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How do we know what DNA looks like

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Question: How do we know what DNA and genes really look like?

We see images in books that look like this, but each individual atom is only a nanometer (1 x 10 -10 m) wide.

No visible light microscope can view objects made with such small pieces.

dna-notes-7-728

 

So the real way that we figured out the atom-by-atom structure of DNA is through a technique called X-ray crystallography.

Our molecule of interest – in this case, DNA – is concentrated and crystallized.

It is placed in front of an X-ray source.

The X-rays scatter off the DNA’s atoms. We capture this diffraction pattern on film (or on a digital X-ray detector.)

Photo 51 DNA Diffraction pattern

X-ray diffraction image of the double helix structure of the DNA molecule, taken 1952 by Raymond Gosling, commonly referred to as “Photo 51”, during work by Rosalind Franklin on the structure of DNA (text Wikipedia)

This diffraction pattern is beautiful but doesn’t directly look like the original molecule.

There is a mathematical relationship between the placement of the atoms, and where the atoms deflect – just like there is a relationship between hitting pool balls and how they deflect:

When you know how a pool table is set up, what balls are made of, and see how the balls move after being it, you could use math to work backwards to figure out where the balls originally where.

Billiards Pool

from Banks and Kicks in Pool and Billiards, Dr. Dave Alciatore, Billiards and Pool Principles, Techniques, Resources

Same here: We can use math to figure out what each individual atom in the DNA originally was.

In this image: X-rays leave a source; some pass through a lead screen

The X-rays hit crystallized molecules. X-rays bounce off of the molecules, and onto a film plate.

We end up with a diffraction pattern on film.

How does one physically interpret diffraction patterns in DNA?

DNA X-ray crystallography

Figure 11.4, Purves’s Life: The Science of Biology, 7th Edition

Once we have a diffraction pattern, we use math to work backwards, and figure out what the shape of the molecule must have been.

The result is an electron density map which almost exactly traces out the shape of the molecule.

Final step: tba

X Ray crystallography and electron density map

Left image: X-ray diffraction pattern, Wikimedia. Right upper image: electron density map. Right lower image: model fitting atoms to the density map.

Can we image DNA more directly?

Yes. One can use a scanning tunneling microscope (STM).) It shows detail at the the atomic level.  Along with the following image please read Livescience: DNA directly-photographed-for-first-time.html

Photo of DNA helix

DNA’s double-helix seen in electron microscope photograph. By Enzo Di Fabrizio, Magna Graecia University in Catanzaro, Italy.

 

Here is another STM image of DNA. You can see how closely it matches the model from X-ray crystallography.

STM image of DNA

External resources

Are there true pictures of the DNA molecule (not synthetic images), showing the double helix?

On DNA’s Anniversary: How Rosalind Franklin Missed the Helix

Sexism in science: did Watson and Crick really steal Rosalind Franklin’s data?.

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