes ...
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...ses, TALEs are shown to bind degenerate DNA sequences, albeit with much lower toxicity than zinc fingers (Carlson, Fahrenkrug et al. 2012). Thus along with a high potential of TALEs, the scientific community today is faced with a number of challenges which need to be answered before TALEs can be used as robust effectors of targeted gene manipulation. In this regard, the structural information about TALE interaction with the DNA which Deng et al. present in this paper is an important first step towards rational design of target DNA specific TALEs that can carry out a variety of effector functions.
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The PBS documentary “Nova – Cracking Your Genetic Code” tells about the genome sequencing technology: its current possibilities, advantages, disadvantages and future potential. The system became cheaper, faster and more available since the first human genome was fully sequenced in 2000. Modern companies use the technology to provide clients with the information about their genes and impacts they can have on owners’ health. Hospitals can provide more accurate diagnosis and personalized treatments with the aid of the genome sequencing. The video shows several examples of these benefits. But it mentions concerns about the quality of services, risks of exaggerated
The main goal for our experiment was to learn how to examine DNA when there is only a small
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consists of a polyhedral head and a tail. The tail is used to inject DNA into a
Raymo uses for this is DNA and its ability to reproduce itself. This tiny double-helix
Chemistry dictates the structure of DNA. DNA is a polymer of monomers called nucleic acids. These are made of a nitrogenous base, a phosphate group and a sugar. It is the negative charge on the phosphate group that makes DNA an acid. There are 4 different bases: adenine, thymine, guanine and cytosine. In groups of three, these four bases can code for any protein coded for in an organism’s genome. Two strands of nucleic acids stack on top of each other in a double helix. The backbone of the nucleic acids consists of the interaction between phosphate groups and the hydroxide groups of nucleic acids. These are held together by covalent bonds called phosphodiester bonds. The helix itself is held together by hydrogen bonds. Although h...
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James Watson: He can be seen as someone who is quick to judge, somewhat condescending, yet intelligent, suave, and dedicated to his work.
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"The discovery of the structure by Crick and Watson, with all its biological implications, has been one of the major scientific events of this century." (Bragg, The Double Helix, p1) In the story of The Double Helix, James Watson tells of the road that led to the discovery of life's basic building block-DNA. This autobiography gives insight into science and the workings within a professional research laboratory that few members of society will ever be able to experience. It also gives the reader an idea of the reality of life for one scientist and how he struggled with the problem of DNA. However, the author's style is marked by his lack of objectivity and inclusion of many biased opinions and personal prejudices.
The birth of genetic engineering and recombinant DNA began in Stanford University, in the year 1970 (Hein). Biochemistry and medicine researchers were pursuing separate research pathways, yet these pathways converged to form what is now known as biotechnology (Hein). The biochemistry department was, at the time, focusing on an animal virus, and found a method of slicing DNA so cleanly that it would reform and go on to infect other cells. (Hein) The medical department focused on bacteria and developed a microscopic molecular messenger, that could not only carry a foreign “blueprint”, or message, but could also get the bacteria to read and copy the information. (Hein) One concept is needed to understand what happened at Stanford: how a bacterial “factory” turns “on” or “off”. (Hein) When a cell is dividing or producing a protein, it uses promoters (“on switches”) to start the process and terminators (“off switches”) to stop the process. (Hein) To form proteins, promoters and terminators are used to tell where the protein begins and where it ends. (Hein) In 1972 Herbert Boyer, a biochemist, provided Stanford with a bacterial enzyme called Eco R1. (Hein) This enzyme is used by bacteria to defend themselves against bacteriophages, or bacterial viruses. (Hein) The biochemistry department used this enzyme as a “molecular scalpel”, to cut a monkey virus called SV40. (Hein) What the Stanford researchers observed was that, when they did this, the virus reformed at the cleaved site in a circular manner. It later went on to infect other cells as if nothing had happened. (Hein) This proved that EcoR1 could cut the bonding sites on two different DNA strands, which could be combined using the “sticky ends” at the sites. (Hein). The contribution towards genetic engineering from the biochemistry department was the observations of EcoR1’s cleavage of
The restriction enzymes SmaI cuts DNA vertically. This results in two DNA fragments with blunt ends. Next, the gene is spliced into a vect... ... middle of paper ... ... le by stopping illness but this process has also been vandalised for many uses which are not necessary.
The scientific and medical progress of DNA as been emense, from involving the identification of our genes that trigger major diseases or the creation and manufacture of drugs to treat these diseases. DNA has many significant uses to society, health and culture of today. One important area of DNA research is that used for genetic and medical research. Our abi...