Well it's not at all clear to me that you would ever use the CIPH chip to perform actual tests - rather you would use the chip to discover what proteins to look for, and then use some sort of immunoassay (like this) to measure the protein levels.
But this does sound interesting - just not competitive with CIPH. Perhaps it would compete with MSD (of Igen infamy).
Incidentally, the Corante chemistry blogger discussed this work a few weeks back:
Sunday, October 5, 2003
Performing Proteins, Jumping Through Hoops
The new way to detect proteins was published in the latest issue of Science (, p. 1884). It's an ingenious idea, because it gets around one of the biggest problems. As I was saying on Friday, proteins have a much greater variety than DNA or RNA, and can take on a gigantic range of shapes. So It's no surprise that there isn't a general technique that picks them up specifically.
The closest thing is the use of antibodies. The immune system is capable of generating a binding protein against something it recognizes as foreign, and these can be very selective. Antibodies are a vital tool in the protein field, but antibody assays don't approach the sensitivity of the DNA/RNA assays that are behind techniques like gene chips.
Over the past ten years or so, several groups have tried to combine the two approaches. Generally, what they've ended up doing is binding the target protein to some solid support, and then using an antibody for it that has a specific stretch of DNA attached to it. Once the antibody binds to the protein, you can use techniques like PCR to amplify the DNA that's hanging off of the complex, and get a much higher sensitivity in the assay. This "immuno-PCR" idea is a good one, but it's had some problems.
From a chemist's standpoint (mine!), one of the biggest difficulties is hooking up the DNA to the antibody. There's no really good way to do that, because nucleic acids and proteins aren't very similar, chemically. I mean, it's certainly possible, but it's not a natural fit. Several methods have been used, but they all have their complications. And when you can get them to work, you typically don't have many DNA strands (maybe only one) coming off your antibody, which isn't optimal.
This is a lurking weakness of many interesting molecular biology schemes, actually. I've come across several of these ideas that have a step in them which says "And then we hook our small ligand to the biomolecule," or "OK, we should be able to chemically link these two protein fragments together with some kind of nonreactive tether, right?" Joining things up like this is pretty difficult, actually. It's a special case each time, and each time you have to make an effort to be sure that you haven't hosed your system up somehow. We organic chemists don't have a toolbox marked "unreactive, uninterfering all-purpose linking groups."
But this latest wrinkle, from Chad Mirkin's group at Northwestern, gets around these problems. They start with small (micrometer-sized) polymer particles that have iron oxide in their core. These magnetic microparticles are functionalized with monoclonal antibodies (mAbs) to the protein of choice - in this case, they went after the well-known diagnostic protein PSA (prostate-specific antigen.) The monoclonals all recognize the same surface region of the PSA. Separately, they take gold nanoparticles and decorate those with plenty of specific DNA strands, as well as attaching polyclonal antibodies for the PSA protein. Both of these technologies have been previously worked out. The polyclonal antibodies recognize PSA, too, but at a number of different sites that don't necessarily overlap with the one that the mAb sticks to.
So, you take your magnetic particles, with the mAbs all over them, and let them contact your blood or tissue sample. PSA proteins stick to the antibodies, as they should. Now you purifiy things by use of the magnetic microparticles - put a strong magnet up there, and all the microparticle/antibody/PSA complexes stick to the wall of the tube! That lets you wash out all the other stuff - other proteins, unreacted PSA, what have you.
Then you come in with your gold nanoparticles, and let the polyclonal antibodies stick to other exposed parts of those bound PSA proteins. Now you've got some real hairballs floating around in there - micrometer-sized magnetic particles, decorated with antibodies which have PSA protein stuck to them, which in turn have other antibodies stuck to them, which antibodies are attached to small gold particles that are furry with strands of DNA. Quite a fearsome sight, no doubt, if we only we could see it. Another magnetic-separation round can clean up this reaction, too.
But now things are set up. Soaking the complexes in pure water allows the DNA to unravel off of them. You use the magnetic separation again to get rid off all the hairballs, which have done their part and are dismissed. That leaves you with a water solution of single-stranded DNA, which (thanks to PCR and cDNA chips) can be detected at laughably low concentrations. The linkage of protein-to-DNA has been accomplished smoothly and cleanly, making for a very nice assay indeed.
Compared to the standard diagnostic PSA method, this one is about a million times more sensitive. And there's more: by using a mix of antibody-coated particles, you could simultaneously detect dozens of proteins in the same sample. Just assign each of them a specific DNA sequence back at the beginning, and they won't interfere with each other at all. The authors call this "bio-bar-coding," and that's a good way of looking at it. This should work for any protein that antibodies can be raised to, which is a goodly selection (and which covers most everything that's diagnostically important, as far as I'm aware.)
I assume that these folks have already patented this idea - heck, I assume that they've already formed a company, selected a letterhead and, most likely, a ticker symbol. If this works out as well as it looks, it's going to be very, very useful, both in the clinic and in the research lab. Congratulations all around.
corante.com
Peter |
