Can Laser Spectroscopy Reveal 3D Molecular Structures and Subsurface Details?

[fredreload]

So I came across this article while looking for laser spectroscopy. From what I see most of the laser spectroscopy requires the laser to beam directly at the ample to retrieve a spectral image about the sample. I want to know if it is possible to reverse the spectral image back into a 3D image of the molecule or how do people go about interpreting this spectral image. Then if there is a way to look beneath the skin, I mean most of the signal received is going to be from the surface. If someone knows how useful this technology is, please let me know, thanks!

P.S. First part is confirmed thanks to Wikipedia, so how do you look beneath the surface?
P.S. I guess this works, but I still want to know how effective it is, if someone got any interesting videos let me know

 

[Simon Bridge]

So I came across this article while looking for laser spectroscopy. From what I see most of the laser spectroscopy requires the laser to beam directly at the sample to retrieve a spectral image about the sample.

You don't have to - but you want to be able to say that the alteration to the laser light is due to the interaction with the sample. Tough to prove if only part of the beam hits the sample. You can take reflection spectroscopy from a glancing contact though. That's pretty much what the article is talking about: they'd point the scanner at you and sensors collect the scattered light.

I want to know if it is possible to reverse the spectral image back into a 3D image of the molecule or how do people go about interpreting this spectral image.

It is not like taking a photograph no. Different molecules scatter light in different ways. The spectra from the sensors is compared with samples that have been taken of known substances.

Then if there is a way to look beneath the skin, I mean most of the signal received is going to be from the surface. If someone knows how useful this technology is, please let me know, thanks!

Light penetrates the skin to some degree - different light penetrates a different amount. It's usually more useful to just use an x-ray machine (which is exactly like taking a photograph).
Note: A CAT scan does reconstruct a 3D image of a slice through the patient by using multiple shots from different angles in rigidly controlled circumstances ... and that can see inside your body. Maybe this is what you are thinking of?

Dunno what you mean by "effective" though ... the tech has been around for quite a while so it is pretty established science.
I gather that dogs are still better in general - a machine like the one in the article would be installed at a checkpoint so the test will be clean.
A positive reading will just mean that the subject gets more attention - maybe swabbed. It will be possible to set such a sensitive machine off in ways that are not prosecutable just like your cell phone coming up positive for cocain does not prove you are a user.

 

[fredreload]

Thanks for the reply, effective as of saying they can scan the entire body and know everything at a molecular level in pico-second. As powerful as this technique should be I have not heard of it applied for a body scan. With hyper-spectral imaging you would be able to get a distribution of different things in a 3D data cube, would it eventually become a 3D image? Well my concern is how detailed is the spectral image I can get from laser spectroscopy, Wikipedia suggests that "the lateral and depth resolutions were 250 nm and 1.7 µm" for Raman Spectroscopy, this video with the attosecond laser suggests it is possible to detect molecular changes of molecules, so the resolution should be even higher with an attosecond laser?

 

[Simon Bridge]

Thanks for the reply, effective as of saying they can scan the entire body and know everything at a molecular level in pico-second.

There are a LOT of molecules in the human body and a picosecond is very small. To "know" everything would involve getting a computer to store and analyze the data involving interactions of more than 10^20 molecules.
The fastest computer can manage a bit under 34 calculations in a picosecond... thousands of times too slow.

As powerful as this technique should be I have not heard of it applied for a body scan.

Yes you have: the article you linked to is about this very application isn't it?

With hyper-spectral imaging you would be able to get a distribution of different things in a 3D data cube, would it eventually become a 3D image? Well my concern is how detailed is the spectral image I can get from laser spectroscopy, Wikipedia suggests that "the lateral and depth resolutions were 250 nm and 1.7 µm" for Raman Spectroscopy, this video with the attosecond laser suggests it is possible to detect molecular changes of molecules, so the resolution should be even higher with an attosecond laser?

That kind of resolution is not like picture resolution on a TV screen. The output of a spectrograph is a wavy line. You can infer stuff from the wavy line.

Currently the way to build a 3D pic of the inside of someones body is with NMR scans.

 

[fredreload]

Well, you are right, it takes time to process this information, something that is not mentioned in the article(did I miss out?).

Well I'm thinking of it being used in a hospital for cancer treatment, need to wait until 2030?

Something like https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2014/moerner-lecture-slides.pdf, I'm thinking of using it to image and analyze DNA molecules at real time, this seems like the closest technique based on the video presented. Some type of molecule tracking technique

 

[Simon Bridge]

The quick time in the article is the amount of time it takes for the laser pulse to return to the unit. Journalists often report the sensational stuff without thinking it through. That is like saying you can take an instant snapshot with a polaroid ... sure, the button press is pretty quick, but the film still has to develop so you don't have a picture yet.
Or is all that just so many archaic terms these days?

So: it takes a nanosecond to collect the raw impression which then has to be stored, sorted, and processed ... then accessed and presented in a human-readable formal. Same as anything really.

Hospitals already have fast hi res 3D scanners that use NMR ... I keep telling you this.
They are good enough that a 3D model of an organ or bone of interest can be computed, then printed in a rapid prototype machine, so the surgeons can practise operations before opening the patient up.

What do you mean "analyse DNA molecules in real time"? All analysis is done in real time: it's the only time we have.
But sure: one could, in principle, image a DNA molecule that you were working on so you can observe the changes as they happen ... it's a big molecule though, you'd see it a bit of string or zoom in for a fuzzy-rung effect.

 

[fredreload]

I know hospitals have MRI, but the resolution isn't high enough to be on a molecular scale

DNA needs to be sequenced to find the four bases. If you can analyze DNA in real time, the whole cellular structure as it develops and protein sequenced. Sure I've seen it in animation, but not in real time

P.S. Well sure I need more understanding of how DNA is analyzed, leave it at this

 

[Simon Bridge]

I think the main this you want to look at is the differences in scale you are talking about, and how much things move about at the molecular level.
The animations you have seen are made up. Fiction.

 

[fredreload]

From what I see there are two ways to track the DNA molecules. You can use Raman Microscopy to identify and track each of the four bases on the DNA molecule in real time and construct an image out of it(that's what laser microscopy do, identify explosives). Or, if you can get a detailed enough image of the DNA with laser microscopy at real time, you can identify the four bases based on the image presented. Either way you might be able to skip the traditional DNA sequencing, I'm not experienced enough to note on this

 

[Mike H]

People are using Raman spectroscopy to develop DNA sequencing methods - http://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/user/1317/documents/review_treffer_2010_recent_advances_in_single_molecule_sequencing.pdf (PDF link).

Of course, sequencing in a laboratory is one thing. If you wanted to do something like monitor DNA in a human cell, that's a different story.

 

[fredreload]

People are using Raman spectroscopy to develop DNA sequencing methods - http://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/user/1317/documents/review_treffer_2010_recent_advances_in_single_molecule_sequencing.pdf (PDF link).

Of course, sequencing in a laboratory is one thing. If you wanted to do something like monitor DNA in a human cell, that's a different story.

Monitor DNA in a human cell is the way to go and how hard is it?

 

[Mike H]

As noted in the review, the SERS-based methods require that the sample molecule (in this case, DNA) adsorb to a metal surface to enhance the signal to permit detection at the single-molecule level. Doing SERS-based measurements in vivo is non-trivial, and are nowhere near the stage necessary to do monitoring of DNA in the manner you desire. People have done in vivo glucose sensing in rats (using a surgically implanted microsphere) - for example, see here - as well as look for various pathological biomarkers using so-called SERS nanotags (a nanoparticle with Raman-active molecules on it, all surrounded by a polymer/protein shell) - see here. They rely upon secreted metabolites in the blood to detect, not inside the cell.

There's another issue I'm surprised you haven't brought up - DNA in eukaryotic cells is bound up with various proteins, ultimately forming chromatin. How do you propose to get the DNA to unbind from chromatin to allow for these experiments you're interested in seeing done?

 

[fredreload]

There's another issue I'm surprised you haven't brought up - DNA in eukaryotic cells is bound up with various proteins, ultimately forming chromatin. How do you propose to get the DNA to unbind from chromatin to allow for these experiments you're interested in seeing done?

Wasn't aware of that, I'll keep that in mind

P.S. Well the important thing is to be able to correctly locate and track the sequence. I am not sure if it is possible to generate an image based on Raman Spectroscopy instead of getting a spectrum, with the improvement of attosecond laser and all the other techniques this seems to be the closest in observing DNA in vivo. As the video I posted suggests that this could happen in year 2030 in observing molecular changes so I sort of did a search on this for the heads up. Interesting light reflection technique

 

[Mike H]

OK, here's the next batch of questions.

When you say locate and track the sequence, again, in every human cell? Like I mentioned, the trick is that DNA is not just floating around in a vacuum for you to do spectroscopic measurements on inside the cell. It's bound up within proteins to form chromatin.

Regarding attosecond laser spectroscopy - really? They do this stuff in vacuum chambers, and while I believe some of it winds up being done in the near-infrared, plenty of it winds up in the XUV to soft x-ray range. You are not going to convince very many people to let you blast them with an XUV or soft x-ray laser. Ultraviolet light causes sunburns, and x-ray exposure is carefully monitored for a variety of health reasons. And you want to do so from head to toe!

More importantly, attosecond spectroscopy isn't well-matched for what you want to apparently want to study - outside of things like light absorption or charge transfer where attosecond spectroscopy might be helpful, most processes in biology aren't at the attosecond timescale. DNA winding, unwinding, DNA strands being formed...none of these require such incredible time resolution.

I also think you should look harder for work done on in vivo spectroscopy, as here is one recent example. I found a number of citations of various spectroscopic methods being used to probe DNA in living cells.

If you're serious about wanting to understand and develop in vivo spectroscopy to the next level, it would help to be a bit more critical of what you read and watch, as well as to do some more in the way of background reading.

 

[fredreload]

OK, here's the next batch of questions.

When you say locate and track the sequence, again, in every human cell? Like I mentioned, the trick is that DNA is not just floating around in a vacuum for you to do spectroscopic measurements on inside the cell. It's bound up within proteins to form chromatin.

Regarding attosecond laser spectroscopy - really? They do this stuff in vacuum chambers, and while I believe some of it winds up being done in the near-infrared, plenty of it winds up in the XUV to soft x-ray range. You are not going to convince very many people to let you blast them with an XUV or soft x-ray laser. Ultraviolet light causes sunburns, and x-ray exposure is carefully monitored for a variety of health reasons. And you want to do so from head to toe!

More importantly, attosecond spectroscopy isn't well-matched for what you want to apparently want to study - outside of things like light absorption or charge transfer where attosecond spectroscopy might be helpful, most processes in biology aren't at the attosecond timescale. DNA winding, unwinding, DNA strands being formed...none of these require such incredible time resolution.

I also think you should look harder for work done on in vivo spectroscopy, as here is one recent example. I found a number of citations of various spectroscopic methods being used to probe DNA in living cells.

If you're serious about wanting to understand and develop in vivo spectroscopy to the next level, it would help to be a bit more critical of what you read and watch, as well as to do some more in the way of background reading.

Well in as many cells as possible all the way from the blastocyst and how it becomes human shape. This is when you need hyperspectral imaging. Imaging a data cube containing information about the DNA in terms of colors but not by structure. For instance, finding the spectral color of one of the four bases would be much easier then identifying it with its molecular structure. My guess is the spectral color would be different on different parts of the chromatin and you isolate the protein out.

It is pretty harmless with a Kickstarter on the way.

I'm following what it's said in the video as its prediction of the attosecond technology by year 2030.

The example shows the use of NMR and you'll need a structural analysis of each to figure out the DNA bases and protein. I didn't know NMR can present chromosome in such resolution as well. I would like to know if DNA information is already being processed with NMR and how they are doing this analysis.

Well I haven't found anything about hyperspectral imaging with DNA so I suppose this is just a speculation. I just think a structural analysis of the chromatin would be pretty hard to do

P.S. If that's not enough I would track the enzyme during DNA replication to find the correct order

 

[Mike H]

Your comment about thinking about DNA in terms of color but not structure has convinced me this will not be a fruitful conversation to continue. Where a sample absorbs and emits in the EM spectrum is dependent on its structure - this is standard physics/chemistry. IR radiation probes vibrational motions, UV/Vis tends to probe electronic transitions, microwaves probe rotational transitions…..these are all things that can be calculated to varying degrees of accuracy. You cannot decouple the two in the way you seem to want to do.

I would suggest foregoing the cutting-edge research and refresh your understanding of physical chemistry/atomic & molecular spectroscopy if you’re serious about this topic.

 

[fredreload]

Hmm, when you are lighting up the four bases on DNA you are lighting the DNA at different points, assuming not the entire DNA molecule is vibrating and emitting EM spectrum then I should be able to get four different spectrum of light based on the four bases of DNA. The key is that only the part of the DNA that is being probed is vibrating but not the entire DNA molecule, which I am not able to prove so I will leave it at that. Through observation I would speculate that you can light up part of the DNA distinctly