First Direct Image of DNA Double Helix

Horrible summary of article by Dahamma · 2012-11-30 21:38 · Score: 5, Informative

Summary: "structure of a single strand of DNA"
TFA: "Here we report on the direct imaging of double stranded (ds) -DNA"

Summary: "using a tunneling electron microscope"
TFA: "with transmission electron microscopy (TEM)"

Yes, the full paper is beyond a paywall, but couldn't you have even summarized the three sentence abstract correctly!?

Re:Horrible summary of article by ColdWetDog · 2012-11-30 22:03 · Score: 4, Interesting

That's a tad confusing, but so is the 'article':

Direct imaging becomes important when the knowledge at few/single molecule level is requested and where the diffraction does not allow to get structural and functional information. Here we report on the direct imaging of double stranded (ds) -DNA in the A conformation, obtained by combining a novel sample preparation method based on super hydrophobic DNA molecules self-aggregation process with transmission electron microscopy (TEM). The experimental breakthrough is the production of robust and highly ordered paired DNA nanofibers that allowed its direct TEM imaging and the double helix structure revealing.
It appears that this was translated poorly from the original Italian. A strand of DNA could be a single polymer of DNA or double stranded - where complementary sequences are bound together in the traditional 'double helix' - 'strand' being a poor choice of words in this context. It's not clear where the tunneling electron microscope idea came from.
It's also not clear that the picture represents and image of either single or double stranded DNA. It appears to be a linear polymer of a number of double stranded DNA molecules. You can see a helical structure, but it appears that that you are looking at a group of DNA molecules bound together. Unfortunately, the paucity of information in the abstract and the poor translation make it unclear what, if anything, we learn with this technique.

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Re:Horrible summary of article by Dahamma · 2012-11-30 22:19 · Score: 4, Informative

It appears that this was translated poorly from the original Italian.
I don't think so. If the full article was in Nano Letters, they published it in English.

It's not clear where the tunneling electron microscope idea came from.
I'm guessing the poster figured "TEM" meant tunneling election microscope, when it really means transmission electron microscope, vs. "STM" (scanning tunneling microscope). Though jeez, the article actually spells it, out, so it's a pretty lame mistake.

It's also not clear that the picture represents and image of either single or double stranded DNA. It appears to be a linear polymer of a number of double stranded DNA molecules. You can see a helical structure, but it appears that that you are looking at a group of DNA molecules bound together.
Yup, from a different summary I read they claimed it was a bundle of 7 molecules (6 around a core), apparently (for what their explanation is worth) because a single one would be destroyed by the TEM.
Re:Horrible summary of article by MagusSlurpy · 2012-11-30 23:45 · Score: 1

It appears that this was translated poorly from the original Italian.
I don't think so. If the full article was in Nano Letters, they published it in English.
You beat me to it. I don't know HOW that abstract made it through. The ACS kept telling me that they could only maintain their current level of quality publishing if I kept giving them money, but I didn't realize they actually meant it!

Yup, from a different summary I read they claimed it was a bundle of 7 molecules (6 around a core), apparently (for what their explanation is worth) because a single one would be destroyed by the TEM.
I am by no means a TEM expert, but I did spend a semester learning to use one in grad school (in a bio class all my materials chemistry classmates taunted me for taking), and it only a minute or two at relatively low acceleration voltages to completely trash each cell I was imaging, so I'm not surprised by this at all.

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Re:Horrible summary of article by Megane · 2012-11-30 23:50 · Score: 1

I seem to recall that DNA strands themselves coil into a helix (I guess you could call it a "meta-helix"), and from the spacing vs the width in the picture, I'm going to guess that's what they actually imaged.

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Re:Horrible summary of article by arisvega · 2012-12-01 02:36 · Score: 1

Yes, the full paper
It is not a paper, it is just a letter.

is beyond a paywall

$35 for 48 hours of access? Really?

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Re:Horrible summary of article by ColdWetDog · 2012-12-01 05:27 · Score: 2

You beat me to it. I don't know HOW that abstract made it through. The ACS kept telling me that they could only maintain their current level of quality publishing if I kept giving them money, but I didn't realize they actually meant it!
"Subscribe to our journal or the article gets it!"

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Re:Horrible summary of article by Anonymous Coward · 2012-12-01 06:14 · Score: 0

the ACS does no proofreading or even spell checking of articles - it is all up to the submitting academic
the result is that the many peer reviewed, highly respected scientific publicatins from the Amer Chemical Society are filled with incomprehensible articles.
You have to really admire the bravery of a foreign scientist willing to not just write a paper (a huge amt of work) but in another language - that is really brave and commendable, and a plus for us english speakers.
but, sadly , most of em don't hire an editor, and as a result basic errors in grammar limit the audience that can veiw and understand their work.
Re:Horrible summary of article by Anonymous Coward · 2012-12-01 14:31 · Score: 0

Yes really, that is the going rate for an individual article. I don't know who pays that. If I wanted an article that much and couldn't get it at my own library, I would request an interlibrary loan. It will take a few days instead of instant, but it will be free.

First confirmation? Really? by Anonymous Coward · 2012-11-30 21:40 · Score: 1

Didn't X-ray crystallography visually confirm the structure of DNA long ago?

Re:First confirmation? Really? by Dahamma · 2012-11-30 21:54 · Score: 4, Insightful

No, X-ray crystallography was an indirect confirmation - sort of like the current methods for detecting extrasolar planets.
This was actually directly photographing the helix, which is novel - though according to other (much better!) summaries it's still not of a single (or even double) DNA molecule:
"This technique will allow researchers to view single molecules of DNA interacting with other molecules. For now, the method only works with cords of DNA, made up of six molecules wrapped around a seventh acting like a core. This was needed because the energy of the electron streams could break apart a single DNA molecule."
Re:First confirmation? Really? by AHuxley · 2012-11-30 23:00 · Score: 4, Interesting

Some fun art from c1910 by a Swedish artist named Hilma Af Klint
http://www.wikipaintings.org/en/hilma-af-klint/what-a-human-being-is-1910

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Re:First confirmation? Really? by cnettel · 2012-11-30 23:18 · Score: 3, Interesting

The main problem of the experiments of the Watson-Crick era was that the diffraction pattern was created by the average along the helix, so you could not really discern individual nucleotides. Considering diffraction by itself to somehow be inferior to transmission techniques is not very convincing, in my opinion. It's not even like the scientists can visually see this with their own eyes - and even if they could, the interpretation would be totally dependent on the design of the equipment, just like reconstruction of diffraction data is dependent on a number of assumptions.
What's relevant and interesting is the fact that we get close to observing individual molecules of DNA in detail, but that could be done with techniques for single-molecule diffraction as well.
Re:First confirmation? Really? by Bartles · 2012-12-01 05:39 · Score: 1

I'm intrigued by this painting. The double-helix structure of DNA wasn't hypothesized until 1953, and the dual strand nature wasn't hypothesized until 1927. Do you know anything about this, or is it just another way cool art thing like Michaelangelo painting god sitting on a big brain in the Sistine Chapel?
Re:First confirmation? Really? by AHuxley · 2012-12-01 15:15 · Score: 1

Saw the pic on a blog back in 1997. Stays with you after you have seen it :)
Some more on her work at http://www.guardian.co.uk/culture/2006/mar/14/2

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Re:First confirmation? Really? by Brian+Feldman · 2012-12-01 19:10 · Score: 2

No, you are confusing it with the Caduceus (which is itself confused with the Rod of Asclepius). The double-helix is stacked/offset, not intertwined.
http://en.wikipedia.org/wiki/Caduceus
http://en.wikipedia.org/wiki/Rod_of_Asclepius
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg

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"news" by Anonymous Coward · 2012-11-30 21:47 · Score: 0

This is HUGE news for those incapable of thinking in reciprocal space.

for those wondering what the picture shows by Anonymous Coward · 2012-11-30 21:51 · Score: 5, Informative

the two pillars in the upper pics (SEM images) are some kind of super hydrophobic structure designed to hold the DNA molecule, the thin line connecting the tops of the columns is the DNA itself, the holes in the bottom allow the TEM electron beam to photograph the helix. the bottom right pic is the TEM image.

Re:for those wondering what the picture shows by Anonymous Coward · 2012-11-30 23:49 · Score: 0

Thank you, no idea why the picture could have a caption such as yours to explain this.
It actually makes sense now what all the pictures are!
Re:for those wondering what the picture shows by tulcod · 2012-12-01 03:44 · Score: 1

Thank you, no idea why the picture could have a caption such as yours to explain this.
Because the audience is not a bunch of nerds on a tech news site, but scientists in a nanofabrication lab.
Re:for those wondering what the picture shows by Brucelet · 2012-12-01 07:07 · Score: 1

Even scientists still need captions sometimes. Generally the audience for a paper is slightly wider than the set of people intimately familiar with your particular experimental techniques, and formatting and display conventions do vary between different people and different labs. That said, I know nothing of this field so maybe this set-up is standard enough that anyone professionally interested in it does recognize it on sight.
Re:for those wondering what the picture shows by Anonymous Coward · 2012-12-01 14:40 · Score: 0

The captions for those figures are in the full text. The journal wants you to pay for access if you are going to actually learn anything. Abstracts are meant to make you want to read the full paper, not give out all the details.

Is it writable by MichaelSmith · 2012-11-30 21:56 · Score: 1

Brings to mind the teams which were using an instrument like the SEM to deposit atoms on to a surface. Could the same be done with DNA, ie, use the needle to modify the molecule?

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Re:Is it writable by UBfusion · 2012-12-02 02:19 · Score: 1

I think you are confusing the TEM (electron transmission) microscope that operates with the help of an electron beam, with an AFM (atomic force microscope) which does indeed use a needle and can displace atoms on the surface of a material.
Re:Is it writable by MichaelSmith · 2012-12-02 08:26 · Score: 1

Yes, probably.

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First Impression by Ukab+the+Great · 2012-11-30 22:33 · Score: 1

DNA is a pipe cleaner.

A TEM is NOT a tunneling electron microscope! by Anonymous Coward · 2012-12-01 00:17 · Score: 0

A TEM is a TRANSMISSION electron microscope. Something completely different! Get your facts straight, editors. Such a blatant error on a site for "nerds" makes me sad.

The Obtuse by Anonymous Coward · 2012-12-01 00:47 · Score: 0

The "Abstract" should have been labeled the "Obtuse". Unreadable. Images not described. Big waste of time.

Polymerase chain reaction by AlphaWolf_HK · 2012-12-01 01:00 · Score: 2

Any chance they could get visual confirmation of DNA replication? That would be neat to watch.

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Re:Polymerase chain reaction by Anonymous Coward · 2012-12-01 01:50 · Score: 0

The second part of this video is a visualization of it. Not the real thing, but still very cool.
Re:Polymerase chain reaction by Biotech_is_Godzilla · 2012-12-01 02:28 · Score: 3, Informative

They already have a visual confirmation of DNA replication, obtained by transmission electron microscopy again.
Google "replication fork TEM" for some images. You have to prep DNA from cells, you can't see it happening inside cells, but it's very strong visual evidence of how replication happens.
There's also a cool visualisation method that allows you to see new DNA being laid down during replication using confocal (laser) microscopy. The way it works is: they feed an artificial version of a DNA base to cells during replication, then stop, and swap the first one out with a different artificial DNA base analogue to see the new DNA being made after the point that you change analogues. They then use fluorescently labelled antibodies to detect both types of bases, using (for e.g.) a red-labelled one for the first period of replication, and a green labelled one for the second period.
This is a good explanation. It can be used for some awesome experiments - here's an example from the same lab (Fig. 3).
Re:Polymerase chain reaction by AlphaWolf_HK · 2012-12-01 04:35 · Score: 1

Hmm...if they saw DNA earlier by seeing a PCR fork, why would this be the first time they "see" DNA? It looks apparent in those other pictures.
Is there something different about this?

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Re:Polymerase chain reaction by Anonymous Coward · 2012-12-01 06:05 · Score: 0

Any chance they could get visual confirmation of DNA replication? That would be neat to watch.
Can you watch something unwinding at 150,000 rpm?
Re:Polymerase chain reaction by Anonymous Coward · 2012-12-01 07:47 · Score: 0

Hmm...if they saw DNA earlier by seeing a PCR fork, why would this be the first time they "see" DNA? It looks apparent in those other pictures.
Is there something different about this?
The most common technique to prepare a sample for TEM is the use of a carbon support film, whereas the authors of this paper used a background-free preparation method.
Quoting from the paper:
"For these main reasons, after almost 60 years since the first X-ray diffraction images, we were able to obtain, for the first time, a clear direct and completely background-free image of DNA double stranded in A conformation by a simple and fast preparation method."
Therefore DNA has been directly imaged before, but not using this exact preparation method.
Re:Polymerase chain reaction by Anonymous Coward · 2012-12-01 11:22 · Score: 0

What kind of sick voyeur are you!
Re:Polymerase chain reaction by Biotech_is_Godzilla · 2012-12-01 14:20 · Score: 1

You mean replication fork. "PCR fork" is not a meaningful term. PCR is an artificial way to replicate DNA, and is very different to, and much less complicated than, in vivo (in the cell) DNA replication.
You're right, though, this is not the first time they've visualised DNA. It may be the first time they've visualised it using electron microscopy at a resolution that means you can actually see what its fine structure looks like, instead of it looking like a smooth line, but we already had a good idea what the structure looked like from X-ray crystallography.
X-ray crystallography is an indirect method that gets its data from a massive crystal made of repeated molecules of DNA which is hence in a pretty unnatural state. The question is whether or not this new method is any better. Is the central bit of DNA in any less unnatural a state if it's stuck between 6 other helices, than if it were stuck in the middle of millions? It is possible to make crystals of DNA in the A-form (the ones in this paper are in the A-form, so are the same as what we've already seen from X-ray crystallography) so I'd say that this isn't that exciting a new technique, but this paper is in a pretty high impact journal, so maybe I'm missing something.

Kids^W Scientists these days by omarius · 2012-12-01 01:36 · Score: 1

I hope everyone on this team has read The Double Helix, so they know just how much imaginative work was done back in the day to figure out what they just confirmed visually. While writing that I also had the amusing thought that I hope James Watson calls them up and tells them to get off his lawn.

Prior Work by Anonymous Coward · 2012-12-01 01:48 · Score: 0

Um... "This marks the first visual confirmation of its structure." statment is untrue. This has already been done with AFM. http://www.asylumresearch.com/Gallery/BioScience/Nucleic/Nucleic10.shtml

Human DNA? by jovius · 2012-12-01 02:17 · Score: 3, Insightful

If it was human this is the first time DNA took a photo of itself. It took a few million years and much learning and understanding to realize the present capabilities, but finally we are there.

Re:Human DNA? by jo_ham · 2012-12-01 05:16 · Score: 2

If it was human this is the first time DNA took a photo of itself. It took a few million years and much learning and understanding to realize the present capabilities, but finally we are there.
Just consider, if you leave hydrogen around for long enough it eventually becomes something that can work out what hydrogen is.

Just Wrong by Anonymous Coward · 2012-12-01 06:11 · Score: 0

how is imaging with an AFM more "direct" then imaging via xray crystallography ?
Or hi res NMR ?
I guess you could say that individual molecules allow you to see the solution phase envelope of conformations, but this is on super hydrophbic surface, so it ain't realistic

A thousand words... by fahrbot-bot · 2012-12-01 08:59 · Score: 2

abstract includes the picture that's worth a thousand words

But only four letters: A, C, T and G.

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Look hard in the tunnel and there it is by Anonymous Coward · 2012-12-01 20:34 · Score: 0

Shrodinger's cat looking back at you hiding in there and it is still alive!

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First Direct Image of DNA Double Helix

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