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Topic: Nanopore sequencing

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	genome.gov \| Advanced Sequencing Technology Awards 2004
		The gene sequencer is based on the nanopore approach and incorporates tunneling current electrodes to sense the individual nucleotides as they transverse the pore.
		However, the cost of sequencing mammalian-sized genomes is currently too high and we remain too far away from being able to afford the use of comprehensive genomic sequence information on a routine basis, in part because such large-scale sequencing requires a great deal of equipment and is labor intensive.
		In a new approach to DNA sequencing, DNA primers synthesized to be complementary to specific sequences on targeted genes are covalently tethered in known locations in an array on the surface of a glass slide and allowed to hybridize with and capture complementary target gene fragments.
	www.genome.gov /12513162 (5394 words)

	Nanopores, methods for using same, methods for making same and methods for characterizing biomolecules using same ...
		In once solid state nanopore of the present invention the width and/or length of the nanopore is defined or established by sharp edges of cleaved crystals that are maintained in fixed relation during the formation of the insulating member including the nanopore.
		The current amplitude through the nanopore is monitored during the translocation process and changes in the amplitude are related to the passage of single- or double-stranded molecules through the nanopore.
		For example, nanopore devices and systems of the present invention are contemplated for use as a molecular comb to probe the secondary structure of RNA molecules, for use in detecting biological warfare agents, and contaminants/pollutants in air and/or water.
	www.freshpatents.com /Nanopores-methods-for-using-same-methods-for-making-same-and-methods-for-characterizing-biomolecules-using-same-dt20070222ptan20070042366.php (5175 words)

	A milestone towards fast DNA sequencing with nanopore devices
		Nanopores function as membrane channels in all living systems, where they serve as sensitive electro-mechanical devices that regulate electrical potential, ionic flow, and molecular transport through the cell membrane.
		For a nanopore to be useful as a single molecule detector, its diameter must not be much larger than the size of the molecule to be detected.
		The nanopores for this research were made in silicon nitride (Si) as an insulating membrane, focused ion beam milling, followed by feedback controlled ion beam sculpting.
	www.nanowerk.com /spotlight/spotid=585.php (690 words)

	CBSE Nanopore Project
		Nanopore detectors are instruments built around a membrane containing a tiny pore called an ion channel, just big enough to allow a single strand of DNA to pass through.
		Nanopore technology makes it possible to measure DNA structure and dynamics with precision at the angstrom level.
		Nanopore technology is well suited to analysis of the terminal ends of double-stranded DNA, and it is amenable to high throughput experiments.
	www.cbse.ucsc.edu /nanopore.html (273 words)

	Sequencing
		In Genetics and Biochemistry, sequencing means to determine the Primary structure (or primary sequence) of an unbranched Biopolymer.
		In chain terminator sequencing (Sanger sequencing), extension is initiated at a specific site on the template DNA by using a short oligonucleotide 'primer' complementary to the template at that region.
		Modern automated DNA sequencing instruments are able to sequence as many as 384 fluoresecently labelled samples in a batch (run) and perform as many as 24 runs a day.
	www.ufaqs.com /wiki/en/se/Sequencing.htm (1454 words)

	NanoSeq: Research
		Gramicidin is the smallest useful nanopore, having a pore diameter of roughly 0.4 nm.
		One approach that can reproducibly fabricate nanopores of a desired dimension is a feedback-controlled ion sputtering system that counts the ions transmitted through the gradually opening pore and extinguishes the ion sputtering erosion process at the appropriate time [26] With feedback control, reproducibility does not depend on precisely matching all conditions and starting dimensions.
		Although nanopore analysis is just emerging as a new research tool, the rapidly developing technology has immense promise as an analytical method for measuring and characterizing linear polyions such as nucleic acids.
	nanopore.bme.ucsc.edu /html/research.html (3878 words)

	Harvard Nanopore Page
		The underlying principle of nanopore sequencing is that a single-stranded DNA or RNA molecule can be electrophoretically driven through a nano-scale pore in such a way that the molecule traverses the pore in strict linear sequence, as illustrated in Figure 1.
		Although this detection mode is extraordinarily sensitive and able to sense small differences in the base composition of the translocating molecule, theory and experiment show that measurement of ionic conductivity alone is unlikely to achieve the resolution required for rapid sequential detection of each nucleotide in a DNA molecule.
		The problem of confining the scan to the length of the DNA molecule is solved by integrating tunneling probe electrodes into a nanopore device and by having ssDNA molecules electrophoretically drawn into and through the confining volume of a nanopore at rates commensurate with the potential sensitivity and bandwidth of the electronics.
	www.mcb.harvard.edu /branton/projects-NanoporeSequencing.htm (1875 words)

	Nanopore will make for speedy DNA sequencing - tech - 10 April 2006 - New Scientist Tech
		The DNA-sequencing nanopore is yet to be built, but you can view the simulation, here (mpeg format).
		The device would work by running an electric current across a DNA strand as it is drawn through a nanopore, using electrodes built into the pore's sides.
		The Harvard group are experimenting with adding a carbon nanotube inside a nanopore — a pore left behind after depositing silicon nitride in a way that leaves a pore behind.
	technology.newscientist.com /article/dn8977-nanopore-will-make-for-speedy-dna-sequencing.html (715 words)

	PROGRAM - NATO Advanced Research Workshop
		Two nanopore detector modes are being developed: in the first, DNA nucleotides modulate the ionic current through the membrane channel or nanopore; in the second, DNA nucleotides modulate local tunneling currents at the nanopore aperture.
		Because nanopores should be as responsive to very long polymers as they are to short polymers, the method should avoid errors associated with repetitive sequences and the time-consuming assembly of contiguous elements.
		A polynucleotide that is pulled through a nanopore by a voltage gradient large enough to assure minimal backward movement of the DNA moves at a rate that will not allow precise measurement of the current associated with each nucleotide.
	www.cstl.nist.gov /nist831/NATO99/abstracts/brant.html (436 words)

	[No title]
		In nanopore sequencing, strands of DNA move through a small hole in a membrane with sensors that read off the base pairs of genetic code one by one.
		The hole, or nanopore, is about the size of a DNA molecule, or 1 to 2 nanometers in diameter, and the membrane separates positively and negatively charged solutions.
		As the DNA moves through the nanopore, researchers should be able to "identify each base as it goes by" using electrical or optical techniques, says David Deamer, professor emeritus of chemistry at the University of California-Santa Cruz.
	www.technologyreview.com /printer_friendly_article.aspx?id=17601 (783 words)

	NHGRI's Sequencing Technologies, October 14, 2004 Press Release - National Institutes of Health (NIH)
		NHGRI's near-term goal is to lower the cost of sequencing a mammalian-sized genome to $100,000, which would enable researchers to sequence the genomes of hundreds or even thousands of people as part of studies to identify genes that contribute to cancer, diabetes and other common diseases.
		DNA sequencing costs have fallen more than 100-fold over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the successful effort to sequence the human genome.
		This is a highly parallel sequencing approach that involves synthesizing short regions of identical DNA fragments on magnetic beads, packing millions of them into a chamber and then extending each of those molecules while detecting the addition of fluorescently labeled DNA building blocks or nucleotides.
	www.nih.gov /news/pr/oct2004/nhgri-14.htm (1779 words)

	Nanopores Have a Zillion Uses, Researchers Say
		Nanopores, the tiny holes formed by proteins, could be used for a variety of applications, including sequencing DNA and detecting anthrax.
		Nanopores are nanometer scale holes formed naturally by proteins or cells, for instance to allow ions to pass between nerve cells.
		Nanopore sequencing would work by looking at changes in ion flow as a single strand of DNA in a solution flows through a nanopore.
	www.aps.org /publications/apsnews/200605/nanopores.cfm?renderforprint=1 (777 words)

	Nanopore Method Could Revolutionize Genome Sequencing
		Because sequencing a person’s genome would take several months and millions of dollars with current DNA sequencing technology, the researchers say that the new method has the potential to usher in a revolution in medicine.
		“Current DNA sequencing methods are too slow and expensive for it to be realistic to sequence people’s genomes to tailor medical treatments for each individual,” said Massimiliano Di Ventra, an associate professor of physics at UCSD who directed the project.
		The nanopore and the electrodes have been made separately, and although it is technically challenging to bring them together, the field is advancing so rapidly that they think it should be possible in the near future.
	www.sciencedaily.com /releases/2006/04/060409153612.htm (1041 words)

	A Milestone Towards Fast DNA Sequencing with Nanopore Devices
		A high-throughput solid state nanopore device that can probe and directly "read" electronically, at the single molecule level, the size, folding, and eventually the sequence of DNA and proteins, will dramatically alter the pace of biology and medical science.
		Solid-state nanopores are eminently suited for DNA and protein detection because they are mechanically robust, have tunable dimensions, and tolerate broad temperatures, pH, and chemical variations.
		The nanopores for this research were made in silicon nitride (Si3N4) as an insulating membrane, focused ion beam milling, followed by feedback controlled ion beam sculpting.
	www.prweb.com /releases/2006/6/prweb404588.htm (681 words)

	DNA sequencing at AllExperts
		DNA sequencing is the process of determining the nucleotide order of a given DNA fragment, called the DNA sequence.
		Currently, almost all DNA sequencing is performed using the chain termination method [1], developed by Frederick Sanger.
		In chain terminator sequencing (Sanger sequencing), which is possible because of the availability of PCR, extension is initiated at a specific site on the template DNA by using a short oligonucleotide 'primer' complementary to the template at that region.
	en.allexperts.com /e/d/dn/dna_sequencing.htm (1635 words)

	NanoBioConvergence.org
		Carl Myerholtz of the Life Science Technologies Laboratory is researching a breakthrough nanopore technology to speed the analysis of nucleic acids.
		Compared to conventional technologies, nanopore sequencing converts nucleic-acid sequences directly into electronic signatures and could make it possible to easily sequence individual, chromosome-length molecules of DNA at very high speeds and for a low cost.
		The nanopore technology allows a single piece of nucleic acid, such as DNA, to be pulled through a small hole called a "nanopore" like a string of pearls.
	www.nanobioconvergence.org /speakers.aspx?ID=27 (364 words)

	Science Notes 2002 \| How to Speed-Read a Gene
		They think nanopores will be able to read DNA far more quickly than the current sequencing methods used in the genome project.
		But with the nanopore method, just one copy of the DNA is all it would take: A single strand could be decoded base by base without any amplifying, chopping, or reorganizing.
		Nanopores could replace both the lasers and these dyes-bringing the whole process down to a smaller, cheaper scale-by directly tallying individual DNA molecules as they whiz through the pore.
	scicom.ucsc.edu /SciNotes/0201/lo/dna (2845 words)

	FuturePundit: Nanopore technology: sequence your DNA in two hours!
		One of the teams attempting to develop nanopore DNA sequencing technology is at Harvard.
		Single molecules of DNA are drawn through a small channel or nanopore that functions as a sensitive detector.
		With 500 nanopores in a single device the human genome could be decoded in less than 2 hours.
	www.futurepundit.com /archives/000017.html (417 words)

	Article : $1,000 Genome Remains the Holiest Genetic Engineering News - Biotechnology from Bench to Business
		The cost of core sequencing has progressively decreased, and in 2005 was estimated to be approximately $7 per combined reaction and run (2006 General Survey of DNA Sequencing Facilities).
		As a DNA strand is threaded through the nanopore, four microscopic electrodes are used to detect the differences in tunneling current of each individual nucleotide.
		While nanopore technology is still in the future, a single-molecule sequencing technology developed by Helicos Biosciences (www.helicosbio.com) is close to commercialization.
	www.genengnews.com /articles/chitem.aspx?aid=2000 (2171 words)

	Music Sequencing Software
		In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer.
		Sequencing results in a symbolic linear depiction known as a sequence which succinctlysummarizes much of the atomic-level structure of the sequenced molecule.
		Though polysaccharides are also biopolymers, it is not so common totalk of 'sequencing' a polysaccharide, because a symbolic linear depiction cannot capture their tendency to branch and to bond to one another in different ways.
	www.altvetmed.com /face/3941-music-sequencing-software.html (839 words)

	Biopharmaceutical Sequencing glossary
		Sequencing was limited to only 200- 300 bases of data from a single sample analysis and many reiterative steps were required to acquire just a few thousand bases of DNA sequence data.
		The obvious alternative [to vertical sequencing] is to perform all four reactions in one vial and determine the sequence by comparing determined oligonucleotide mass differences with expected data (horizontal sequencing).
		Sequencing method which involves randomly sequencing tiny cloned pieces of the genome, with no foreknowledge of where on a chromosome the piece originally came from.
	www.genomicglossaries.com /content/sequencing_gloss.asp (6341 words)

	biology - Sequencing
		In genetics terminology, sequencing is determining the nucleotides of a DNA or RNA strand.
		Currently, all sequencing is performed using the chain termination method, created by Frederick Sanger.
		Two of the mainstream chain termination strategies are chromosome walking and shotgun sequencing.
	www.biologydaily.com /biology/Sequencing (231 words)

	Business 2.0 - Magazine Article - Printable Version - A Genetic Hole in One (Site not responding. Last check: )
		Gene sequencing typically requires complex chemical processes and serious computing power to identify and catalog each genetic base, or letter, on a DNA strand.
		With single-base resolution, a nanopore sequencer could decode patients' genomes in 24 to 48 hours with a 500-nanopore device costing about $20,000.
		Even at the lower resolution, nanopores could be used to detect important differences in a patient's DNA much more easily than can be done with "gene chips" -- small plates currently used to analyze DNA strands by comparing them with control samples.
	www.timeinc.net /b2/subscribers/articles/print/0,17925,530509,00.html (466 words)

	Nanopore will make for speedy DNA sequencing - tech - 10 April 2006 - New Scientist Tech
		A new technique harnessing a “nanopore” to detect electrical changes as a strand of DNA is passed through it could speed up DNA sequencing more than 200 times.
		The DNA-sequencing nanopore is yet to be built, but you can view the simulation, here (mpeg format).
		Because DNA is a kind of acid, it has a negative charge and can be drawn through a nanopore by a positive electrode on the other side.
	www.newscientisttech.com /article/dn8977-nanopore-will-make-for-speedy-dna-sequencing.html (705 words)

	FuturePundit: Nanopore Design For Cheap DNA Sequencing Identified
		Because sequencing a person’s genome would take several months and millions of dollars with current DNA sequencing technology, the researchers say that the new method has the potential to usher in a revolution in medicine.
		“Current DNA sequencing methods are too slow and expensive for it to be realistic to sequence people’s genomes to tailor medical treatments for each individual,” said Massimiliano Di Ventra, an associate professor of physics at UCSD who directed the project.
		The nanopore and the electrodes have been made separately, and although it is technically challenging to bring them together, the field is advancing so rapidly that they think it should be possible in the near future.
	www.futurepundit.com /archives/003358.html (1201 words)

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