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Topic: Nanopore

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	Nanopore sequencing - Wikipedia, the free encyclopedia
		Nanopore sequencing is a currently under development method for determining the order in which nucleotides occur on a strand of DNA.
		Certain transmembrane cellular proteins act as nanopores, and nanopores have also been made by etching a somewhat larger hole (several tens of nanometers) in a piece of silicon, and then gradually filling it in using electron beam methods which results in a much smaller diameter hole: the nanopore.
		However, the scale of the nanopore ensures that the DNA is forced through the hole as a long string, one base at a time, rather like thread through the eye of a needle.
	en.wikipedia.org /wiki/Nanopore_sequencing (286 words)

	Nanopore detector shows discriminating taste in DNA molecules
		The instrument used to perform the analysis, called a nanopore detector, is built around a membrane containing a tiny pore just big enough for a single strand of DNA to pass through.
		The pore in this nanopore detector is actually a kind of toxin, known as the alpha-hemolysin ion channel, produced by Staphylococcus bacteria to punch holes in cell membranes.
		The DNA molecules used in the nanopore detector experiments had a "hairpin" structure, consisting of a single strand of DNA folded back on itself to form a double-stranded segment (the "stem") with a single-stranded loop at one end.
	www.eurekalert.org /pub_releases/2001-03/UNKN-Ndsd-1303101.php (896 words)

	Facts about topic: (Nanopore) (Site not responding. Last check: 2007-10-13)
		A nanopore is a small pore in an electrically insulating membrane (A pliable sheet of tissue that covers or lines or connects organs or cells of animals), that can be used as a molecular probe.
		The size of the nanopore must be made to be just a little larger than the molecule which is to be detected, a molecule entering the nanopore will change its electrical properties in ways which can be measured.
		To make measurements with a nanopore, polymers and electrolytes in solution are applied a voltage, i.e.
	www.absoluteastronomy.com /encyclopedia/n/na/nanopore.htm (128 words)

	Nanopores with a spark for single-molecule detection - Nature Biotechnology
		When a short complementary polynucleotide is drawn into the lumen of the nanopore by a voltage bias, it is likely to form a DNA duplex with the tethered oligomer, producing a characteristic current reduction that may last tens of milliseconds.
		When an individual oligonucleotide with an unknown codon sequence is tethered to the nanopore and analyzed by the application of a series of different untethered polynucleotides of known sequence, the unknown codon sequence of the single tethered oligomer molecule can be determined.
		The single-nucleotide discrimination observed suggests that if a DNA molecule could be induced to slowly translocate through a suitable nanopore, the atomic-scale changes in the chemical and electrostatic environment within the nanopore might be sufficient to directly reveal the sequence of the translocating DNA as a series of ionic conductivity "signatures".
	www.nature.com /nbt/journal/v19/n7/full/nbt0701_622.html (1169 words)

	About Jiali Li
		Solid-state nanopores are mechanically robust, have tunable dimensions, tolerate broad temperatures, pH, and chemical variations, and are therefore ideally suitable for DNA and protein detection as well as integrated electronic device development.
		The research goal is to develop a nanopore technique to record single DNA and protein translocations in their denatured aqueous solution environment through a solid-state nanopore, probe the biopolymer’s length, diameter, secondary structure, charge, and eventually the sequence at high speed, high resolution, and low cost.
		The principle and idea of nanopore detection for single charged polymer is: a single nanopore in an insulating solid state membrane separates two ionic solution filled compartments, a voltage across the membrane is applied by a pair of electrodes.
	www.uark.edu /depts/physics/about/li.html (603 words)

	[No title] (Site not responding. Last check: 2007-10-13)
		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.
		nanopore structure has a cis and trans side that, during use of the device, separates the fluid sample from the another fluid, that may be the same or different than the solvent component of the fluid sample (i.
		Translocation or movement of the nucleic acids in the sample through the nanopore is achieved using any convenient means, where generally movement is achieved by applying an electric field to the sample and across the nanopore.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=01/18251.010315&ELEMENT_SET=DECL (3341 words)

	Encyclopedia: Nanopore
		Nanopore technology is expected to accelerate advances in personalized medicine where therapies are tailored to the patient and their particular form of the disease.
		Nanopore technology can distinguish between and count a variety of different molecules in a complex mixture.
		Nanopore technology is a direct measurement technique; therefore nanopore-based sequencing is expected to provide far greater speed than conventional methods.
	www.nationmaster.com /encyclopedia/Nanopore (476 words)

	NASA - Solid-state Nanopores for Gene Sequencing
		The nanopore channel with a diameter and length of less than 5 nm is made in a silicon-based chip that has nanoelectrodes placed adjacent to the pore.
		The nanopore sensor is expected to have unmatched speed and sensitivity of DNA detection and sequencing, enabling personalized molecular medicine, revolutionary modification of agriculture and food industry, and decoding of ecosystem-wide genetic variation.
		The approach to the development of a solid-state nanopore device is novel in the use of nanofabrication, nanoelectronic components, and high-speed signal acquisition.
	www.nasa.gov /lb/centers/ames/research/technology-onepagers/nanopores_gene_sequencing.html (444 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 /research/research_nano.shtml (273 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)

	Science Notes 2002 \| How to Speed-Read a Gene
		The prototype nanopore lives in a cramped corner of his lab, within the walls of a cubicle.
		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)

	[No title] (Site not responding. Last check: 2007-10-13)
		Of particular interest is the heptameric nanopore or channel produced from a-hemolysin, particularly a- hemolysin from Staphylococcus aureus, where the channel is preferably rectified, by which is meant that the amplitude of the current flowing in one direction through the channel exceeds the amplitude of the current flowing through the channel in the opposite direction.
		Typically, an aqueous nanopore or channel comprising solution is introduced into the cis chamber and an electric field is applied across the lipid bilayer in a manner sufficient for a single channel to insert or intercalate into the lipid bilayer.
		In such methods, the polymer is moved relative to the nanopore in a manner such that each different monomeric unit of the polymer causes a correspondingly different current to flow through the nanopore.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=00/28312.000518&ELEMENT_SET=DECL (6809 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.
	golgi.harvard.edu /branton/projects-NanoporeSequencing.htm (1875 words)

	Nanopore sequencing (Site not responding. Last check: 2007-10-13)
		Nanopore sequencing is a currently under development method for determining the order in which nucleotidesoccur on a strand of DNA.
		However, the scale of the nanopore ensuresthat the DNA is forced through the hole as a long string, one base at a time, rather like thread through the eye of a needle.
		The potential is that a single molecule of DNA can be sequenced from a single pass through a nanopore, and without the needfor an intervening PCR amplification step.
	www.therfcc.org /nanopore-sequencing-107910.html (152 words)

	Agilent \| Agilent Labs \| News \| Feature: Agilent and Harvard Develop Nanopore Technology (Site not responding. Last check: 2007-10-13)
		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's size is such that it permits only a single nucleic acid strand to pass through it at any one time.
		Compared to existing techniques, nanopore technology is expected to provide direct characterization of individual nucleic acid and protein molecules directly derived from biological samples, thereby making it applicable to a wide set of analyses.
	www.labs.agilent.com /news/2001features/fea_nanopore.html (1040 words)

	NanoPore Incorporated
		NanoPore HP-150 can be used at temperatures up to 300°C, but for higher temperature use NanoPore produces a special high temperature insulation, NanoPore HT-170 which can be used up to 800°C and above in some cases.
		NanoPore thermal insulation begins as a proprietary blend of nanoporous powders which are pressed into semi-rigid boards.
		For applications where a VIP cannot be used (such as high temperature applications) NanoPore has experience working with customers to design, and if needed, build custom containment for the insulation.
	www.nanopore.com /thermal.html (533 words)

	Tiny Holes Offer Giant Glimpse into Future
		Li, the first UA physicist to receive NIH funding, is fine-tuning a microscope-like device she and her former colleagues invented known as the single-molecule nanopore detector.
		Nanopores are essentially holes as tiny as 30 atoms across that exist within all living systems.
		With the nanopore "microscope," Li and her research group can look not only at a single molecule, but can measure the interaction between molecules.
	www.physorg.com /news2503.html (496 words)

	Molecular Electronic Devices (Site not responding. Last check: 2007-10-13)
		Using the nanopore process and a 4-thioacetatebiphenyl SAM we constructed a diode.
		Using the nanopore process and a 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate SAM we have demonstrated low temperature negative differential resistance (NDR) and using a 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate SAM we have demonstrated room temperature NDR.
		Using the nanopore process and a 4,4'-di(ethynylphenyl)-2'-nitro-1-benzenethiolate SAM we have demonstrated a room temperature memory cell which can be configured as a RAM.
	www.eng.yale.edu /reedlab/research/device/mol_devices.html (575 words)

	The Daily Californian
		Artificial nanopores developed by UC Berkeley researchers may offer a portable method of detecting and identifying biological weapons.
		The nanopores would be incorporated into a small cartridge similar to the technology that diabetics use to test their blood sugar level, that could be carried in a soldier's gear.
		Similar applications of nanopore technology are being applied in the field of DNA sequencing and other related fields.
	www.dailycal.org /article.php?id=13667 (560 words)

	Translocation of DNA through Synthetic Nanopores
		These nanopores have been used as Coulter counter devices for detecting single DNA molecules, resolving their length and diameter.
		For synthetic nanopores observed blockades presently show irregular shapes due to fluctuations of the reduced current within one blockade event; some blockades have a positive spike of the ionic current above the open pore level at the end of the blockade.
		The electromechanics of DNA in a synthetic nanopore.
	www.ks.uiuc.edu /Research/nanopore (3327 words)

	Encyclopedia: Nanopore sequencing
		SDS-PAGE autoradiography Gel electrophoresis is a group of techniques used by scientists to separate molecules based on physical characteristics such as size, shape, or isoelectric point.
		A nucleotide consists of a heterocyclic nucleobase, a pentose sugar, and a phosphate or polyphosphate group.
		In genetics and biochemistry, sequencing means to determine the primary structure (or primary sequence) of an unbranched biopolymer.
	www.nationmaster.com /encyclopedia/Nanopore-sequencing (557 words)

	Biophysical Journal: Nanopore Unitary Permeability Measured by Electrochemical and Optical Single Transporter Recording
		Prototypic protein nanopores were formed in bilayer membranes by addition of Staphylococcus aureus α-hemolysin (α-HL).
		Using the stable nongated nanopore (Song et al., 1996) formed by Staphylococcus aureus α-hemolysin (α-HL) the blockade of the single channel current caused by substrate molecules in transient was used to obtain information about the identity, concentration, and primary structure of the substrate (Kasianowicz et al., 1996; Bayley and Cremer, 2001).
		In this study, OSTR was extended to a prototypic biological nanopore reconstituted in artificial bilayers.
	www.findarticles.com /p/articles/mi_qa3938/is_200506/ai_n13642542 (1268 words)

	Biomolecular Engineering
		Examples include protein engineering (the computational design of proteins to enhance or modify their functions), the development of sensors that integrate biomolecules with electronic components, and new laboratory devices and analytical tools for studying gene regulation, protein expression, and other complex biological systems.
		One project that illustrates several aspects of biomolecular engineering is the nanopore analytical instrument being developed by research scientist Mark Akeson with Deamer, Haussler, and their students.
		The nanopore instrument is built around a membrane containing a tiny hole just a few nanometers in diameter (a nanometer is one-billionth of a meter).
	currents.ucsc.edu /03-04/02-16/biomolecular.html (729 words)

	Paper: No Job Name :: (Site not responding. Last check: 2007-10-13)
		The nanopore geometries fabricated with AR NSL and RIE corresponded well with the theoretically determined geometries for values of e 30°.
		All nanopores were made with 720 nm nanosphere etch masks on Si (111).
		The RIE variant of AR NSL yields a further reduction in nanopore in-plane widths by approximately a factor of 3.
	www.medical-papers.com /nanopores+nanopore+nsl+nanosphere+etch/4 (596 words)

	genome.gov \| Advanced Sequencing Technology Awards 2004
		The nanopores will then be physically characterized to determine their ion transport dynamics, and in conjunction with the modified oligonucleotides, to find a combination that meets the R21 milestone specifications.
		The gene sequencer is based on the nanopore approach and incorporates tunneling current electrodes to sense the individual nucleotides as they transverse the pore.
		In addition, since the nanopore readout does not rely on the relatively slow enzymatic incorporation of nucleotides, and because it can be applied to read the sequence of single molecules, an extremely high throughput is expected, resulting in a cheaper and faster approach.
	www.genome.gov /12513162 (5394 words)

	Detecting individual DNA molecules with a solid-state nanopore
		A voltage bias is applied over the nanopore, resulting in a strong electric field inside the pore.
		By measuring the ionic current through a voltage-biased nanopore, we detect the passing molecules, as shown in Figure 1.
		We used nanopores with a diameter of 10 nm, which is relatively large compared to the 2 nm diameter of DNA.
	www.mb.tn.tudelft.nl /projects/solid_state_nanopore/nanopore.htm (761 words)

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