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Similar DNA Molecules Able to Recognize Each Other
Chroniton brings us a story about research into DNA which has shown that free-floating DNA strands are able to seek out similar strands without the assistance of other chemicals. From Imperial College London:
"The researchers observed the behaviour of fluorescently tagged DNA molecules in a pure solution. They found that DNA molecules with identical patterns of chemical bases were approximately twice as likely to gather together than DNA molecules with different sequences. Understanding the precise mechanism of the primary recognition stage of genetic recombination may shed light on how to avoid or minimise recombination errors in evolution, natural selection and DNA repair. This is important because such errors are believed to cause a number of genetically determined diseases including cancers and some forms of Alzheimer's, as well as contributing to ageing."
(They hate it when you do that.)
The World Wide Web is dying. Soon, we shall have only the Internet.
are there any other compounds, perhaps naturally-occurring compounds that exhibit similar behavior? If so, that might go aways towards explaining how the first primordial single-celled organisms came about.
The higher the technology, the sharper that two-edged sword.
With all of its advances, I sure hope a code of conduct is built into societies laws to help contain its tech to good uses. Of course there may be gene doping, etc. But antidiscrimination laws may need to be written at some point.
gang up to throw the nerdy molecules into their lockers?
- in germ cells for "crossover" diversification of offspring, and
- in somatic cells to repair already damaged DNA.
Though there are other genetic mechanisms of aging (Telomere shrinkage), and still more non-genetic.They already do this, it's called hybridization .
If I had two strands of magnets, arranged with random orders of polarity, identical strands would be able to stick together along the entire length in a "head to tail" fashion. Dissimilar strands would have "weak spots" where they didn't want to stick together. If you wiggled them, they'd be more likely to come aparts.
At the molecular level, electrical forces (analogous to the magetic attraction above) and thermal forces (analogous to the wiggling) dominate but the analogy is similar. This just doesn't seem like such an amazing thing to me.
Come on, let's try it. It probably won't be as cool as using mouse traps and ping-pong balls to demonstrate chain reactions; but it might still be interesting.
For all intensive purposes, "whom" is no longer a word. That begs the question, "who cares"?
or does eliminating certain DNA errors seem like a possibly very bad idea? I mean, let's say that a gene causes Alzheimer's disease later in life, but it gives its carrier immunity to a new virus that appears. Eliminating this gene from the entire species could wind up killing us all off in the end. Just because something appears to be a disadvantage doesn't mean that it's always so.
what's that now?
I believe that the article is saying that the molecules seem to "seek" each other out in solution, over and above just randomly bumping into each other.
Is there a bad?
"What's the use of a good quotation if you can't change it?" - Doctor Who
I was quite suspicious of their claim, so I read the original article.
The claim is that long DNA molecules (200bp) that have double helix structure (dsDNA) can "detect" each other over long distances -- as long as nanometers. Their claim is that sequence specific electrostatic type interactions -- which scale as 1/r -- lead to such recognition. Since the base interactions themselves are through H-bonds, the claim is that the base-pairs have subtle effects on the phosphodiester backbone (and the counter-ions around them) such that identical dsDNA molecules can recognize each other electrostatically without opening up. As stated in their introduction, this is quite controversial.
DNA molecules already "recognize" themselves by opening up and hybridizing, and the lower energy molecular pairs -- i.e. sequence matched strands -- are more populated than mismatched molecules. They try to address this : "We consider it to be rather unlikely in this instance, since the probability of bubble formation in unstressed linear DNA of the studied length is very small in contrast to the case where topological strain is relieved by bubble formation in small circular DNA molecules."
I'm not so sure that I would rule this option out because even partial hybridization changes the diffusivity constants of ssDNA/dsDNA molecules, which could lead to "pockets" of higher local concentration. I'm surprised that this wasn't elaborated more carefully, and that reviewers didn't jump all over this. Furthermore, I think they should have screened the electrostatics and changed the Debye length of these molecules and demonstrated a change in "recognition", at the very least.
In any case, I am quite suspicious of their conclusions, as many other biophysicists are.
You misunderstood the conclusion they're trying to push from the result. (This isn't surprising because the summary didn't get the article.)
As you've stated, DNA molecules that open up and close will more likely hybridize with molecules with a similar sequence. It's basic thermodynamics. The more complementary hydrogen bonds you can make between the bases of two DNA molecules, the more stable that molecule will be, and therefore, there will be a much greater population of that combination of DNA molecules in solution. Site directed mutagenesis works on this principle.
What they're proposing in this article is that you have DNA molecules that recognize each others sequences without opening up. Two double stranded DNA molecules (dsDNA) *recognize* each other without seeing each other's bases -- purely an electrostatic effect and not a hydrogen-bonding effect. In B-form DNA, the bases are hidden by the DNA backbone, and their conclusion strikes many people (including myself) as crazy. I have another post that elaborates on this.
...so much for Opposites Attract.
Take that Paula Abdul!
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nü!