chemical biology

Polymerase chain reactions, so good they invented it twice.

I’ve recently been preparing some new courses which have given me the opportunity to browse through the literature from the dawn of molecular biology. And in the process I came across a 43 year old paper entitled  “Studies of Polynucleotides XCVI. Repair replication of short synthetic DNA’s as catalyzed by DNA polymerase.” by Kleppe  and Khorana in the Journal of Molecular Biology. Its an elegant manuscript that describes how DNA polymerase can replicate a DNA strand but only if there is a section of duplex DNA, known a as primer, from which it can start.

So Klepper started off with a bit of DNA that looked like this:

and after incubating with DNA polymerase ended up with a DNA sequence with the gaps filled in, like so.


Well isn’t that nice?

But the really intriguing bit is the last paragraph of the discussion.

.. the DNA duplex would be denatured to form single strands. This denaturation step would be carried out in the presence of a sufficiently large excess of the two appropriate primers. Upon cooling, one would hope to obtain two structures, each containing the full length of the template strand appropriately complexed with the primer. DNA polymerase will be added to complete the process of repair replication. Two molecules of the original duplex should result. The whole cycle could be repeated, there being added every time a fresh dose of the enzyme. … After every cycle of repair replication, the process of strand separation would have to be repeated. Experiments based on these lines of thought are in progress.

Wow, what a cliff hanger. Kleppe has just described polymerase chain reactions (PCR), the now ubiquitous method for amplifying DNA. But this was 14 years before Kary Mullis (with Saikia as first authur)  published the first application of  PCR in Science.

But despite the tantalising ending to Kleppe’s paper, nothing else emerges from Khorana’s group to that effect. He never published those experiments. And indeed no one else picked up on the idea until Kary Mullis ran with it.

Its an interesting story that’s been brought up plenty of times before, but having stumbled across the original paper describing the ‘invention’ of PCR and given the big DNA anniversary next week, I thought I’d put it out there again.

By April 15, 2013 2 comments chemical biology, Uncategorized

Now we can’t drink tea!

If you’re a man and you live in Scotland do not drink tea. According to a BBC report  >7 cups a day give you a >50% greater chance of developing prostrate cancer than “normal” tea drinkers. This was the result of a  study over 37 years involving 6000 volunteers aged between 21 & 75 years of age. I’m surprised they didn’t choose whisky and/or beer (they have probably been checked at some point in distant past). This is in direct contrast to a National Cancer Institute report which suggests the opposite, at least for green tea.

What’s next I wonder, coffee is already on the black list, as well as fatty foods smoking, no doubt sex will also rear it’s ugly head in the list of cancer producing agents, water is also dangerous, fish swim in it and you can drown as well.

Wiki tells us the exact opposite to the results reported by the Glasgow study. Tea is actually beneficial for you in all sorts of ways.

So what’s in tea that makes it so harmful or so good for you? Well there is theanine and caffeine, making up about 3% of its dry weight up to 90mg per cup, depending upon the tea. Theanine moves across the blood brain barrier (quite distant from the prostrate) and has a synergistic effect with caffeine, high doses even providing a neuroprotective effect. Caffeine is a stimulant and the author of the Wiki page suggests that it may even have moderately protective effect against certain cancers.


There are also things like theobromine (or should it be teaobromine) and theophylline. So those compounds are  probably not the cause of this higher prostrate cancer risk.

What else?

Up to 30% of the dry weight of tea are the catechins. These look like a possible candidates! Some present in green tea are shown below.


Just look at all those nasty phenols, they may even have antioxidant properties, but as carcinogens, well,  I think they are not very high on the list.

The tea plant apparently has the capacity to absorb lots of the pollutants we pump out every day, e.g. fluoride and aluminum, the latter  can be present up to 30,000ppm by dry weight! Exactly what the form of the fluoride and aluminum is I don’t know, presumably sodium fluoride, perhaps someone can enlighten me as to the aluminum source.

So everyone, what shall we drink now? How about red wine, with all that reservatrol it must be good for you perhaps the chances of developing cancers will be reduced. It’s like everything we do (apart from working and paying tax), taken in moderation it is very enjoyable, but taken in excess, well I guess we have all suffered a hangover at some time.

Enjoy your tea breaks.


Glucose Fuel Cell for Medical Implants

Professor Rahul Sarpeshkar and colleagues at MIT have created an implantable fuel cell which relies on glucose as its fuel. The device could potentially be used as a power source for the computers needed to decode brain signals and manipulate prosthetic or perhaps paralyzed limbs. The article was published in PLos ONE.

There are many layers of cool in this story. Implantable glucose fuel cells have been invented before – back in the 70s – but contained enzyme-based anodes which degraded over time and needed to be replaced. Because of this, implants like pacemakers rely on lithium ion batteries – which also drain over time, but have a much longer lifespan. This design utilizes a platinum anode to oxidize glucose ultimately to gluconic acid, liberating 2 electrons. The cathode is a matrix of single-walled carbon nanotubes which reduce dissolved oxygen to water.

What strikes me as the coolest part of this story, the fuel cell is fabricated on a silicon chip and would be placed in the cerebralspinal fluid next to the brain. Platinum is already known for being fairly biocompatable, but placing the chip in the cerebrospinal fluid is beneficial as there are very few white blood cells in the CSF to trigger an immune response and potential rejection. The CSF contains roughly the same concentration of glucose as plasma, and is not predicted to consume enough glucose fuel so as to impair brain function.

via DOI:10.1371/journal.pone.0038436

To avoid short circuiting the fuel cell, the platinum anode is enclosed in a ring of the carbon nanotube cathode. The cathode sequesters the dissolved oxygen for the reduction reaction, creating a concentration gradient across the cathode such that dissolved oxygen does not penetrate past the cathode. The nanotubes do not oxidize glucose, but are permeable to glucose, so the glucose passes through the cathode unreacted. The cathode is separated from the anode by a strip of nafion, a biocompatable perfluorniated polymer similar to teflon, but with branched sulfonate groups throughout. The sulfonate groups allow protons to flow through the nafion from the anode to the cathode, and nafion is permeable to glucose as well. The anode is at the center and can be as large as 2.5cm x 2.5cm.

The oxidation reaction at the anode is considerably less efficient than other implantable glucose fuel cells, but the biocompatability and long lifespan of the fuel cell makes this a really nice step forward in the treatment of paralysis and spinal cord injuries.

#ToxicCarnival: Nitroglycerin

Tonight, we make soap.

Matt over at Sciencegeist is organizing this blog carnival in an effort to reclaim the word chemical from the hands of ignorant people who blindly assume anything with ‘chemicals’ in it must be evil. This is not a moment too soon.  I’m not exactly sure how the pendulum of public opinion swung from products being advertised as ‘Better living through chemistry’ to products being advertised as ‘chemical free’ (whatever that means). Soaps and other skin care/beauty products are certainly in the cross-hairs of the ‘chemical free’ crowd, but that’s not what I’m talking about today.

As the tallow renders, you skim off the layer of glycerin. If you were to add nitric acid, you got nitroglycerin.  If you were to add sodium nitrate and a dash of sawdust, you’d have dynamite. 

Read more ›