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A New Innovative Hitech Nanobiotech Chip Design "DNA BRAID GENESEQ"

Arun Kumar*, 1and Ajith Kumar2

1Srkac Hospital,
Trivandrum, Kerala 695003 India

2Medical College

This is an abstract for a presentation given at the
11th Foresight Conference on Molecular Nanotechnology

 

DNA BRAID GENESEQ Inc. technologies address these two needs with a highly innovative and efficient system which optimize DNA sequencing at both the efficiency and cost level.

There are various methods to sequence DNA. The most relevant one are based on electrophoresis, capillary action, capillary gel electrophoresis, ion separation, phase transition etc. The most widely used are based on capillary electrophoresis separation of DNA strands followed by detection, again by various methods.

Capillary electrophoresis separation involves flowing different molecular weight or different size DNA segments through a porous or gel material which allows smooth and easy movement in the presence of an electric field. The DNA segments are obtained by the use of several restriction enzymes which, acting each as a different chemical scissor, are able to cut the DNA at a specific site along its sequence. The flow patterns, which include the different DNA segments, are then plotted on a particular material in time and scale and the segments are detected using usually lasers (or other detection methods) in combination with certain base-specific fluorescent dyes.

The majority of DNA sequencers available on the market today incorporate the basics of the method described above.

Although capillary electrophoresis sequencers have undergone several evolutionary improvements, they all share the following common disadvantages:
a) They are plagued by overlapping problems: overlapping of different DNA fragments, as they move accross the gel or membrane, makes sequencing and detection inefficient and expensive, since it slows down the sequencing process and imposes the use of expensive reagents which brings the commercial cost of sequencing at $10-12 dollars per base pair.
b) Only few DNA fragments are flown in the separation columns at any given time.
c) Can only sequence up to a maximum of 600 to 700 Base pairs at any given time.
d) Use laser detection which severely restricts the use of low molecular weight dyes with fluoresent properties.

DNA BRAID GENESEQ has developed a system which reduces or eliminates most of the above mentioned disadvantages, dramatically improves sequencing precision and throughput and, as result, significantly reduces sequencing cost per base pair. DNA BRAID GENESEQ has developed an innovative sequencing system design consisting of two key components:
a) The Hardware component
b) The Software component

The hardware component of DNA BRAID GENESEQ' sequencing system is the most critical component since it speeds of the process of DNA sequencing altogether. It has been designed as a silicon chip in which DNA segment separation and detection is much more efficient than currently-used electrophoretic methods. Separating DNA fragments by length is the single most important step of the sequencing process. The traditional method is to place a 'restriction enzyme digested' sample at one end of a column of an organic gel and apply an electric field to the column. The electrical field causes the flow of the DNA fragments through the gel and the rate of flow of each fragment is directly related to its molecular weight. As they slowly make their way through the tiny pores of the material, fragments of different lengths moves at different speeds and eventually collect in a series of bands as a ladder like structure that can be photographed using fluorescent or radioactive tags. One of the major problems with this conventional scheme is the overlapping of DNA fragments caused by the intense density of the media (gel or membrane) acting as a 'viscous' substrate through which the fragments move. DNA fragment overlapping is the first problem that DNA BRAID GENESEQ's system eliminates.

DNA BRAID GENESEQ has developed NANOCHIP a a microelectronic device, a chip-like system, which allows DNA fragments to travel freely without intense density filling. It has been designed through the use of fractal geometrical methods, which are genetical algorithms which can be modelled to develop a porous geometry architecture which allows DNA samples to move in non-viscous media, such as water and other low/zero resistance media, using an electric field. In conventional schemes the second rate-limiting step is that only a few DNA fragments can be flown through the columns to avoid overlapping.


*Corresponding Address:
Arun Kumar
Srkac Hospital
tc 11-1266, Nanthancode
Trivandrum, Kerala 695003 India
Phone: ++91-471-2310179 Fax: ++91-471-2333614
Email: ajitharun@yahoo.com



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