toms@fcs260c2.ncifcrf.gov (Tom Schneider) (11/02/90)
The discussion about STM makes me wonder whether anyone is planning on watching individual atoms decay? Imagine putting down some radioactively labeled DNA and observing the 32P go boom! Broken DNA! Does it leave a pit in the surface? :-) Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov
ems@buttermilk.princeton.edu (Ed Strong) (11/06/90)
In article <Nov.1.20.18.17.1990.8002@athos.rutgers.edu> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: > >The discussion about STM makes me wonder whether anyone is planning on watching >individual atoms decay? Imagine putting down some radioactively labeled DNA >and observing the 32P go boom! Broken DNA! Does it leave a pit in the >surface? :-) > > Tom Schneider > National Cancer Institute > Laboratory of Mathematical Biology > Frederick, Maryland 21702-1201 > toms@ncifcrf.gov I'm not an expert, (obligatory disclaimer inserted here :-) but it seems to me there are a few problems with this scenario. You generally can't tell which individual atoms of a radioisotope are about to decay, half-life is a statistical measure of a large number of atoms. Also 32P is lighter than iron so you can't fission it. Assuming you knew where to look, normal radioactive decay of an individual atom is a comparatively tame event, compared to fission of an atom. I can't say whether it would be energetic enough to break DNA bonds. ------------------------------------------------------------------------------ Ed Strong, Technical Staff Member ems@princeton.edu Princeton University (609) 258-1747 35 Olden Street Department of Computer Science Princeton, NJ 08544-2087 ------------------------------------------------------------------------------ [My guess is that anything ionizing could break bonds. --JoSH]
landman@eng.sun.com (Howard A. Landman) (11/06/90)
In article <Nov.1.20.18.17.1990.8002@athos.rutgers.edu> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >The discussion about STM makes me wonder whether anyone is planning on watching >individual atoms decay? Imagine putting down some radioactively labeled DNA >and observing the 32P go boom! How about *listening*? You could leave the probe tip on a radioactive atom and use a fast digital oscilloscope to capture the trace when it decays, then frequency-shift those samples and play them back at audio rates. Of course, it might be so fast it would just sound like a click. -- Howard A. Landman landman@eng.sun.com -or- sun!landman
toms@fcs260c2.ncifcrf.gov (Tom Schneider) (11/08/90)
In article <Nov.5.18.06.01.1990.14534@athos.rutgers.edu> ems@buttermilk.princeton.edu (Ed Strong) writes: > >In article <Nov.1.20.18.17.1990.8002@athos.rutgers.edu> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >> >>The discussion about STM makes me wonder whether anyone is planning on watching >>individual atoms decay? Imagine putting down some radioactively labeled DNA >>and observing the 32P go boom! Broken DNA! Does it leave a pit in the >>surface? :-) >I'm not an expert, (obligatory disclaimer inserted here :-) but it >seems to me there are a few problems with this scenario. You generally >can't tell which individual atoms of a radioisotope are about to decay, >half-life is a statistical measure of a large number of atoms. Right. So you label up some DNA as hot as possible, or simply put some hot radioactive compound on your 'stage'. The compound chosen should be easy to recognize by STM. Then you use the STM to scan a field of the molecules. One should be able to calculate the number of radioactively labeled atoms in the field given the way they were labeled. DNA is nice because it is easy to recognize by STM (right handed helix). It shouldn't be too hard to watch 200 base pairs of DNA. Anyone have the specific activity on hand? How many of the 400 phosphates could one get hot by current body labeling techniques? The next step is to calculate how long one needs to wait for a decay. 32P has a half life of about 2 weeks, so it should be pretty easy to observe events! In 2 days 1/8 of the atoms --- 50! --- should have gone if all of them were labeled initially. Of course it will be tougher than that because not all the atoms will be hot. > Also 32P is lighter than iron so you can't fission it. Do you mean cause it to fission by bombarding it with neutrons? That would take a lot more equipment than I was thinking about... >Assuming you knew where to >look, normal radioactive decay of an individual atom is a comparatively >tame event, compared to fission of an atom. > I can't say whether it would be energetic enough to break DNA bonds. Anybody know? >------------------------------------------------------------------------------ >Ed Strong, Technical Staff Member ems@princeton.edu >Princeton University (609) 258-1747 >35 Olden Street >Department of Computer Science >Princeton, NJ 08544-2087 >------------------------------------------------------------------------------ > >[My guess is that anything ionizing could break bonds. --JoSH] Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov [The only problem I can see with this scheme is that to get DNA with a high percentage of any atomic type in a radioactive isotope, one may have had to cause synthesis to occur with the isotope as a constituent, and it's easy to imagine a level of radioactivity seriously impeding the synthesis. This would be obviated is it were possible to transmute the marker in place (by neutron irradiation) without destroying the DNA in the process. I don't know whether this is true. --JoSH]
toms@fcs260c2.ncifcrf.gov (Tom Schneider) (12/05/90)
>>In article <Nov.1.20.18.17.1990.8002@athos.rutgers.edu> >toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >>> >>>The discussion about STM makes me wonder whether anyone is planning on watching >>>individual atoms decay? Imagine putting down some radioactively labeled DNA >>>and observing the 32P go boom! Broken DNA! Does it leave a pit in the >>>surface? :-) >[The only problem I can see with this scheme is that to get DNA with > a high percentage of any atomic type in a radioactive isotope, one > may have had to cause synthesis to occur with the isotope as a > constituent, and it's easy to imagine a level of radioactivity > seriously impeding the synthesis. This would be obviated is it > were possible to transmute the marker in place (by neutron > irradiation) without destroying the DNA in the process. I don't > know whether this is true. > --JoSH] Molecular biologists label DNA this way all the time! I'm looking this up in the latest edition of "Molecular Cloning": a laboratory manual, second edition, Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory Press, 1989, page 10.6-10.8. Mix together: dATP dTTP dGTP dCTP (each with 32P on the alpha position, so it stays in the final product) DNA buffer (with salts and water) DNA polymerase The DNA polymerase will bind to the DNA at nicks, and run along, replicating the DNA, replacing the 'cold' bases with the 'hot' bases. They say that one can use all four radiolabeled to get things really hot: "By replacing the preexisting nucleotides with highly radioactive nucleotides, it is possible to prepare 32P-labeled DNA with a specific activity well in excess of 10^8 cpm/ug." Now, that should tell us how frequently the bases are hot, if I knew what to calculate next. Lesee.... The rule is if we divide the ug by the length in kb and multiply by 1.5 we get the number of picomoles. So we have for 1 ug 1500 pmole of bases. but there are about 10^23 molecules per mole, and a pmole is 10^-12 mole, so that's 1.5x10^11 basepairs. Each could bust up, so that's 3x10^11 base pairs. With 10^8 counts per minute, that's 3x10-4 cpm per base. If we were to watch 100 bases for an hour, we should see about 2 events. This is a rough calculation, and I haven't checked it closely (could someone confirm please?) but it looks like the experiment is practical! Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov
jgsmith@bcm.tmc.edu (James G. Smith) (12/05/90)
I think watching radioactive DNA decay is both do-able and worth doing. The following is a real quick lesson in DNA structure. The building blocks of DNA are 4 bases, each of which is attached to a sugar. (They're all attached to the same kind of sugar: deoxyribose). A strand of DNA is made by linking the sugars together with phosphates. The bases are simply hanging off the sugars. The actual starting material for adding a base to the end of the DNA is the base attached to the sugar attached to three phosphates in a row. During synthesis, the two phosphates on the end get cut off and the phosphate closest to the sugar gets connected to the last sugar in the DNA strand. It is a routine procedure to radioactively label DNA by allowing the synthesis to occur using building blocks in which the phosphate closest to the sugar is radioactive (32-P). Thus, part of the chain which holds the DNA together is a radioactive atom. I don't know if much is known about what happens to DNA when the 32-P decays. That's why I think the experiment is worth doing. * (maybe they could look at other kinds of radiation, especially UV. How about tritium? What? You don't want to wait around for a few years?)
mike@everexn.com (Mike Higgins) (12/05/90)
In <Nov.7.15.17.08.1990.26991@athos.rutgers.edu> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >ems@buttermilk.princeton.edu (Ed Strong) writes: >toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >>>The discussion about STM makes me wonder whether anyone is planning on watching >>>individual atoms decay? Imagine putting down some radioactively labeled DNA >>>and observing the 32P go boom! Broken DNA! Does it leave a pit in the >>>surface? :-) There is a sampling problem you all seem to be overlooking: The STM doesn't take snapshots, it's this little needle waving around. Even if it is scanning the area of say a DNA molecule where a 32P is about to go boom, all you will see is one picture whith everything in place, and the next scan will show something broken. Big deal. If the needle happened to pass over the 32P at the exact moment (low probability) when it goes boom, the most likely result is that the rest of that horizontal scan is messed up. Still not exciting. mike@everexn.com [Actually, seeing "something broken" could be quite useful. However, see the recent Sci. Am. article on "photographing" molecular reaction transition states--a new technology that bids to contribute substantial useful understanding for nano-designers. --JoSH]
landman@eng.sun.com (Howard A. Landman) (12/05/90)
>In article <Nov.5.18.06.01.1990.14534@athos.rutgers.edu> >ems@buttermilk.princeton.edu (Ed Strong) writes: >>Assuming you knew where to >>look, normal radioactive decay of an individual atom is a comparatively >>tame event, compared to fission of an atom. >> I can't say whether it would be energetic enough to break DNA bonds. In article <Nov.7.15.17.08.1990.26991@athos.rutgers.edu> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes: >Anybody know? >>[My guess is that anything ionizing could break bonds. --JoSH] You're all overlooking something very obvious, which is that after a radioactive decay you've got an atom of a *different* *element* there, which will have different bonding properties than your original atom. This has some severe implications for the survival of any affected bonds! -- Howard A. Landman landman@eng.sun.com -or- sun!landman
hayes@hpuxa.ircc.ohio-state.edu (Patrick W. Hayes) (12/14/90)
About watching atoms decay with an STM: isn't it true that every time you scan over an atom with the needle, you have observed it, thus collapsing the wave function to "I'm not even thinking about decaying now" state? So the more often you scan it, the less likely it will become that it decays? Just asking, Patrick Hayes [This isn't as nutty as it sounds. There are in fact demonstrated physical systems where repeated measurement can prevent quantum- mechanical transitions. However, in the specific case of the STM, my guess is that the measurement of the state of the nucleus is far too indirect for it to have that kind of effect. --JoSH]
landman@eng.sun.com (Howard A. Landman) (12/14/90)
In article <Dec.4.22.18.49.1990.24170@athos.rutgers.edu> mike@everexn.com (Mike Higgins) writes: > There is a sampling problem you all seem to be overlooking: The STM >doesn't take snapshots, it's this little needle waving around. Even if it is >scanning the area of say a DNA molecule where a 32P is about to go boom, all >you will see is one picture whith everything in place, and the next scan will >show something broken. Big deal. My notion was, you scan perhaps once a second to make sure you haven't drifted, but spend most of the time (more than 98%) hovering over the atom of interest. That gives you an excellent chance of seeing everything in the Z dimension. That's why I suggested treating it as an audio-like signal. For video you have to trade off time resolution to get spatial resolution. -- Howard A. Landman landman@eng.sun.com -or- sun!landman
toms@fcs260c2.ncifcrf.gov (Tom Schneider) (12/19/90)
In article <Dec.13.17.07.53.1990.17437@athos.rutgers.edu> landman@eng.sun.com (Howard A. Landman) writes: >In article <Dec.4.22.18.49.1990.24170@athos.rutgers.edu> mike@everexn.com (Mike Higgins) writes: >> There is a sampling problem you all seem to be overlooking: The STM >>doesn't take snapshots, it's this little needle waving around. Even if it is >>scanning the area of say a DNA molecule where a 32P is about to go boom, all >>you will see is one picture whith everything in place, and the next scan will >>show something broken. Big deal. No, it would be the first time somebody saw an 'atomic explosion' at the atomic level. You don't know what might come from that. For one thing, even present day electronics are degraded by the radioactive materials imbedded in their matrix (there was a paper on that in Science (?) sometime before 1987), so learning what kind of local damage occurs could be very important for nanotechnology. And it's an easy experiment that somebody can do TODAY with the right equipment. I realized that one must scan, and that one would not see the actual event. But one would see the damage created. (Assuming the parties are anywhere nearby afterwards!) >My notion was, you scan perhaps once a second to make sure you haven't drifted, >but spend most of the time (more than 98%) hovering over the atom of interest. >That gives you an excellent chance of seeing everything in the Z dimension. >That's why I suggested treating it as an audio-like signal. For video you have >to trade off time resolution to get spatial resolution. The experiment is not practical with one atom, unless the half-life is very short. If it's short then it is hard to prepare the materials without them falling apart before you get to look at them. Since 32P decays with a half life of about 14 days, it hangs around long enough for the experiment to be done. But 32P is convenient also because one can label DNA with it, and that takes only a day. But I DO like the idea of setting up the STM to listen to one phosphate for a MONTH, to 'hear' the actual explosion! I think that would make a nice second experiment, once one had seen the decay by scanning a large population repeatedly. > Howard A. Landman > landman@eng.sun.com -or- sun!landman Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov