Next gen sequencing – Nanopores

Since the advent of dideoxy sequencing method by Sanger, important biological data has accumulated explosively. Several automations  to this method, has made sequencing routine work in molecular biology research. But several new sequencing technologies do emerge in aim of reducing cost and time further. One such technology is Nanopore sequencing technology.

Nanopore is simply a hole and the internal diameter is in the order of 1 nanometer ranges. When two chambers containing different electrolyte concentrations are separated by a nanopore containing membrane a potential difference is formed between the two chambers. If this voltage is disrupted (say for example by blocking the pore), the resulting ionic current can be measured using standard techniques. Thus it was independently proposed by two researchers from University of California and University of Harvard, that the modulation of this current could also be done by electrophoretically driving a strand of DNA or RNA through a nanopore of appropriate diameter. If the internal diameter of the nanopore is approximately equal to a nucleotide of a ssDNA molecule, two important properties could be achieved.
1. The unraveling of coiled DNA upon mobilizing through the nanopore
2. Translocation of a single nucleotide in the nucleic acid molecule through the pore in sequential order

Due to the partial blockage of current through the nanopore upon nucleotide translocation, there is a relative reduction of ionic current compared to the current through the nanopore when it is empty. Thus each nucleotide in the nucleic acid molecule produced a unique current modulation upon passage through the nanopore. However several problems persist given the extraordinary ability of nanopores for sensing single molecules.

Solving all drawbacks, Oxford Nanopore technologies has introduced the world’s first miniaturized 900$ sequencing machine. It may be possible to sequence a whole human genome in just hours, which took 13 years less than a decade ago.

Source:

1. http://www.nature.com/naturebiotechnology – The potential and challenges of nanopore sequencing

2. http://www.nature.com/news/nanopore-genome-sequencer-makes-its-debut-1.10051

The ultimate athlete – Doped Epo gene

Gene therapy is an amazing tool which could pave way to efficient treatment for many diseases that were previously not treatable due to lack of efficient treatment procedures. However the human mind is so infinite that even the greatest findings could cause serious damage. Gene therapy is also one such finding that may be used as a performance enhancer in athletes.

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DNA vaccines – Basics

Several reports exist on delivery of naked DNA into mammalian cells that could induce protein expression within. Thus it is no wonder that vaccination could be experimented with the delivery of heterologous DNA into mammalian cells. One form of DNA vaccination is the use of plasmid DNA to immunise against an array of diseases.

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Hybridize within – Principles of in-situ hybridization

When a target DNA sequence and a complementary sequence are proximal enough and are properly oriented the two anneal together to what we call a hybrid. The complementary sequence is usually known as a probe. Several hybrids may exist such as DNA-DNA hybrids, DNA-RNA hybrids etc. The chemical reaction between the target and the probe is referred to as hybridization. If hybridization is carried out to analyze a sequence of interest that is present inside cells, tissue sections or isolated chromosomes it is known to be in-situ hybridization. However in contrast an in-vitro technique is carried out within suitable apparatus or typically in a test tube.

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Get it out – DNA

Isolation of DNA is one of the prime processes carried out in any research or experiment involving analysis of DNA. Extraction of DNA is not a very cumbersome process as many amateurs may think but rather simple and logical. I found this process to be exciting too when I first thought about isolating the molecules that have all the information about who you are.

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