Posts Tagged DNA

Computer modellers for the win Grant Jacobs Oct 10

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As a computational biologist I rather like the look of this year’s Nobel Prize for Chemistry – it’s been awarded for contributions to computational modelling, to Martin Karplus (University de Strasbourg/Harvard), Michael Levitt (Standford) and Arieh Warshel (University of Southern California).

Molecular modelling takes several forms. The twist in the work the prize has been awarded for is multi-scale modelling, in their case bridging classical (Newtonian) and quantum modelling.

Take a ball. Given the forces on the ball you can apply the ‘classical’ physics of Sir Isaac Newton (and those that furthered his work) to determine where the ball will be at a given time in the (near) future. That’s Newtonian modelling.

Peter Murray-Rust, CC 2.5. Source: Wikimedia Commons.

Peter Murray-Rust, CC 2.5. Source: Wikimedia.

We can think of molecules—chemicals of several atoms or many more—as balls connected by sticks, chemical bonds.

To the right is a ball-and-stick model of a single amino acid, proline.

If you can treat atoms in a molecule as balls, you can apply Newtonian physics to them.

Atoms are joined to each other by chemical bonds. Different types of bonds have different rotational properties. Some rotate freely, others less so. So we can add rotational properties to our model.

There’s the different forces atoms have on eachother. We can simplify these to something like compressing springs that draw together or push apart atoms or groups that attract or repel eachother.

Keep going and we can built up a method to simulate the motion of molecules.

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How to spot a badly-drawn DNA helix Grant Jacobs Jul 22


The DNA double helix is one of the icons of our time. You’d wish people would draw it right.

You’d think getting it wrong would make the artist feel like a complete mug, as if they’d drawn the Statue of Liberty holding up a lump of coal instead of a flaming torch.[1]

But the DNA helix in all sorts of places is simply wrong.

You don’t need to be a TV drama-smart science geek to know which artists have screwed up.

Let me show you an easy way. (And impress your non-scientist friends!)

Does it turn the right way?

Look at the DNA with the ‘rungs’ of the ladder horizontal and the helix standing vertically.

LH-w-arrow-80pxRH-w-arrow-80pxLook for the diagonal ‘stripes’ that make up the spiral of the helix, as they cross the front of the helix.

Apply this rule:

From the right downwards, means the helix is right-handed. (Shown to the right.)

From the left downwards, means the helix is left-handedwhich is wrong. (Shown to left.)

(Modified from original image at Georgia Perimeter College webpage.)

So, this is right-handed,


By jscreationzs, published on 22 October 2011; from, ID: 10061973.

but these are left-handed,


By dream designs, published on 04 October 2012; from, ID: 100105102.


By dream designs, 09 April 2012;, ID: 10079201.

Flip it over

One way to correct a left-handed DNA cartoon is simply to flip the picture over to it’s left-right mirror image.

No excuses for artists not to put their errors right – that’s click-of-a-button stuff.

A plague of wrongness

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Crick’s letter to son, aged 12, explaining DNA structure model Grant Jacobs Feb 27


Yesterday I wrote about how the Crick family is to sell Francis Crick’s Nobel Prize medal. In that post I mentioned how my attention was drawn to that the family is also considering selling Crick’s letter to his son Michael, then aged 12, explaining his and James Waton’s model for the structure of DNA.

It struck me as I was curious to see how he’d write to a non-scientist at close to the time of creating their model.

I was unsure if this letter had already been published and I now see that The New York Times has posted a copy of the letter on-line as a part of an article about Crick writing to his son.

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Animating our DNA* Grant Jacobs Jan 20


One part of biology that fascinates me is the three-dimensional structure of genomes and all that goes with them within the nucleus, the central organelle in our cells containing our genomes and the molecular machinery that organises, moves and processes our genetic information.

In the TED lecture below Drew Berry speaking in Sydney, Australia, shows off animations of molecular life.

The animations he shows are of DNA, chromosomes and the proteins that work with them.

Here, let me get out of the way so you can watch it -

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Arsenic life – more criticism, formally published Grant Jacobs May 29


Science magazine has lined up eight Technical Comments on-line in advance-of-print release, along with a response to these from the authors, that will stand alongside ’the’ arsenic life paper to be published in in print next week’s edition after a wait of roughly six months. With the exception of the accompanying editorial, these are all open-access.

For those new to the story, the ‘lite’ gloss–i.e., for a non-scientist readership–of this research arguing that a bacteria uses arsenic in place of phosphate in it’s DNAgoes something like this.

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