Our blogs and videos choice: single molecule dna sequencing

Research Demonstrates Progress Towards DNA Strand Sequencing

UCSC researchers are collaborating with Oxford Nanopore Technologies Ltd in the development of a new generation of electronic, single-molecule DNA sequencing technology. In the 'strand sequencing' method, current through a nanopore is [more...]

Date: 2010-10-02 15:03:00

Blog posts (39) | Videos (17)
 


Efficient light collection and high frame rates a must for high ...

To harness this powerful single-molecule detection modality for high-throughput DNA sequencing, each of the four nucleotides (A, C, G and T) in the target DNA has to be converted into a predefined sequence of oligonucleotides, using a technique called Circular DNA Conversion. Each pre-defined sequence is then hybridized to a self-quenching molecular beacon. In their experimental setup, the Meller team recorded DNA translocation through a 4 nm pore in a SiN membrane immersed between two aqueous solutions. With the camera in place, the researchers were able to detect fluorescence bursts in two [more...]

Date: 2010-06-15 11:25:33


Biocurious: Hot off the Press: Single molecule DNA sequencing

Building on the work in the single-basepair resolution paper, the Block lab has a new result in this week's Science, where they are (mostly) able to sequence a 32 bp section of DNA upon which an RNA polymerase is stepping. [more...]

Date: 2006-08-11 07:00:00


Scientist Solutions - DNA MicroArray Basics

Just came across this resource today, while looking up MicroArray companies. Its pretty nice and a great beginner step. DNA microarrays can be thought of as the massively parallel version of Northern blotting. While the Northern blotting technique is capable of analysing for each experiment the expression of one single gene in different conditions, microarrays allow the exploration of the expression levels of thousands of genes in several different conditions in one single run. As Northern blotting and many other classic techniques widely used in molecular biology, the fundamental basis of [more...]

Date: 2009-03-19 19:31:20


Graphene may hold key to speeding up DNA sequencing

(Nanowerk News) In a paper published as the cover story of the September 9, 2010 Nature, researchers from Harvard University and MIT have demonstrated that graphene, a surprisingly robust planar sheet of carbon just one-atom thick, can act as an artificial membrane separating two liquid reservoirs. By drilling a tiny pore just a few-nanometers in diameter, called a nanopore, in the graphene membrane, they were able to measure exchange of ions through the pore and demonstrated that a long DNA molecule can be pulled through the graphene nanopore just as a thread is pulled through the eye of a [more...]

Date: 2010-08-19 07:00:00


Research Associate, Enzyme Screening

Details: We are seeking a highly motivated Research Associate to perform enzyme screening using our single molecule DNA sequencing system. The successful candidate will be detail-oriented, proficient at multitasking, and focused on [more...]

Date: 2010-10-09 05:06:41


Popular Mechanics Posts 2010 BREAKTHROUGH Awards — The Gadgeteer

While working at the National Institutes of Health in the early 1990s, Venter developed a way to rapidly discover genes by exploiting snippets of DNA called expressed sequence tags. In 1992, he founded The Institute for Genomic Research, and, three years later, he and a team decoded the first genome of a free-living organism. That led to Venter’s best-known breakthrough, mapping the human genome. Last May, he achieved a defining moment in the history of biology when he inserted digitally created DNA into a living bacterium, forming the first synthetic life. His ultimate goal is to design [more...]

Date: 2010-09-28 20:43:25


Cancer Genomes — Continuing Progress — NEJM

... we now sit at the beginning of a revolution in cancer genomics resulting from the systematic application of highly parallel, single-molecule DNA-sequencing techniques to a large number of human cancers.1 The prediction is that many [more...]

Date: 2009-09-09 20:56:09


DNA sequencing » Blog Archive » DNA Sequencing Methods

DNA Sequencing – How DNA Sequencing Works – Methods for … An explanation of how DNA sequencing works. … Typically, the automated sequencing method is only accurate for sequences up to a maximum of about 700-800 base-pairs in length. … DNA Sequencing Simulation (Sanger Method) Within each reaction mixture are the following items: a DNA segment of unknown … The other DNA sequencing method (named for Allan Maxam and Walter … Next-Generation DNA Sequencing Methods 921k – Adobe PDF – View as html generation DNA sequencing technologies highlight the striking impact … [more...]

Date: 2010-09-28 04:29:58


Graphene may hold key to speeding up DNA sequencing

Researchers from Harvard University and MIT have demonstrated that graphene, a surprisingly robust planar sheet of carbon just one-atom thick, can act as an artificial membrane separating two liquid reservoirs. By drilling a tiny pore just a few-nanometers in diameter, called a nanopore, in the graphene membrane, the researchers were able to measure exchange of ions through the pore and demonstrate that a long DNA molecule can be pulled through the graphene nanopore just as a thread is pulled through the eye of a needle. "By measuring the flow of ions passing through a nanopore drilled in [more...]

Date: 2010-09-30 15:48:46


PLANT TISSUE CULTURE TECHNIQUE AND PCR TECHNOLOGY

SSR assays require a minimal amount of genomic DNA. Most of the crop improvement programs are confined to evaluation and selection of naturally occurring clonal variations. In vitro culture techniques provide an alternative means of plant propagation and an important tool for crop improvement. The in vitro cultures are also of low risk for genetic variation since it is more resistant to genetic changes while occurrence of cell division in vitro condition. Gel electrophoresis is an important molecular biology tool which enables us to study DNA. It can be used to determine the sequence of [more...]

Date: 2010-09-08 04:07:38


IPO News: Pacific Biosciences of California sets terms for $200 ...

Pacific Biosciences of California, which is developing a system that performs DNA sequencing using single molecule real-time technology, announced terms for its IPO on Tuesday. The Menlo Park, CA-based company plans to raise $200 [more...]

Date: 2010-10-05 13:45:33


FinchTalk: From Reads to Data Sets, Why Next Gen is not like ...

The first widely-used sequencing systems were based on the “Sanger” method. DNA was synthesized in the presence of chain terminating radioactive dideoxy-nucleotides (1). Mixtures of DNA fragments were separated by size using gel electrophoresis and the bases were identified and entered into a computer through manual techniques. Automated DNA sequencing instruments arrived later. These instruments made DNA sequencing thousands of times more efficient by detecting fluorescently labeled fragments and sending the information directly to a computer (2). For the first time, it became possible [more...]

Date: 2009-01-06 19:16:00


Genomics and Gene Sequencing IPOs Booming?

The Company was founded in 2005, has 159 employees, and has a proprietary DNA sequencing platform with integrated software and bioinformatics providing services for genomic based research (see Raygent profile). Applications for the complete genome sequencing services are cancer research, Mendelian Disease research, Rare Variant Disease research, and clinical trial optimization. The Company has raised $95.4M since inception through six VCs and 5% shareholders: Orbimed Advisors, Essex Woodlands Health Ventures, Prospect Venture Partners III, OVP Venture Partners, Enterprise Partners and [more...]

Date: 2010-10-05 04:13:00


.ada.aimi.kisah: dna replication.ape tu?

in this chapter, there's three processes to synthesis protein from DNA. replication(DNA>DNA)> Transcription(DNA>RNA) > Translation(RNA>Protein) just focus on Eukaryotes jea tau. prokaryotes tak masuk dalam syllabus. :) replication of DNA - separation of double strands of DNA is by Helicase. and to prevent the rewinding of the strands, there is SSBp.(Single strand Binding protein) to help. - Leading strand (5' to 3') is copied by DNA Polymerase III which functioned as template for the replication. - lagging strand ( 5' to 3') is produced by DNA Polymerase III and form Okazaki Fragment. [more...]

Date: 2010-08-18 19:04:00


The Structure of the DNA Molecule

Working with nucleotide models made of wire, Watson and Crick attempted to put together the puzzle of DNA structure in such a way that their model would account for the variety of facts that they knew described the molecule. Once satisfied with their model, they published their hypothesis, entitled “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid” in the British journal Nature (April 25, 1953. volume 171:737-738.) It is interesting to note that this paper has been cited over 800 times since its first appearance! Here are their words: “…This (DNA) [more...]

Date: 2010-09-28 22:15:45


DNA strides into organic synthesis

The walker and three 'stations', made from specific DNA sequences, organise themselves along the track using the normal pairing of DNA bases. 'The walker will move unidirectionally along the track,' Liu says. 'We attached chemical reactants to the walker and each station on the track. As the DNA walker moves from station to station, a programmed series of chemical reactions takes place.' The walking strand of DNA moves to each station (blue, red and green) in turn and reacts with the attached reagent © Nature Nanotechnol. In this way, the Harvard team was able to perform three acylation [more...]

Date: 2010-10-10 22:46:00


DNA Sequencing Development Scientists – Company Confidential ...

scientists, nad computer scientists. Must have single molecule or nanotechnology experience. Excellent pay, perks, and stock options. Thanks for your… From ActiveHire – 23 Sep 2010 01:11:16 GMT – job details – View all Boston jobs View full post on nanotechnology Jobs | [more...]

Date: 2010-09-23 02:00:05


Helicos sequencing: Single-Molecule DNA Sequencing of a Viral ...

Single-Molecule DNA Sequencing of a Viral Genome Timothy D. Harris, Phillip R. Buzby, Hazen Babcock, Eric Beer, Jayson Bowers, Ido Braslavsky, Marie Causey, Jennifer Colonell, James DiMeo, J. William Efcavitch, Eldar Giladi, Jaime Gill, John Healy, Mirna Jarosz, Dan Lapen, Keith Moulton, Stephen R. Quake, Kathleen Steinmann, Edward Thayer, Anastasia Tyurina, Rebecca Ward, Howard Weiss, and Zheng Xie (4 April 2008) Science 320 (5872), 106. The M13 viral genome has been resequenced by a single-molecule method that allows simultaneous sequencing of 280,000 [more...]

Date: 2008-04-04 15:36:31


Venture Development Center NobleGen Biosciences joins VDC

With a proof of concept in hand, startup NobleGen Biosciences is setting up at the VDC to develop and commercialize a single-molecule sequencing technology that uses arrays of solid-state nanopores and optical detection. The method comes from the lab of Amit Meller at BU and colleagues at the University of Massachusetts Medical School. Meller filed his first patents on the technology while working at Harvard. NobleGen recently licensed a patent portfolio from Harvard and BU that includes additional IP from Meller’s research at BU. The company is led by CEO Frank Feist and Phil Buzby, former [more...]

Date: 2010-10-06 12:41:09


EpiCentral: Examining blocking lesions in ancient DNA

Blocking lesions prevent amplification and sequencing of affected molecules, thus limiting the analysis of DNA derived from ancient samples. Heyn et al. recently developed a new method--polymerase extension profiling (PEP)--that reveals occurrences of polymerase stalling on DNA templates. This sequencing-based technology allows detection of damage on a single-molecule level. The technique used CircLigase™ ssDNA Ligase for high-efficiency ligation of single-stranded adaptors (containing the Roche 454 A sequence) to the 3’ ends of primer-extension products. The authors found evidence of [more...]

Date: 2010-10-07 20:29:00


Nanotechnology could provide a rapid DNA sequencing and economic

These last three years, a third generation methods, ” Single Molecule Sequencing Real Time ” made its appearance . She is already using nanotechnology in progress to optimize the pyrosequencing methods . It is again to build the complementary strand of DNA using an enzyme. This time , the fluorophores are directly attached to nucleotides . A nanophotonic structure , called “zero -mode wave guide ” , composed of holes 70 nm in diameter and 100 nm long in a layer of aluminum deposited on a glass ensures effective detection of light signals and allows parallel sequencing many strands . [more...]

Date: 2010-09-06 16:19:36


Craig Venter Profile - Breakthrough Leadership Winner Craig Venter ...

Having a clear definition of which genes are essential is going to be important for future design projects. As the population goes from 6.8 billion people to more than 9 billion over the next 40 years, we’re going to need a lot more food, clean water, medicine and fuel to power all these things. We’re now a society that’s 100 percent dependent on science for our survival. It’s not a gentleman’s sport. We think this is one of the most powerful tools—at least on the biology side—that we can apply to all these critical needs. Q: How did a former surf bum, as some have called you, make [more...]

Date: 2010-10-04 11:30:00


Pacific Biosciences Adds More Than $50 Million

“We believe Pacific Biosciences' third-generation, single-molecule sequencing technology has the potential to play an important long-term role in strategically valuable, high-growth clinical diagnostics markets such as oncology, [more...]

Date: 2010-06-18 12:28:48


Optical Recognition of Converted DNA Nucleotides for Single ...

Nano Letters, Volume 10, Issue 6, Page 2237-2244, June 9, [more...]

Date: 2010-06-09 04:49:07


Visualising DNA sequences

Current single molecule mapping methods have a timeframe of around one week for analysing individual genomes.  Kalim Mir, an expert in DNA sequencing and genomics at the Wellcome Trust Centre for Human Genetics, University of Oxford, comments, ‘the advantage the system has over conventional optical mapping is that it can provide ultra-high density mapping of genomic DNA and could easily be extended to much longer fragments from larger genomes, from bacteria to humans. The most significant challenge the authors face is to scale the technique up to the human genome.’  The group now plan [more...]

Date: 2010-08-16 15:07:06


Ultrafast EMCCD cameras point the way to faster DNA sequencing

To harness this powerful single-molecule detection modality for high-throughput DNA sequencing, each of the four nucleotides (A, C, G and T) in the target DNA has to be converted into a predefined sequence of oligonucleotides, using a technique called Circular DNA Conversion. Each pre-defined sequence is then hybridized to a self-quenching molecular beacon.In their experimental setup, the Meller team recorded DNA translocation through a 4nm pore in a SiN membrane immersed between two aqueous solutions. With the camera in place, the researchers were able to detect florescence bursts in two [more...]

Date: 2010-06-10 07:00:00


csirhrdg.res.in | CSIR UGC NET 2011 Life Science Syllabus 2011 ...

Analysis of RNA, DNA and proteins by one and two dimensional gel electrophoresis, Isoelectric focusing gels. Molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems. Expression of recombinant proteins using bacterial, animal and plant vectors. Isolation of specific nucleic acid sequences Generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC and YAC vectors. In vitro mutagenesis and deletion techniques, gene knock out in bacterial and eukaryotic organisms. Protein sequencing methods, detection of post translation modification of proteins. DNA [more...]

Date: 2008-06-21 07:00:00


Leading Edge DNA Sequencing Method Nets Major NIH

Described in the May 12 online edition of Nano Letters, their novel, highly efficient, optically-based method to detect single DNA molecules in nanopores could significantly reduce the cost of DNA sequencing and the time required to sequence a complete human genome. “We are the first to employ optical detection from individual nanopores, and this allows us to probe multiple pores simultaneously using a single high-speed CCD camera,” said Meller, referring to the charge-coupled devices that science and medical researchers use to obtain high quality images. “As a result, our method can [more...]

Date: 2010-09-13 04:00:00


New Paper Shows Enzyme-Controlled Movement of DNA Polymer Through ...

This paper addresses a key challenge for DNA strand sequencing: fine control of the translocation of the DNA strand through the nanopore, at a rate that is consistent and slow enough to enable accurate identification of individual DNA bases. The Nature Nanotechnology work shows for the first time that the motion of a strand can be controlled using electronic feedback and that an enzyme can move a strand against a field while located on top of the nanopore. "The techniques described in this paper are an advance towards electronic, single molecule DNA sequencing of DNA strands" said [more...]

Date: 2010-09-28 17:46:34


DNA Replication

How does DNA replicate?The DNA molecule consists of two strands held collectively by hydrogen bonds. DNA replication commences together with the breaking of those bonds, by the motion within the enzyme helicase, with a purpose to yield two father or mother strands. This construction, of unpaired DNA, is known as the DNA fork. Considering that the bottom sequence of your two strands is complementary to one another, they have to be replicated by two completely different mechanisms i.e. the foremost chain process as well as lagging chain system. Within the principal chain device and enzyme named [more...]

Date: 2010-10-09 06:44:35


Basics: Sequencing DNA, Part 1 « Genetic Inference

However, in certain respects Sanger Sequencing is still top-of-the-range. The 4-channel capillary approach lets you sequence DNA pretty fast, and each machine can often do hundreds of reactions at once. It was these machines that first sequenced the human genome. In addition, you can sequence relatively long sequences of DNA; up to 1000 nucleotides (after that, it gets difficult to tell the difference between molecules of different sizes). We have yet to make a machine that can sequence DNA fragments of this length faster than Sanger Sequencing (yet…). The modern Sanger Sequencing machines [more...]

Date: 2009-04-17 21:31:39


Heliscope builds world's fastest DNA sequencer | Singularity Hub

The Short: Technology Review reports that for just $1,350,000 USD you can have have the worlds fastest commercially available DNA sequencer, called the Heliscope. The machine developed by Helicos BioSciences takes just one hour to read 1.3 billion base pairs from a strand of DNA. Here is a picture of the beauty: HeliScope™ Single Molecule Sequencer The Long: The Heliscope is being marketed as a DNA microscope. It is unique in the field of DNA sequencing because it sequences an actual DNA strand whereas most other sequencing technologies use PCR to create millions of copies of an original [more...]

Date: 2008-07-14 16:58:33


My Helical Tryst: Single Molecule DNA Sequencing

There are a number of companies that have recently launched competing technology platforms that are capable of sequencing DNA at the single molecule level. You may ask, why? Well, the answer is simply cost-effectiveness. DNA sequencing technology has been around for several decades, and to date, the Human Genome Project (HGP) is considered the pinnacle application of that technology. The cost of the HGP was approximately $3 billion and took about a decade and half. It was the molecular biology equivalent of putting a man on the moon. But what is the next step? Well, if we can systematically [more...]

Date: 2009-02-11 22:17:00


Harvard-MIT study examines Graphene | UWIRE

Pore length is crucial when identifying individual DNA bases, Branton said, adding that the study “represents the first time that a molecule—DNA in our case—has been put through a nanopore that is extremely short.” Scientists in the past have studied protein-based nanopores that span five to 10 nanometers in length. But because the distance between two bases in a DNA molecule is 0.5 nanometers, such pores are ineffective, as they obstruct the resolution of 10 to 15 bases at a time. In contrast, graphene nanopores—which span a length of 0.5 nanometers—allow a single base to occupy [more...]

Date: 2010-10-05 20:48:04


Chemistry World blog » Chemistry World's weekly round-up of money ...

Oxford Nanopore has secured £17.4 million in new funding to develop its label-free single molecule DNA sequencing platform based on protein nanopores (see this Chemistry World article for more details), as well as related projects on protein analysis. The cash came from a mixture of existing and new investors including the company’s marketing partner, Illumina, which has already invested £11.8 million in the company. Phillip Broadwith and Matt [more...]

Date: 2010-02-05 16:02:54


Slowing the translocation of double-stranded DNA using a nanopore ...

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA [more...]

Date: 2010-09-02 17:18:59


Fastest Evolving Technology – DNA Sequencing | Impact Lab

Human DNA sequence Investing in technology-driven fields is risky, especially when everyone touts them as the Next Big Thing. Sure, it’s easy to see quick gains, but you’re just as likely to see those gains vanish as the next-generation technology sneaks in and replaces it — the disruptor becomes the disrupted, so to speak. Perhaps the fastest evolving technology right now isn’t computer tech, but rather is found in DNA sequencing. We’ve gone from sequencing the first genome for about $2.7 billion in the Human Genome Project just a few years ago and rather quickly come down to [more...]

Date: 2009-08-24 22:52:00


New nanopore method for DNA sequencing

(Nanowerk News) Sequencing DNA could get a lot faster and cheaper – and thus closer to routine use in clinical diagnostics – thanks to a new method developed by a research team based at Boston University. The team has demonstrated the first use of solid state nanopores — tiny holes in silicon chips that detect DNA molecules as they pass through the pore — to read the identity of the four nucleotides that encode each DNA molecule. In addition, the researchers have shown the viability of a novel, more efficient method to detect single DNA molecules in nanopores. "We have employed, for the [more...]

Date: 2010-05-21 06:27:21



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