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High Speed Single Molecule DNA Sequencing using Nanopores

A group of researchers from the Institute of Physics in Belgrade is developing a novel method for the human DNA molecule decoding, which can greatly contribute to the advancement of modern medicine, i.e. personalized therapy.

Professor Radomir Žikić with his team of young scientists, from the Institute of Physics in Belgrade (IPB), is giving a large contribution to this extremely popular field of research. Prof. Žikić is the coordinator of the NanoDNASequencing FP7 project which focuses on developing technologies for ultrafast sequencing of the human genome. This project represents one of two FP7 European projects which are focused on this area of research. Method based on nanotechnology is being investigated, and besides the IPB, four other distinguished Universities are also contributing to this project – EPFL (École polytechnique fédérale de Lausanne), The Hebrew University of Jerusalem, Trinity College Dublin, University of Regensburg and a start-up company NuWave System Ltd, London.

This new approach has the potential for sequencing one million base pairs per minute, which means that the entire human genome (three billion base pairs) could be sequenced in only a few hours. This is truely revolutionary, especially when compared to the famous Human Genome Project, in which sequencing took about 10 years. Also, the novel sequencing method excludes DNA copying steps and chemical reactions, which make the process expensive and error prone. This means that the cost of the entire human genome sequencing can be reduced to only USD 1000. After the complete development of the technology and the sequencing device, it is intended to make it available at the global level i.e. to medical facilities and specialized laboratories.

“Our research could bring a major progress in modern medicine and can potentially save lives. Doctors will be able to use this crucial information obtained by DNA sequencing to detect, diagnose and treat patients based on their own unique DNA structure,” says prof. Žikić. The medical approach that is mentioned by prof. Žikić is in fact the basic principle of personalized therapy. This kind of therapy tends to adapt preventive measures and the therapy itself to the individual patients, based on the patients’ genetic profile and additional information in the field of proteomics and metabolomics. “One of the important facts is that the NanoDNASequencing project also represents a key step in the further development of the biotechnology and nanotechnology industries, so its significance goes beyond the field of health care and pharmacy”, says prof. Žikić.

Nanopore sequencing

Nanopore sequencing is a method for determining the order in which nucleotide bases—adenine, guanine, cytosine, and thymine occur on a strand of DNA, as it passes through a nanopore. This is one of the sequencing methods that can overcome the limits of existing technologies – prohibitively high cost of a time consuming sequencing procedure.

New technology being developed within the NanoDNAsequencing project is based on the electrical characterization of the individual nucleotide bases, while DNA passes through a nanopore with integrated nanotube side-electrodes. The task that the team of researchers from the Institute of Physics has, is to determine the characterization of the electrical properties, which will help them answer the proof-of-principle question – is it possible to detect different types of DNA bases by their electrical properties? Even though this matter raises many doubts, mainly due to insulator properties of adenine and guanine, which further hamper their identification, prof. Žikić with his team is on the right track to prove otherwise.

Serbian scientists have determined that nucleotides become conductive at the voltage about 2 V. They have also discovered that the reason for this behavior lies in the specific property of a DNA strand – delocalized molecular states (spanning the entire length of a nucleotide) participate predominantly in the electrical conduction through a single-strand DNA. This makes possible both the identification of nucleotide bases, as well as reading of the genetic code by measuring conductivity of nucleotides. Another new feature is that adenine becomes conductive under positive, while guanine becomes conductive under negative voltage. The results show that, after all, it was possible to identify adenine and guanine, in a very easy way – simply by fast changing the polarity of the voltage.

“Developing a product of such capability represents a great scientific challenge. Our aim is to, at the same time, increase the sequencing speed, lower the costs and eliminate the need for excessive reagents. The first results of the electrical measurements are promising and we are expecting further progress and success,” says prof. Žikić with great confidence.

 

Source: www.inovacionifond.rs