Biocurious

/ a biophysics blog

DNA Conductivity, Finally?

Posted 15 March 2008 by Andre under

Last month, there was a Nature Nanotechnology article [abstract, full text is toll access] reporting new measurements of DNA conductivity from Jacqueline Barton’s and Colin Nuckolls’ groups.

The team began with a nanotube—a tiny tube of carbon about as thick as DNA itself—that was integrated within a simple electrical circuit. A 6-nm section of the nanotube was removed using plasma ion etching. This procedure not only cuts the tube, but also oxidizes the remaining tips. This makes it possible to bridge the gap with a DNA molecule with ends that have been designed to form strong chemical bonds with the oxidized tips.

This meant that they had a reliable, well defined connection between the bridging DNA molecules and the nanotube electrodes that allowed them to do their measurements in water at room temperature. Since everything is bathed in water they could add a DNA cutting enzyme to show that this breaks the circuit they formed and could also de-hybridze their bridging double strands, leaving only a single strand with a known sequence. Then, by flowing in an almost complementary strand, they could measure the effect of single base mismatches. Even a single mismatch increased the DNA’s resistance by 300 fold.

This structural sensitivity poses a significant challenge to anyone dreaming of making self-assembled circuits directly from DNA, but their system might also make a nice miniaturizable device for detecting single nucleotide polymorphisms, or SNPS. For this to be feasible, one of the first things they would need to improve is the rate at which they get successful DNA bridging. Right now it’s a bit low for commercial applications with their method producing “10 working devices out of 370 that were tested.”

For more, check out my news story at physicsworld.com.

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A New Kind of Conduction in DNA?

Posted 4 January 2008 by Andre under

My latest Physics World news story discusses some recent work on DNA conduction [free signup required to read the whole article]:

Not long after the double-stranded structure of DNA was revealed by Watson and Crick in 1953, scientists suspected that the molecule might support electrical conduction. This is because the bases in the middle of the double helix stack in a way reminiscent of graphite – which is an excellent conductor. At about the same time, the physicist Leon Brillouin suggested that the DNA backbone, rather than the bases, might support conduction because of its periodic structure.

While the conductive properties of DNA have been studied using a wide range of techniques, most experiments have focused on understanding conduction in terms base stacking and have yielded conflicting results. Alternative or complementary conduction mechanisms – such as Brillouin’s backbone conduction – have been largely ignored.

Now there’s been some new experimental work by Hiromi Ikeura-Sekiguchi and Tetsuhiro Sekiguchi that shows that electrons can in fact delocalize through the backbone of DNA as well:

What they found is that electrons in the backbone delocalize in less than one femtosecond (10-15) in wet DNA. These results imply that electron movement occurs a thousand times faster in the DNA backbone than in the bases stacked in the core.

This work is important because it might help to reconcile some of the seemingly contradictory conduction measurements made so far and it might spark some new ideas on re-engineering DNA to improve its electronic properties but what I found most interesting about this field from my background reading for the story are the potential biological implications of DNA conduction.

One interesting possibility is that enzymes communicate through DNA conduction in order to efficiently find sites of DNA damage that need repairing. This idea has been proposed by Jacqueline Barton, one of the people responsible for a resurgence of interest in DNA conduction in the early 1990s. It has also been proposed that DNA conduction could allow cathodic protection of important segments of DNA by transporting holes injected by oxidants to sites where the damage would have a smaller biological impact. This is one of those ideas that has a nice balance of craziness, potential importance, and plausibility. It might even turn out to be true.

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Protein calms the waters

Posted 20 November 2007 by Andre under

Here’s my latest Physicsworld.com news story:

Living organisms contain both proteins and water and the complex interactions between the two are thought to be the driving force behind many biological processes.

Now, biophysicists in the US have discovered that a protein called myoglobin can coordinate the motion of surrounding water molecules, slowing them down significantly – perhaps to allow certain interactions to occur (PNAS 104 18461). The team has also shown that the motion of these water molecules can be associated with the shape and function of the protein – information that could improve computer simulations of protein dynamics and lead to a better understanding of diseases like Alzheimer’s and Parkinson’s, which involve drastic protein shape changes.

The rest of the article is here and the original article is available from the author’s website [pdf].

They measured the ultrafast decay of fluorescence from tryptophans after they were excited by femtosecond pulses of UV. To get information over the surface of the protein they did a tryptophan scan and I’m sure it was a lot of work to prepare all those mutants so it’s nice that they could see some systematic trends in hydration dynamics with local surface charge.

Since Philip is the one doing ultrafast protein stuff now we can ask him to comment.

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