Nanotechnology Now

Our NanoNews Digest Sponsors





Heifer International

Wikipedia Affiliate Button


android tablet pc

Home > Press > Researchers Report Novel Approach for Single Molecule Electronic DNA Sequencing

Schematic of single molecule DNA sequencing by a nanopore with phosphate-tagged nucleotides. Each of the four nucleotides will carry a different tag. During SBS, these tags, attached via the terminal-phosphate of the nucleotide, will be released into the nanopore one at a time where they will produce unique current blockade signatures for sequence determination. A large array of such nanopores will lead to high throughput DNA sequencing.
Schematic of single molecule DNA sequencing by a nanopore with phosphate-tagged nucleotides. Each of the four nucleotides will carry a different tag. During SBS, these tags, attached via the terminal-phosphate of the nucleotide, will be released into the nanopore one at a time where they will produce unique current blockade signatures for sequence determination. A large array of such nanopores will lead to high throughput DNA sequencing.

Abstract:
DNA sequencing is the driving force behind key discoveries in medicine and biology. For instance, the complete sequence of an individual's genome provides important markers and guidelines for medical diagnostics and healthcare. Up to now, the major roadblock has been the cost and speed of obtaining highly accurate DNA sequences. While numerous advances have been made in the last 10 years, most current high-throughput sequencing instruments depend on optical techniques for the detection of the four building blocks of DNA: A, C, G and T. To further advance the measurement capability, electronic DNA sequencing of an ensemble of DNA templates has also been developed. Recently, it has been shown that DNA can be threaded through protein nanoscale pores under an applied electric current to produce electronic signals at single molecule level. However, because the four nucleotides are very similar in their chemical structures, they cannot easily be distinguished using this technique. Thus, the research and development of a single-molecule electronic DNA sequencing platform is the most active area of investigation and has the potential to produce a hand-held DNA sequencer capable of deciphering the genome for personalized medicine and basic biomedical research.

Researchers Report Novel Approach for Single Molecule Electronic DNA Sequencing

New York, NY | Posted on September 22nd, 2012

A team of researchers at Columbia University, headed by Dr. Jingyue Ju (the Samuel Ruben-Peter G. Viele Professor of Engineering, Professor of Chemical Engineering and Pharmacology, Director of the Center for Genome Technology and Biomolecular Engineering), with colleagues at the National Institute of Standards and Technology (NIST) led by Dr. John Kasianowicz (Fellow of the American Physical Society), have developed a novel approach to potentially sequence DNA in nanopores electronically at single molecule level with single-base resolution. This work, entitled "PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis" is now available in the open access online journal, Scientific Reports (2, 684 DOI:10.1038/srep00684, 2012),from the Nature Publication group.

The reported nanopore-based sequencing by synthesis (Nano-SBS) strategy can accurately distinguish four DNA bases by detecting 4 different sized tags released from 5'-phosphate-modified nucleotides at the single molecule level for sequence determination. The basic principle of the Nano-SBS strategy is described as follows. As each nucleotide analog is incorporated into the growing DNA strand during the polymerase reaction, its tag is released by phosphodiester bond formation. The tags will enter a nanopore in the order of their release, producing unique ionic current blockade signatures due to their distinct chemical structures, thereby determining DNA sequence electronically at single molecule level with single base resolution. As proof-of-principle, the research team attached four different length polymer tags to the terminal phosphate of 2'-deoxyguanosine-5'-tetraphosphate (a modified DNA building block) and demonstrated efficient incorporation of the nucleotide analogs during the polymerase reaction, as well as better than baseline discrimination among the four tags at single molecule level based on their nanopore ionic current blockade signatures. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.

In previous work, the Center of Genome Technology & Biomolecular Engineering at Columbia University, led by Professor Ju and Dr. Nicholas J. Turro (William P. Schweitzer Professor of Chemistry), developed a four-color DNA sequencing by synthesis (SBS) platform using cleavable fluorescent nucleotide reversible terminators (NRT), which is licensed to Intelligent Bio-Systems, Inc., a QIAGEN company. SBS with cleavable fluorescent NRTs is the dominant approach used in the next generation DNA sequencing systems. Dr. Kasianowicz and his group at NIST pioneered the investigation of nanopores for single molecule analysis. They previously reported that different length polymers, polyethylene glycols (PEGs), could be distinguished by their unique effects on current readings in a α-hemolysin protein nanopores at single molecule level and subsequently developed a theory for the method. Their results provide the proof-of-concept for single molecule mass spectrometry. The combination of the SBS concept with the distinct nanopore-detectable electronic tags to label DNA building blocks led to the development of the single-molecule electronic Nano-SBS approach described the current Scientific Reports article (09/21/2012).

As lead author Dr. Shiv Kumar points out, "The novelty of our approach lies in the design and use of four differently tagged nucleotides, which upon incorporation by DNA polymerase, release four different size tags that are distinguished from each other at the single molecule level when they pass through the nanopore. This approach overcomes any constraints imposed by the small differences among the four nucleotides, a challenge which most nanopore sequencing methods have faced for decades." Moreover, the technique is quite flexible; with PEG tags as prototypes, other chemical tags can be chosen to provide optimal separation in different nanopore systems.

With further development of this Nano-SBS approach, such as the use of large arrays of protein or solid nanopores, this system has the potential to accurately sequence an entire human genome rapidly and at low cost, thereby enabling it to be used in routine medical diagnoses.

The authors of the Scientific Reports article were Shiv Kumar, Chuanjuan Tao, Minchen Chien, Brittney Hellner, Arvind Balijepalli, Joseph W.F. Robertson, Zengmin Li, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, and Jingyue Ju. The study was supported by a grant from the National Institutes of Health, a National Research Council/NIST/NIH Research Fellowship, and a grant from the NIST Office of Law Enforcement Standards.

####

For more information, please click here

Contacts:
Beth Kwon

212-854-6581

Copyright © Columbia University

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related News Press

News and information

Silicene Labs Announces the Launch of Patent-Pending, 2D Materials Composite Index™ : The Initial 2D Materials Composite Index™ for Q2 2014 Is: 857.3; Founders Include World-Renowned Physicist and Seasoned Business and IP Professionals July 24th, 2014

Iranian Scientists Produce Transparent Nanocomposite Coatings with Longer Lifetime July 24th, 2014

Deadline Announced for Registration in 7th Int'l Nanotechnology Festival in Iran July 23rd, 2014

A Crystal Wedding in the Nanocosmos July 23rd, 2014

Govt.-Legislation/Regulation/Funding/Policy

NNCO Announces an Interactive Webinar: Progress Review on the Coordinated Implementation of the National Nanotechnology Initiative 2011 Environmental, Health, and Safety Research Strategy July 23rd, 2014

Nano-sized Chip "Sniffs Out" Explosives Far Better than Trained Dogs: TAU researcher's groundbreaking sensor detects miniscule concentrations of hazardous materials in the air July 23rd, 2014

NIST shows ultrasonically propelled nanorods spin dizzyingly fast July 22nd, 2014

Penn Study: Understanding Graphene’s Electrical Properties on an Atomic Level July 22nd, 2014

Nanomedicine

Researchers create vaccine for dust-mite allergies Main Page Content: Vaccine reduced lung inflammation to allergens in lab and animal tests July 22nd, 2014

NIST shows ultrasonically propelled nanorods spin dizzyingly fast July 22nd, 2014

SentiMag® Now Available in Australia and New Zealand July 21st, 2014

More than glitter: Scientists explain how gold nanoparticles easily penetrate cells, making them useful for delivering drugs July 21st, 2014

Discoveries

Iranian Scientists Produce Transparent Nanocomposite Coatings with Longer Lifetime July 24th, 2014

UCF Nanotech Spinout Developing Revolutionary Battery Technology: Power the Next Generation of Electronics with Carbon July 23rd, 2014

A Crystal Wedding in the Nanocosmos July 23rd, 2014

Nano-sized Chip "Sniffs Out" Explosives Far Better than Trained Dogs: TAU researcher's groundbreaking sensor detects miniscule concentrations of hazardous materials in the air July 23rd, 2014

Announcements

Silicene Labs Announces the Launch of Patent-Pending, 2D Materials Composite Index™ : The Initial 2D Materials Composite Index™ for Q2 2014 Is: 857.3; Founders Include World-Renowned Physicist and Seasoned Business and IP Professionals July 24th, 2014

Iranian Scientists Produce Transparent Nanocomposite Coatings with Longer Lifetime July 24th, 2014

Deadline Announced for Registration in 7th Int'l Nanotechnology Festival in Iran July 23rd, 2014

A Crystal Wedding in the Nanocosmos July 23rd, 2014

Nanobiotechnology

Production of Non-Virus Nanocarriers with Highest Amount of Gene Delivery July 17th, 2014

Physicists Use Computer Models to Reveal Quantum Effects in Biological Oxygen Transport: The team solved a long-standing question by explaining why oxygen – and not deadly carbon monoxide – preferably binds to the proteins that transport it around the body. July 17th, 2014

Tiny DNA pyramids enter bacteria easily -- and deliver a deadly payload July 9th, 2014

Artificial cilia: Scientists from Kiel University develop nano-structured transportation system July 4th, 2014

NanoNews-Digest
The latest news from around the world, FREE



  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoTech-Transfer
University Technology Transfer & Patents
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More














ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project







© Copyright 1999-2014 7th Wave, Inc. All Rights Reserved PRIVACY POLICY :: CONTACT US :: STATS :: SITE MAP :: ADVERTISE