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February 12, 2010

DNA Nucleosides in a Tunneling Gap and Carbon Nanotube Nanopore DNA Reading Could Speed DNA Sequencing 1000 Times

Tunneling measurements with functionalized electrodes. (A) A gold probe and a gold substrate are functionalized with a monolayer of 4-mercaptobenzoic acid, and the size of the gap between two electrodes maintained under servo control at a value such that the two monolayers do not interact with one another, resulting in a tunnel current signal that is free of spikes (B). When a solution of nucleosides is introduced, current spikes appear, as shown here for24 0.7 μM deoxyadenine in trichlorbenzene with a baseline tunneling current of 6 pA at a bias of 0.5 V (C). Hydrogen-bonding schemes for all four nucleosides are shown in panels D-F. “S” represents the modified deoxyribose sugar (Supporting Information) and the hydrogen bonds are circled.

Arizona State University scientists have come up with a new twist in their efforts to develop a faster and cheaper way to read the DNA genetic code. They have developed the first, versatile DNA reader that can discriminate between DNA's four core chemical components⎯the key to unlocking the vital code behind human heredity and health.

The present work shows that the two major impediments to sequence readouts by tunnelings - a wide range of molecular orientations and a large contact resistancescan be overcome using functionalized electrodes.

Next, Stuart Lindsay's group is hard at work trying to adapt the reader to work in water-based solutions, a critically practical step for DNA sequencing applications. Also, the team would like to combine the reader capabilities with the carbon nanotube technology to work on reading short stretches of DNA.

If the process can be perfected, DNA sequencing could be performed much faster than current technology, and at a fraction of the cost

In the current issue of Science, Stuart Lindsay, director of Arizona State University's Center for Single Molecule Biophysics at the Biodesign Institute, along with his colleagues, demonstrates the potential of one such method in which a single-stranded ribbon of DNA is threaded through a carbon nanotube, producing voltage spikes that provide information about the passage of DNA bases as they pass through the tube — a process known as translocation.

The team carried out molecular simulations to try to determine the mechanism for the anomalously large ionic currents detected in the nanotubes. Observation of current-voltage curves registered at varying ionic concentrations showed that ion movement through some of the tubes is very unusual, though understanding the precise mechanism by which DNA translocation gives rise to the observed current spikes will require further modeling. Nevertheless, the characteristic electrical signal of DNA translocation through tubes with high ionic conductance may provide a further refinement in ongoing efforts to apply nanopore technology for rapid DNA sequencing.

Critical to successful rapid sequencing through nanopores is the precise control of DNA translocation. The hope is that genetic reading can be significantly accelerated, while still allowing enough time for DNA bases to be identified by electrical current traces. Carbon nanotubes provide an attractive alternative, making the control of nanopore characteristics easier and more reliable.

If the process can be perfected, Lindsay emphasizes, DNA sequencing could be carried out thousands of times faster than through existing methods, at a fraction of the cost.



Nanoletters - Electronic Signatures of all Four DNA
Nucleosides in a Tunneling Gap


Nucleosides diffusing through a 2 nm electron-tunneling junction generate current spikes of sub-millisecond duration with a broad distribution of peak currents. This distribution narrows 10-fold when one of the electrodes is functionalized with a reagent that traps nucleosides in a specific orientation with hydrogen bonds. Functionalizing the second electrode reduces contact resistance to the nucleosides, allowing them to be identified via their peak currents according to deoxyadenosine > deoxycytidine > deoxyguanosine > thymidine, in agreement with the order predicted by a density functional calculation.



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