Gene genie

There’s a lot of cool things you can do with DNA – much better than the stuff I see in CSI on an almost nightly basis…

The last week or so has brought us a few more examples, including a self-assembled DNA bipyramid in yesterday’s JACS ASAP from Turberfield’s group at Oxford. This follows hot on the heels of a review article he wrote with Jonathan Bath that appears in our current issue of Nature Nanotechnology – free access here.

In addition, Ned Seeman from NYU – who was featured in our Reactions series last week – has a paper in yesterday’s Nano Lett. ASAP on DNA nanotubes. Finally, there’s a DNA catenane paper from last week’s JACS ASAP, that uses everyone’s favourite – click chemistry.

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

Crazy frogs

A paper in PNAS has just caught my eye, because it emphasizes a problem common in natural product research – where do these funky molecules really originate?

This collaborative effort looks at alkaloids — including the synthetically challenging pumiliotoxins — that are isolated from Oophaga pumilio poison frogs. But these toxic amphibians don’t make the alkaloids themselves. It turns out that they get them by eating mites. What’s more, these mites contain lots of new alkaloids that hadn’t previously been discovered.

This reminded me of a story I once heard about another famous natural product, epibatidine, which was also isolated from a frog. Someone had the bright idea of farming the frogs, so that the precious compound could be harvested. But the farmed frogs didn’t have any epibatidine in their skins, because they hadn’t been eating the right food. Bang goes another brilliant idea…

So the next time you see a natural product synthesis, think of the story behind the compound, and the complex biological chains that originally led to it. Not forgetting of course, the unsung heroes who chase insects all over Costa Rica to work out the links of these chains.

Andy

PS If you’re interested in other tales of natural product isolation, have a look at this paper in Angewandte Chemie which reports the identification of Platencin (an antibiotic structurally related to platensimycin, which was reported in Nature last year).

Andrew Mitchinson (Associate Editor, Nature)

Nanotubes – Pasteurized!

I don’t often plug Nature Nanotechnology papers here on the blog, but I couldn’t resist this one… (mostly because of the title I get to use!)

A couple of days ago we published a paper on our website by Naoki Komatsu and co-workers, entitled, “Optically active single-walled carbon nanotubes”. As we all know, however you go about cooking up a batch of nanotubes, you get a mixture – different diameters, different lengths and different chiralities. Now, what is meant by ‘different chiralities’ in this context, is different degrees of twist when you roll up your graphene sheet – not really ‘chirality’ as the chemist knows it. Methods have been developed to sort carbon nanotubes by length and diameter (and also by degree of twist to some extent – see this free paper here and associated News & Views article here).

What is largely ignored/forgotten, is that chiral nanotubes are, wait for it…, chiral! They come as left- and right-handed forms, depending on which may you roll your graphene sheet, i.e., you can either curl the edges up and over to form a tube, or down and under. (If you want to try this at home, take a couple of overhead transparencies – for those of you under 25 years of age, you may want to look up what one of those is – and draw a hexagonal lattice on each one and roll them up in opposite directions – hey presto, enantiomeric nanotubes!).

Now, Pasteur, all those years ago, separated the enantiomers of tartaric acid by painstakingly sorting through mirror-image crystals, presumably with a microscope and a pair of tweezers. What Komatsu and colleagues have done is to make what they call ‘nano-tweezers’ – chiral gable-type diporphyrins that can discriminate between left- and right-handed nanotubes. One enantiomer of the nano-tweezers forms a stronger complex with either the left- or right-handed nanotubes and these diastereoisomers have different solubility properties, which means that they can be separated by centrifugation. You can then wash away the tweezers and record a CD spectrum of your resolved nanotubes!

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

I’d like to buy the world a Coke

The office coffee machine broke down this morning, so I’ve been using Coca-Cola to fight off the postprandial dip. I rarely drink soda (aside from the occasional Cuba Libre), so I’m usually the last to know about (crazy) new kinds of soda. But there’s a case of Diet Coke Plus in our office refrigerator – you might not have seen it in your local supermarket, but it’s a new version of Diet Coke that contains several vitamins and minerals:

Each eight-ounce serving of Diet Coke Plus provides a good source of Niacin (vitamin B3), vitamins B6 and B12, zinc and magnesium (15% Daily Value [DV] for Niacin, B6 and B12, 10% DV for zinc and magnesium).

Great news, no? Now you don’t have to take that pesky multi-vitamin every day. Just have a few cans of Diet Coke Plus and you’ll be all set…

Not a fan of Diet Coke? Not a problem: PepsiCo is responding with the launch of Tava this fall, which will contain “”https://www.iht.com/articles/2007/03/07/business/soda.php?page=1">vitamins B3, B6 and E, and chromium." (Chromium?)

I’m just waiting for them to combine soft drinks with OTC medication: “have a hangover and can’t stay awake at your morning meeting? Try new Coke NSAID – it comes in two flavors: cherry aspirin and vanilla ibuprofen…” Yum…

Joshua

Joshua Finkelstein (Senior Editor, Nature)

Reactions – Nadrian Seeman

1. What made you want to be a chemist?

I took high school biology from a person who spent the first third of a semester teaching us about atoms and molecules, because he saw life as a chemical phenomenon. I’ve been entranced with the edge of life ever since, and have spent my entire career on that cusp, sometimes venturing into biology, and sometimes into chemistry. The structural beauty of crystallography and informational nature of nucleic acids seduced me into working at their interface. Being able to make things, rather than just analyze them, vectored me into structural DNA nanotechnology.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

Chemistry gives me an outlet for my creative urges. If I couldn’t do that, I’d probably try to be an artist (though I lack talent in that direction). I’m a totally visual person, with not a lot of response to acoustic phenomena.

3. How can chemists best contribute to the world at large?

By doing what they do – creating and analyzing new forms of matter, and gaining control over the structure of matter on the finest possible scale. Saying that, one cannot forget that chemists are subject to the same social responsibilities as other citizens of the world, and they must recognize them.

4. Which historical figure would you most like to have dinner with – and why?

Probably one of the early empiricists, such as Bacon. It was a huge conceptual leap to go from arguing about what might happen in some circumstances, to actually looking to find out. I would hope my dinner companion had eclectic culinary tastes.

5. When was the last time you did an experiment in the lab – and what was it?

I’ve never done much in the wet lab. Mostly, I’ve programmed and modeled. I continue to model.

6. If exiled on a desert island, what one book and one CD would you take with you?

My favorite author is Thomas Pynchon, but if exiled alone on a desert island, his paranoiac tilt would not resonate with the isolated circumstances. I’d probably try to take a book on how to build boats from earth, air, fire and water, or more conducive materials if they were present. I don’t listen to music, so I would trade in the CD for a DVD, probably of ‘Casablanca’.

Ned Seeman is in the Department of Chemistry at New York University and works on structural DNA nanotechnology. He builds objects, lattices, and nanomechanical devices from DNA.

Ich muss einen Blog schreiben…

So I’ve just returned from Germany, one of many lands of superior chocolate goodies… Oops – that’s not related.

Anyway, while I was riding the train across central Germany, and eating some food of some sort, I noticed that I was getting my daily dose of Natrium (that’s Sodium for us Americans, in case that isn’t clear…). It made me wonder how much easier it would be to learn the periodic table if the names actually matched the symbols. Unfortunately, since most of the original names appear to have Latin roots, it’s unlikely that any particular current language is using all of the ‘real’ names. (although please correct me if I’m wrong?!)

So, since changing the symbols seems unlikely, I suggest we revert to the original names of these crazy elements. Let’s call them Natrium and Wolfram, and Aurum, Argentum and Kalium. Ok, maybe not Kalium, as that sounds like something out of Superman.

Alternatively, we could make up new names entirely, like Nancy and William, Aurelius and Agamemnon… what do you guys think? Is Na by any other name still as reactive?

In any case, hope you like the food for thought.

Catherine (associate editor, Nature Chemical Biology)

Reactions – John Anthony

1. What made you want to be a chemist?

I’ve always enjoyed building things, looking for ways to improve some feature or combine functionality. Synthetic chemistry is all about building things – except at a very small scale. The field of organic electronics provides a beautiful opportunity to enjoy both pico-scale construction (molecules) and macro-scale construction (devices). It’s always a real thrill to take an idea all the way from initial target molecule, through synthesis and then into a working device in a matter of a few weeks.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I think I’d still be designing and building things. I’m already an avid woodworker – I could envision myself in architecture / homebuilding, furniture design / construction – any job where I can use my hands to create something beautiful, new and useful.

3. How can chemists best contribute to the world at large?

I suppose at first blush we contribute by doggedly pursuing our intellectual curiosity. Chemistry is central to so many endeavors – from understanding the fundamental science of molecules and molecular assemblies, to synthesizing compounds for pharmaceutical or materials applications. However, I see my most important contribution as the education of a new generation of scientists. I have had the pleasure of working with some exceptionally talented graduate and undergraduate students, and feel confident that their curiosity and enthusiasm will carry them into productive careers as chemical researchers.

4. Which historical figure would you most like to have dinner with – and why?

I’ve always been fascinated by the history of early England, and the one person I’d love to have the chance to converse with is Eleanor of Aquitaine. She exercised an incredible amount of power in an era critical to the development of modern Europe.

5. When was the last time you did an experiment in the lab – and what was it?

Last week – I performed an Ullman coupling to put a perfluoroalkyl chain onto an iodothiophene compound. While I don’t spend nearly as much time in the lab as I would like, I do try to do at least one reaction every few weeks, just to maintain credibility with the students that I instruct.

6. If exiled on a desert island, what one book and one CD would you take with you?

The CD question is tough – my musical tastes are strongly influenced by what I’m doing at the time. When writing, the von Karajan recording of Beethoven’s 4th and 7th symphonies is a top pick. In the lab, lately I’ve loaded my i-pod with Tool’s “Undertow”. When grading, Blues are more appropriate, such as Tom Waits’ “Real Gone”. But the one CD I would never want to be without is Pink Floyd’s “Wish You Were Here”. As for books – since the 5th grade I’ve been fascinated by the works of J.R.R. Tolkien, and his complete works would serve as an entertaining read as well as a phenomenal example of literary creativity.

John Anthony is in the Department of Chemistry at the University of Kentucky and works on the design, synthesis and application of high-performance organic semiconductors for display and photovoltaic applications.

The yellow (and red, blue and green) brick road

My fellow Cambridge-London commuters; did you work it out? Once you know that it depicts a gene, it’s annoyingly obvious. But despite travelling past it by train about three days per week, I failed to identify the thousands of brightly coloured bars painted on the cycle path next to the rail track near Cambridge’s Addenbrooke’s hospital as a nucleotide sequence. It should have been a clue that only four colours are used.

It probably comes from generally not being very biochemistry minded, as a straight-physics editor. Nevertheless, a friend of mine mentioned he had heard about the biology-inspired cycle path artwork and after some quick Googling, the rumour was confirmed; the colourful sequence stands for the BRCA2 gene, implicated in breast cancer and discovered in 1995.

What a good idea to combine scientific topics with railway scenery. After five years of commuting I would welcome more of these puzzles along the rail track to keep me entertained!

Liesbeth

Liesbeth Venema (Senior Editor, Nature)

A nanotube fix

Being an associate editor of Nature Nanotechnology, I now know a lot more about carbon nanotubes that I ever thought I would. There’s a lot I don’t know, however, and I was surprised by what I learned today…

Every now and then I need to look up some interesting (or otherwise) little fact about nanotubes and just get an idea of what the popular terminology is, i.e., is it a ‘chirality vector’ or a ‘chiral vector’? I won’t spoil that one for you. Anyway, first port of call, as with a lot of people, is the web, and, in particular, Wikipedia. Now, I know that any information garnered from Wikipedia might not necessarily be 100% accurate, but it’s a good place to start for casual references.

So, as I was scanning through the entry on carbon nanotubes, I was interested to see how their cost is normalized to the price of a more widely known chemical product in society:

Single-walled nanotubes are still very expensive to produce, around $1500 per gram as of 2000 (compared to marijuana, which generally costs between $10 and $30 per gram, depending on who you know and how sweet the nug is), and the development of more affordable synthesis techniques is vital to the future of carbon nanotechnology.

I don’t know if this is Wkipedia vandalism or not… anyway, maybe this new standard will give the Big Mac index a run for its money…

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)