aptamer sensors patched up

My astrobiology co-author Kevin Plaxco has been pioneering the development of biosensors based on aptamers (the artificially generated DNA equivalent of antibodies) for many years now and every once in a while I write about the progress in this fascinating field. Now the work has reached its first clinical trial, so I wrote a news story for Chemistry World to help spread the word.

The news story is out now:

World first for clinical trial of skin patch to monitor therapeutic drugs in real time

Chemistry World 5.2.2026

Source: © Marsilea A Booth et al/Springer Nature America 2026

Previous episodes in this serie are listed here.

carbon ring hooked up

I don't write about real chemistry very often these days, but it's always great to hear about the creative (supra)molecular architectures and new allotropes of carbon developed in Harry Anderson's lab here in Oxford. The latest news from his lab, published in Science magazine this week, is the first molecular carbon ring stable enough to be investigated in solution by normal spectroscopy methods. Previous carbon rings were produced by atom manipulation on solid surfaces, a method requiring extremely low temperatures (see here and here).

I wrote a news story for Chemistry World about this new work, which is out now:

Ring of pure carbon stabilised by its catenane connections

Chemistry World 15.8.2025

I believe it is freely accessible as long as you haven't used up your monthly quota of free articles from CW.

The three macrocycles helped to stabilise the C48 molecule, allowing the first isolation in solution of this class of molecule. Image source: © Yueze Gao et al 2025

PS It looks like I forgot to blog some of the CW news stories of recent years, I'll list the missing ones here so I have them somewhere on this blog in case I ever get round to updating my publications list.

Proteins behind diatoms’ intricate nanoscale-patterned shells revealed
Chemistry World 5.1.2023

Light-harvesting wheel reinvented by chemists copying bacterium
Chemistry World 7.7. 2020

Hydrogens seen crystal clear in small molecules
Chemistry World 31.5. 2016

For a complete list of all my pieces in Chemistry World, see my profile page.

more carbon rings

I reported the discovery of a new allotrope of carbon, the C18 cyclocarbon, back in 2019. It took a while, but the groups involved in that paper have now presented another new ring molecule made only of carbon, C16. This time the extra challenge is in the fact that it is anti-aromatic (hosting 4n rather than 4n+2 atoms in the ring). A group in China has also produced several such rings in different sizes with a similar method. Their papers aren't officially published yet but available as preprints.

My news story in Chemistry World is out now (open access if you haven't used up your monthly quota of free stories):

Carbon's anti-aromatic allotrope is ringing the changes

The paper is out in Nature online (but not in this week's issue) and is on open access. UPDATE The paper is now in the issue of 29.11.2023, page 977, together with one of the papers from the Wei Xu's group, on page 972

And here is the recipe:

Source: © Yueze Gao et al 2023

The precursor 4 is deposited on a NaCl surface and the carbon monoxide and halogen masking groups are then eliminated to give the cyclocarbon C16

visualising extraterrestrial molecules

I cover atomic force microscopy every once in a while, which results from my residual connections in chemistry and interest in the nanoworld, and because of the astrobiology book I am of course interested in all extraterrestrial molecules.

So the great news is that now these two threads of my work have met and I have been able to report the first AFM work on actual extraterrestrial molecules, which is really exciting, even though it hasn't taught us anything fundamentally new - except that you can visualise extraterrestrial molecules. So anybody who has meteorite materials, send a sample to my namesake Leo Gross, and he will get you lovely pictures of the organic molecules contained in them.

Read all about it on the Chemistry World website (open access if you restrain yourself and don't read more than two stories per month):

Chemical ecosystem of Murchison meteorite molecules revealed in snapshots

Diels Alder revisited

I don't often write about chemistry these days, but every once in a while I have great fun revisiting things that are so elementary and easy that even I can still remember them. Such as the Diels Alder reaction, which on paper goes like this:

Source

I wrote a news story for Chemistry World on an effort to observe the Diels Alder reaction happening on a surface, using atomic force microscopy (AFM). You can read the story here (open access if you haven't used up your quota of CW stories).

Sadly, the researchers had to make this very simple and elegant reaction quite complicated to achieve this. It made me wonder (after sending off the news piece) if biomolecules might offer a way of positioning a pair of simpler Diels Alder reactants on a surface.

It was long believed that nature didn't have Diels Alder enzymes, so various researchers took up the challenge to fill this gap and produced:

• a ribozyme
• an enzyme
• and a catalytic antibody

to catalyse the reaction.

More recently, however, natural Diels-Alderases were discovered, including this one earlier this year.

So there are plenty of biomolecules that by definition recognise and bind Diels Alder reactants. Surely one of them can be persuaded to handle the reaction in a way that is amenable to AFM studies?

aromatics go extra large

A news story I had published in Chemistry World in January and forgot to brag about:

Harry Anderson's group stitched together porphyrin rings in very clever ways to create aromatic molecules with up to 162 pi electrons, which still obey Hückel's rule. Considering that Erich Hückel developed his concept of aromaticity based on benzene with 6 pi electrons, I find this quite mindboggling. And it also looks stunning.

Largest molecular wheel ever made pushes limits of aromaticity rules
Chemistry World, 22.1.2020
Open Access (Chemistry World allow you to read a few articles for free each month, so as long as you haven't used up your quota this one should be free)



Artist's impression.

carbon rings

It's always interesting to catch up with what Oxford chemist Harry Anderson is up to - and his latest work, characterising a new allotrope of carbon, no less, even made it onto the cover of Science:



(Note however that the cover graphic misrepresents the findings in an important way. Anderson and colleagues found that the C18 ring has alternating triple and single bonds, while the graphic suggests the bonds are all the same.)

When the paper appeared online in August, I wrote a short news story about it for Chemistry World:


New form of pure carbon made by manipulating atoms

which neatly builds on last year's story about polyyne nanowires:

Most complex reaction ever triggered by atomic manipulation creates molecular wire
.

The C18 paper in Science is here (paywalled).

And C18 has its own flickr album, too.

chemistry stories

These days, I don't write as much about chemistry as I used to as the features for Current Biology keep me reasonably busy, but here's a couple of news stories I did for Chemistry World. The one that came out today involves Harry Anderson's lab at Oxford - I consulted him about something else and asked what he was up to these days, so I found out about this:

Most complex reaction ever triggered by atomic manipulation makes molecular wire
Chemistry World August 2018, vol 15, issue 8, page 32

And the other was something that Chemistry World commissioned while this one was sitting around waiting for the original paper to come out. This is about new ways of predicting how several elements may be combined to form new materials:


AI teaches itself to identify materials – and predict new ones too
Chemistry World August 2018, vol 15, issue 8, page 38






Image source

crispr sensing

The revolutionary gene-editing technique known as Crispr-Cas has been embroiled in a patent dispute between two leading US research institutions. In one corner, the University of California at Berkeley, where Jennifer Doudna discovered it in collaboration with Emanuelle Charpentier, and in the other, MIT’s Broad Institute, where Feng Zhang’s group first demonstrated its use in living cells.

Now the two institutions are competing against each other again, as both recently demonstrated the usefulness of a different Crispr system for the detection of pathogens. Doudna’s and Zhang’s groups had shown in 2016 that a Crispr-type enzyme called C2c2, now renamed Cas13, targets single stranded RNA, unlike the ones used in gene editing, such as Cas9, which edit double-stranded DNA. Moreover, it doesn’t stop cutting once it has destroyed its target. It goes on to cleave thousands of other RNA molecules that happen to be nearby. This collateral damage provides a useful amplification step enabling the sensitive detection of the original target RNA, whose recognition can be programmed just as in the gene-editing method.

Aiming to turn this into a clinically usable sensor, Zhang teamed up with Jim Collins, also at MIT, who was involved in the race to develop practical methods for rapid detection of the Zika virus.

Read all about it in my latest news story in Chemistry World which is out now (free access if you haven't read any other CW stories this week, they have a free quota):

Crispr enables rapid disease detection

disorder turns 20

Open archives


Today I’ll exceptionally present a feature from the archives that was published in Chemistry World, not in Current Biology.

The occasion is that today is the 20th anniversary of one of my favourite and most impactful papers from my research career, even though it did not result from actual research I did.

What happened back in 1997 was that my friend and colleague Kevin Plaxco happened to know about a paper from molecular biologists coming out on a weird mechanism controlling the growth of the tail (flagella) that certain bacteria use to swim. The tail is a hollow tube, and while it is being built, a certain signalling protein escapes through the tunnel and is lost to the cell. When the tube is finished and closed, the protein accumulates in the cell and thereby signals that no more bricks are needed to extend the tunnel.

What Kevin noticed was an aspect that left the molecular biologist authors of the original paper gloriously uninterested – namely the fact that to carry out its biological signalling function this protein needed to be an unfolded, 1D thread, as opposed to a complex 3D structure as all functioning proteins were supposed to be according to the prevailing dogma that sequence determines structure determines function.

So Kevin told me about this and suggested to write a News & Views piece for Nature, which we did, and which came out 20 years ago today. At the time there were only two or three other examples of “intrinsically disordered” proteins that are functional while unstructured. Mostly the evidence relied on NMR spectroscopy, which invites the objection that maybe the researchers didn’t get the conditions quite right and maybe the protein would be more orderly if they did x instead of y.

The beauty of the system we discussed was that the biological function of the protein made it absolutely necessary to unfold, as it wouldn’t fit through the tube in its folded state.

Anyhow, this turned out to be the beginning of a whole new research field which grew quite impressively over the next years, so in 2010 I had the pleasure of attending a research conference at Barcelona that was all about intrinsically disordered proteins.

And summarising what I learned at this conference, I wrote a feature about the topic which appeared in 2011, and which is freely accessible:

Anarchy in the proteome
Chemistry World, August 2011, pp 42-45
FREE access to PDF file




screenshot of our 1997 News & Views (PDF - if you hit the paywall, try this)

aptamer update

I don't do all that many news stories these days, but I did pick up this one from the lab of my old friend and astrobiology co-author Kevin Plaxco, as it is a further step on a path I have followed since the beginnings more than a decade ago.

So the latest news is that electronic aptamer sensors can now work inside a living, moving mammal, as you can read in Chemistry World today:

Personalised medicine boost as cancer drug monitored in real-time

Previous steps on the way:

Chemists crack cocaine detection Chemistry World 2006

MEDIC to kick-start personalised medicine revolution Chemistry World 2013

Biosensors in real time Feature in Chemistry & Industry 2014, No. 4, pp42-45.

Aptamerensoren für kontinuierliche Bluttests Chemie in unserer Zeit 2014,48, 88

bees can't help it

Another news story on bees and and neonicotinoids. Over the last few years it has become clear that sublethal effects of the pesticides are very bad news for the success of bee colonies. The UK govt seems to think that bees could just say no to poisoned nectar.

Research from Geraldine Wright's lab now shows that they can't detect the poison with their sense of bitter taste. Worse still, they have a tendency to eat more of the toxic stuff. Full story out in Chemistry World, free access:

Bees 'prefer' neonicotinoid-laced nectar
Chemistry World 22.4.2015

The story also appears in the June issue of the printed magazine, on page 29.

own photo (not sure if I've used this one before?)

PS related news that came in just after this:

• Bumblebee genomes
• Bumblebees self-medicate with nicotine

viral DNA

Many DNA viruses pack their DNA so tightly inside their capsids (protein shells) that the molecular chain can no longer move and remain frozen in a glassy state. But how does it get out of that freeze when the virus infects a cell? The answer is in my latest news story in Chemistry World:

Viruses melt ‘glassy’ DNA (free access)

source: found floating around on tumblr

building molecules made easy

Let's have a news story for a change, here's one that just appeared in Chemistry World online, on a new combinatorial approach that is apparently so simple everybody could create new molecules. Just mix the building blocks and test if any of the resulting combinations has the properties you're looking for.

Bringing chemical synthesis to the masses

Chemistry World online 7.9.2014

Free access

Those lucky enough to get the print edition of Chemistry World can find the piece on page 21 of the October issue.

By the way, I may have forgotten to mention one or two other CW news stories in the last couple of years, such as this one:

Speeding up the experiment to fit the simulation

Thankfully, the CW website keeps track of my contributions here.

the unbearable lightness of party balloons

As befits the two months covering both carnival and April Fools day, the roundup of German pieces published in March/April includes an equal mix of serious and not so serious pieces. We find the unbearable lightness of party balloons, the equally unbearable inability of humans to handle antibiotics responsibly, quantum cubism, and the Microfluidic Electrochemical Detector for In vivo Continuous monitoring, or MEDIC, for short.

Aptamerensoren für kontinuierliche Bluttests
Chemie in unserer Zeit 2014,48, 88 DOI: 10.1002/ciuz.201400659 [abstract and limited access to full text]

See also my story in Chemistry World on the same topic: Free Access

Ausgeforscht: Die Leichtigkeit der Partyballons
Nachrichten aus der Chemie 2014, 62, 395

Ausgeforscht: Quanten-Kubismus
Nachrichten aus der Chemie 2014, 62, 495

Blickpunkt Biowissenschaften: Auf Resistenzen besser reagieren
Nachrichten aus der Chemie 2014, 62, 445-447

latest spin on carbohydrates

Even though I did much of my PhD thesis with the characteristic whining of two ancient, wardrobe-sized Beckman model E analytical ultracentrifuges in the background, I didn't really expect to get a chance to write something about this technique any time soon. It was widely used to study molecular weight and assembly of proteins back in the 1970s but for a time it became so unfashionable that there was no company left making or servicing the instruments, and only hardcore fans like my PhD supervisor, Rainer Jaenicke, kept the last of these dinosaurs alive.

By now, the technique has been rediscovered, new centrifuges have been developed and built, and various groups are using the technique. In an intriguing development, the groups of Steve Harding and Thomas Heinze have shown that certain carbohydrates can assemble reversibly just like oligomeric proteins. Read all about it in my news story which is out now in Chemistry World online, free access:

Self-assembling carbohydrates behave like proteins

Searching for an illustration for this article, I discovered this video of a simulation showing what happens to protein molecules in the cell of an ultracentrifuge. Simulation is of lysozyme in water, so nothing to do with carbohydrates, but I thought it's a lovely visualisation of the technique:

Source: Díez A, Ortega A, Garcia de la Tore J (2011). "Brownian dynamics simulation of analytical ultracentrifugation experiments". BMC Biophysics. DOI:10.1186/2046-1682-4-6.

via wikimedia commons.

foam from the horse's mouth

In a late follow-up to the frog foam story from 2009, I covered the structure of an equine protein coming from the same groups. Latherin is found in the sweat and saliva of horses and has unusual surfactant properties suggesting a new mechanism.

Read all about it in Chemistry World (free access):

A foaming protein from the horse’s mouth

NB: this came out so quickly that I actually missed it when it appeared, hence the slight delay in horn-tooting.

Some not so sweaty horses salivating over buttercups in a field near our house.

paradox lost

My review of the book Paradox: the nine greatest enigmas in science, by Jim Al-Khalili is out in Chemistry World online:

FREE ACCESS

It also appears in the print issue on page 69 (together with lots of other book reviews, worth checking if you're hunting for presents ...).

molecular puzzles

I love rotaxanes - they are assemblies consisting of a ring loosely wrapped around a dumbbell shaped molecule, whose endgroups are so bulky that they stop the ring from escaping. They hold the same fascination as those puzzles made of chromed wire, one just can't help wondering: how on earth did that thing get around the other one? Or maybe it's just me.

Anyhow, I was pleased to hear from Oxford chemist Harry Anderson that his group and others have now succeeded in creating rotaxanes with polyynes (polyacetylenes) as the axle. Puzzles apart, such constructs are also of interest as possible molecular wires and as a first step towards a new modification of carbon. So I wrote a news story about all this, which is now out in Chemistry World:

Running rings around molecular wires

Free access.

Cartoon: Wikipedia

UPDATE (4.8.2012): you can now find the piece in this month's print edition as well, on page 33.

chaperone movies

Back in the 90s I did some research on the molecular chaperone GroEL, which at the time didn't even have a crystal structure to its name. It is a great pleasure to see that the accumulation of structural and functional knowledge on this protein has now reached the stage where researchers can assemble snapshots to a movie showing plausible twists and turns that the seen subunits of each ring may carry out during their functional cycle.

The paper from Helen Saibil and colleagues at Birkbeck College, London, appeared in Cell (online) yesterday (D K Clare et al, Cell, 2012, DOI: 10.1016/j.cell.2012.02.047) and I wrote a news item for Chemistry World which has gone live today:

Molecular chaperones caught on film.


PS (23.4.2012): a related paper that just came out in Biophys J. and is freely accessible: Prying Open Single GroES Ring Complexes by Force Reveals Cooperativity across Domains Akiko Ikeda-Kobayashi, Yukinori Taniguchi, David J. Brockwell, Emanuele Paci and Masaru Kawakami Biophysical Journal, Volume 102, Issue 8, 1961-1968, 18 April 2012 doi:10.1016/j.bpj.2012.03.046