Blackpapa said:
rgrekejin said:
As an actual professional geneticist...
DNA FLASH DRIVE!
1. Can DNA strands get tangled?
2. What's the maximum length for loose DNA/RNA in a solution?
3. Would you pack the DNA into higher-order structures or just settle with a soup of short fragments?
4. What's the upper physical limit on DNA write/read speeds?
5. Is DNA/RNA a good candidate for fast-access chemical data storage?
6. As I understand it, reading and writing DNA goes in this slow roundabout way. What's stopping us from interfacing directly?
Before I'd begin, I'd like to point out that addressing actual the actual engineering problems behind DNA data storage is not really my specialty (I do more gene therapy-related stuff) - there may be recent advances in this field that I am not aware of, so don't jump down my throat if I don't know them.
1. Sure, DNA can get tangled. Often, the speed of molecular motion is such that the DNA will often spontaneously untangle itself before this becomes a problem, but lots of organisms have special enzymes like topoisomerases that untangle tangled DNA. In higher organisms this is less of a problem, as the higher-order structures DNA packs itself in leave less of it free to move (so there's usually not enough free length at any given time to get tangled), but they still have a variety of topoisomerases around for instances like replication when longer lengths of free DNA are exposed.
2. Well... this is actually kind of a tricky question. It depends a lot on what the solution you're dissolving it in is, and what degree of condensation you're willing to allow the DNA to have. In human cells, whole chromosomes are the same piece of linear DNA, and chromosome one is something like 250 million base pairs. Naked DNA (DNA with no protein or other modifications) *can* exist in solution in really, really large sizes - it's just that it's fragile this way, and tends to break apart when perturbed.
3. This really depends on what you're trying to do with the DNA. The most basic unit of DNA condensation, the nucleosome, involves wrapping DNA around a protein called a histone. These nucleosomes can then be condensed further. The problem is that in order for DNA to be read, it must be removed from the nucleosome.
4. Actually, read and write speed are more or less the same because in most current technologies, the same enzyme is used for both. DNA is synthesized by a DNA polymerase enzyme. The fastest commercial one I've seen claims to do something like 1,000 bases per enzyme molecule per second. DNA is usually sequenced, or "read", by performing the same synthesis reaction with nucleotides that are labeled in some way, giving off a specific wavelength of light when they are added to the strand. These signals are detected and interpreted as the order of the bases in the DNA. Now, for a known sequence (like anything you're trying to record would be), that would probably be synthesized chemically, rather than using an enzyme. As far as the theoretical upper limit... I'm not sure. I'd ask a physical chemist.
5. With current technology? No. Never say never, because there are certainly smarter people than me working in this field, but at the moment, due to the nature of how DNA is synthesized and sequenced, you can't take advantage of DNA's awesome ability to condense itself and still have something that could be read even relatively quickly. At the moment, though, it's a much better option for long-term archival storage than for something rapid access.
6. I'm afraid I'm not really sure I understand the question. What do you mean by "interfacing with it directly"? If you mean directly manipulating the DNA, the answer is simple - the scale. Molecules of DNA are incredibly tiny - measured on the scale of atoms. We can interface with them chemically, or by utilizing existing enzymes, proteins, or other molecules that exist at their scale, but there's no way to mechanically manipulate them at the moment.
Hope that was interesting to you! I'm never sure what level to write these things at, so I apologize if I was either talking above your head or mostly telling you stuff you already knew.