Researchers report novel approach for single molecule electronic DNA sequencing

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Researchers report novel approach for single molecule electronic DNA sequencing

September 21, 2012

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. (Phys.org)—

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.

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, from the Nature Publication group.

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Researchers extract, sequence spider DNA from spider web
Nov. 25, 2015 - The study's authors want to follow up their study with more field tests involving a wider array of species.

As part of a recent proof-of-concept study, scientists at the University of Notre Dame successfully sequenced DNA extracted from spider web samples. In analyzing the DNA, researchers were able to correctly identify the spider who wove the threads and the insect victims who became the arachnid architect's dinner.

Their successes are described in a new paper, published this week in the journal PLOS ONE. For the experiment, scientists fed black widow spiders house crickets, and then took web samples and extracted mitochondrial DNA. Perfecting noninvasive DNA sampling could help researchers monitor and study a variety of species without interfering.

The noninvasive extraction and sequencing process could be tweaked for use in conservation research, pest control and biodiversity surveys. But the study's authors say more field tests involving a wider array of species is necessary to confirm the broader potential of their early findings. "Sticky spider webs are natural DNA samplers, trapping nearby insects and other things blowing in the wind," study author Charles Cong Xu said in a press release. "We see potential for broad environmental monitoring because spiders build webs in so many places."

Researchers extract, sequence spider DNA from spider web

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Scientists induce flatworms to grow head, brains of other species
Nov. 24, 2015 - Researchers hope their findings will improve birth defect treatments and tissue regeneration technology.

Without manipulating their DNA, researchers at Tufts University have induced flatworms to grow heads and brains of another species of flatworm. By manipulating the worms' electrical synapses, biologists coaxed the specimens into growing different types of heads and brains. The research is proof of a new types of physiological governing systems, separate from the genome. "It is commonly thought that the sequence and structure of chromatin -- material that makes up chromosomes -- determine the shape of an organism, but these results show that the function of physiological networks can override the species-specific default anatomy," researcher Michael Levin, director of Tufts' Center for Regenerative and Developmental Biology, said in a press release. "By modulating the connectivity of cells via electrical synapses, we were able to derive head morphology and brain patterning belonging to a completely different species from an animal with a normal genome."

Researchers manipulated the electrical synapses of flatworms to induce the worms to grow the heads and brains of other species.​

Scientists attempted to induce the regeneration of a variety of head types, and found the easiest were the heads and brains of those to whom the flatworm was most closely related to on the evolutionary timeline. By better understanding the interactions between genes and bioelectrical circuitry, researchers hope they can improve birth defect treatments and tissue regeneration technology.

The new research was detailed in a new paper, published this week in the International Journal of Molecular Sciences. "We've demonstrated that the electrical connections between cells provide important information for species-specific patterning of the head during regeneration in planarian flatworms," said first author Maya Emmons-Bell, an undergraduate at Tufts. "This kind of information will be crucial for advances in regenerative medicine, as well as a better understanding of evolutionary biology." But unlike experiments which have used gene manipulation to coax different shaped bodies and features from flatworms, the morphological changes weren't permanent. The flatworms reverted to their original anatomy after a few weeks. Researchers plan to do further testing to figure out how this works.

Scientists induce flatworms to grow head, brains of other species