DNA Scanners?
- Thread starter Rick
- Start date
There aren't any scanners like the one you describe as far as I know. Most require a pure DNA sample removed from the rest of the cell components, a large machine, and a day or two (at least for a genome the size of a human's). Of course, I could be wrong, and please correct me if I am.
scanners
Idle Mind is right, no such thing exists, and the process of DNA sequencing, at least as the technology stands now, would prohibit such a machine (let's not get into mumbo jumbo about government secret technology and ya da ya da).
DNA sequencing is not tremendously difficult, if you have an idea of what the sequence should be, but it is harder if you're starting from scratch. Even now, knowing the human genome sequence, it would take longer than a day or two to sequence a human genome. Even the best sequencer (that I know of) can only give a max read of 1000 nucleotides/reaction, and since the human genome is huge (2.9 billion bases) according to this article in Science Genome 99% complete
it would take a long time even with an army of sequencers.
Sequencing a genome requires breaking it up into little bits, and is usually done using what is called the "shotgun approach."
Anyway, I digress, let's just say it is unlikely that a machine will ever exist that could scan your entire genome like the one you suggest. Perhaps someday machines will exist that can harvest DNA straight from your blood and sequence a set of predetermined genes looking for single nucleotide polymorphisms or mutations (taking some time in the process).
Now it takes me two days to get a sequence, some people can get it faster if they do the whole procedure themselves.
Idle Mind is right, no such thing exists, and the process of DNA sequencing, at least as the technology stands now, would prohibit such a machine (let's not get into mumbo jumbo about government secret technology and ya da ya da).
DNA sequencing is not tremendously difficult, if you have an idea of what the sequence should be, but it is harder if you're starting from scratch. Even now, knowing the human genome sequence, it would take longer than a day or two to sequence a human genome. Even the best sequencer (that I know of) can only give a max read of 1000 nucleotides/reaction, and since the human genome is huge (2.9 billion bases) according to this article in Science Genome 99% complete
it would take a long time even with an army of sequencers.
Sequencing a genome requires breaking it up into little bits, and is usually done using what is called the "shotgun approach."
Anyway, I digress, let's just say it is unlikely that a machine will ever exist that could scan your entire genome like the one you suggest. Perhaps someday machines will exist that can harvest DNA straight from your blood and sequence a set of predetermined genes looking for single nucleotide polymorphisms or mutations (taking some time in the process).
Now it takes me two days to get a sequence, some people can get it faster if they do the whole procedure themselves.
This is my field!
It depends on what you want, let’s say you want a full-nucleotide map of your genome, this is how we would do it:
1. We take some for your blood, skin or other cell sample.
2. We extract the DNA from the cell sample by lysing and then running the goop through several centrifuge stages and not to mention all the nice chemicals we use to digest all the unwanted cellular components, all this takes at the very least several hours.
3. We take your DNA and run it through a PCR (polymerase chain reaction) think of it as a copying machine for DNA in which we make a unlimited amount of copies of your DNA.
4. We cut (lyse) your DNA into manageable chucks.
5. We make copies of your DNA using DNA dyes (one dye for each type of nucleotide), these dyes also cut up your DNA even more. Lets say we have a segment of your DNA that reads ATGCAG, after using these dyes we know have 6 segment that go: A-Dye_A, AT-Dye_T, ATG-Dye_G, ATGC-Dye_C, ATGCA-Dye_A, ATGCAG-Dye_G. All of the above steps could be done in under a week.
6. These DNA dye segments are run through TLC plate in which as they travel through the plate they get spread out according to size, at the end of the plate we (today, back in the old days you had to do this by hand!) a UV laser and spectrometer that will read the colors of the dyes as they pass, the smallest DNA/dye segment (A-Dye_A) would be read first followed by the rest in order until we would read your whole segment (ATGCAG). Great 6 nucleotides read, another 3 billion to go! Modern Automated systems can read about 200,000 nucleotides a day but remember a lot of re-reading and backtracking is needed as well, After several years we will be done and give you your results.
The internship I am doing now is making a device that will read the fluorescence profiles of DNA dyes so we will have another property besides color in sequencing your DNA. By characterizing both the color and fluorescence decay profiles of DNA dyed fragments as they pass by on a TLC plate we can increase the accuracy and general efficiency of the sequencing process (hence less re-readings and backtracking)
Now lets say you don’t have the time or the needs for the above kind of accuracy, well then we could do a lot of simpler mappings of your genome that are much quicker, For example instead of ready the nucleotide sequence we could just look at all the fragments that we get using common DNA lysing enzymes, Since these enzymes cut your DNA at a specific nucleotide sequence, we can map this with a TLC plate, this could be done in under a week. This is how most forensic DNA tests are done.
Modern technology has made a even quicker genome mappers, by having dyed RNA probes with very specific sequences we can just slap your lysed DNA on a plate with a grid of different RNA probes and take a image of what probes the DNA sticks to and what it does not stick to. All of this can be done in one step in just minutes. Remember though this is not a nucleotide map this is just a map of a few DNA sequences you have: it’s only useful for forensics and gene testing.
The future is believe to be a device that can read a single DNA strand one nucleotide at a time. By pumping a DNA strand through a nanometer wide channel and reading its fluorescence spectra and profile with some kind of unbelievably thin laser beam it is hypothesis that you could read 100,000 nucleotides a second! When that happens we could have full nucleotide maps of your genome in just hours.
It depends on what you want, let’s say you want a full-nucleotide map of your genome, this is how we would do it:
1. We take some for your blood, skin or other cell sample.
2. We extract the DNA from the cell sample by lysing and then running the goop through several centrifuge stages and not to mention all the nice chemicals we use to digest all the unwanted cellular components, all this takes at the very least several hours.
3. We take your DNA and run it through a PCR (polymerase chain reaction) think of it as a copying machine for DNA in which we make a unlimited amount of copies of your DNA.
4. We cut (lyse) your DNA into manageable chucks.
5. We make copies of your DNA using DNA dyes (one dye for each type of nucleotide), these dyes also cut up your DNA even more. Lets say we have a segment of your DNA that reads ATGCAG, after using these dyes we know have 6 segment that go: A-Dye_A, AT-Dye_T, ATG-Dye_G, ATGC-Dye_C, ATGCA-Dye_A, ATGCAG-Dye_G. All of the above steps could be done in under a week.
6. These DNA dye segments are run through TLC plate in which as they travel through the plate they get spread out according to size, at the end of the plate we (today, back in the old days you had to do this by hand!) a UV laser and spectrometer that will read the colors of the dyes as they pass, the smallest DNA/dye segment (A-Dye_A) would be read first followed by the rest in order until we would read your whole segment (ATGCAG). Great 6 nucleotides read, another 3 billion to go! Modern Automated systems can read about 200,000 nucleotides a day but remember a lot of re-reading and backtracking is needed as well, After several years we will be done and give you your results.
The internship I am doing now is making a device that will read the fluorescence profiles of DNA dyes so we will have another property besides color in sequencing your DNA. By characterizing both the color and fluorescence decay profiles of DNA dyed fragments as they pass by on a TLC plate we can increase the accuracy and general efficiency of the sequencing process (hence less re-readings and backtracking)
Now lets say you don’t have the time or the needs for the above kind of accuracy, well then we could do a lot of simpler mappings of your genome that are much quicker, For example instead of ready the nucleotide sequence we could just look at all the fragments that we get using common DNA lysing enzymes, Since these enzymes cut your DNA at a specific nucleotide sequence, we can map this with a TLC plate, this could be done in under a week. This is how most forensic DNA tests are done.
Modern technology has made a even quicker genome mappers, by having dyed RNA probes with very specific sequences we can just slap your lysed DNA on a plate with a grid of different RNA probes and take a image of what probes the DNA sticks to and what it does not stick to. All of this can be done in one step in just minutes. Remember though this is not a nucleotide map this is just a map of a few DNA sequences you have: it’s only useful for forensics and gene testing.
The future is believe to be a device that can read a single DNA strand one nucleotide at a time. By pumping a DNA strand through a nanometer wide channel and reading its fluorescence spectra and profile with some kind of unbelievably thin laser beam it is hypothesis that you could read 100,000 nucleotides a second! When that happens we could have full nucleotide maps of your genome in just hours.