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Similar DNA Molecules Able to Recognize Each Other 84

Posted by Soulskill
from the dna-gps dept.
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."
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Similar DNA Molecules Able to Recognize Each Other

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  • by FooAtWFU (699187) on Sunday January 27, 2008 @01:59PM (#22201070) Homepage
    (They hate it when you do that.)
  • ..how to eliminate errors during the 'homologous recombination' process we get to stay forever young?
    • by cobaltnova (1188515) on Sunday January 27, 2008 @02:35PM (#22201252)
      No. Homologous recombination occurs for two purposes [wikipedia.org] [wikipedia.org]:
      1. in germ cells for "crossover" diversification of offspring, and
      2. in somatic cells to repair already damaged DNA.
      Though there are other genetic mechanisms of aging (Telomere shrinkage), and still more non-genetic.
      • Ah. Close, but no cryogenic freeze mode as default (or even as an optional extra).
      • by csoto (220540)
        Random recombination would result in "diversification" (read: "mutation"). Homologous recombination in germ cells serves exactly the same purpose as #2 (somatic DNA repair). It helps assure that the "very different" is left out of the end product. It's one of the reasons that asexual reproduction tends to lead to higher mutation rates (plus it takes all the fun out).
  • by ScrewMaster (602015) on Sunday January 27, 2008 @02:09PM (#22201112)
    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.
    • by wizardforce (1005805) on Sunday January 27, 2008 @02:36PM (#22201260) Journal
      RNA likely does the same thing as the only differences being that uracil replaces thymine and there's a hydroxyl group in the 2' position. RNA is thought to be one of the most important or the most important chemicals in the formation of life on Earth. it forms complex structures that can be catalytic [self cleaving, primitive peptidase activity etc..] just like proteins and it is a carrier of genetic information. in many organisms, RNA segments are "charged" with an amino acid and the amino acids are strung together like a bead necklace by ribosomes that match RNA anticodons to specific amino acids although in certain viruses, RNA acts primarily as an information carrier in several virus classification groups.
      • I think you are referring to the RNA world hypothesis, and this finding definately would explain how similar RNAs could segregate themselves from a community of many dissimilar RNAs. Part of this hypothesis tries to explain how a self-replicating RNA could form, but a difficulty in the proposal is how this RNA would be able to replicate other RNAs nearby, too. So it's interesting to wonder if the association allowed for more efficient selection. But the RNA world hypothesis is a hypothesis/speculation/educa
  • GATTACA (Score:3, Insightful)

    by Bananatree3 (872975) on Sunday January 27, 2008 @02:21PM (#22201168)
    I doubt it will get to that, but I really am concerned. If you have not seen the movie Gattaca, check out the trailer [youtube.com].

    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.

    • Re:GATTACA (Score:5, Insightful)

      by FooAtWFU (699187) on Sunday January 27, 2008 @02:29PM (#22201222) Homepage
      While I appreciate that there will be all sorts of concerns raised with the rise of biotechnology, do realize that Gattaca's world is a bit... oversimplified. Think about it. There are basically two classes of people: astronauts and janitors.

      The real world is going to be more complicated than that. This is a good thing.

      • I find it an interesting commentary on humanity that we see something that would in theory allow us to become paragons as probably more harmful than good, especially since the vast majority of individuals want what benefits could be had, i.e. near perfect health, beauty, physique and intelligence. I believe this is an example of crabs in a bucket - No one can have it unless I can, and first.

        From a futurist standpoint, I see the probable inability to retroactively apply genetically engineered DNA to an indiv
      • While I appreciate that there will be all sorts of concerns raised with the rise of biotechnology, do realize that Gattaca's world is a bit... oversimplified. Think about it. There are basically two classes of people: astronauts and janitors.
        And police inspectors, and doctors, and 12-fingered musicians.
      • There may be more than astronauts and janitors in the future. There may be alphas, betas, deltas and gammas too.
    • Re: (Score:3, Funny)

      by MacarooMac (1222684)
      Look on the bright side: in 2020 slashdot's DNA detector will scan all would-be posters and automatically discriminate against subjects possessing the Troll Gene(TM) and the evolution-defying 'Sh*t For Brains' condition. Elitist? Yes. Popular? Definitely.

      Mind you, I for one'll need to undertake some wide-scale homologous recombos beteen now an then...
    • Re: (Score:2, Insightful)

      by Beavertank (1178717)
      If I remember the movie correctly there were anti-discrimination laws, which were technically followed, but when you can extract the genetic information you need from a lost hair or even the epithelial cells contained in a urine sample (for drug testing, of course) you can fairly simply come up with another excuse for not hiring the person and it can never be proved that you did not, in fact, hire them because you knew they'd be dead by 40 of heart disease.

      Which was all pretty clearly spelled out in the

  • by Anonymous Coward on Sunday January 27, 2008 @02:24PM (#22201194)
    gang up to throw the nerdy molecules into their lockers?
  • I don't know much at all about molecular biology, but I wonder if this finding be used to develop a new method of DNA testing?

    If two strands of DNA clump together under the right circumstances, then couldn't we decide whether a person's DNA is at a crime scene or not(for example) by putting that person's DNA in a dish with DNA from the crime scene and watching how well they clump together?

    Or is this just too inexact?

  • I think this is No News.
  • base pairing (Score:1, Insightful)

    by mattb112885 (1122739)
    My guess is they tend to accumulate more with similar DNA molecules because they can base pair with each other [since they have similar base sequences] better than they can with different DNA molecules and therefore interactions between them are more stable...so if they happen to find each other in solution they're more likely to remain together. Why is this surprising again?
    • by mOdQuArK! (87332)
      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.
    • by Anonymous Coward
      "Similar" DNA molecules do NOT always base pair each other. In fact, the only ones who base pairs are complements to each other.
    • by omris (1211900)
      almost, but you misunderstand what they are saying. base pairing is what will allow two complementary strands of DNA to bind together into one single strand with the double helix we all saw in biology class.

      they are demonstrating that in a random pile of DNA, the double stranded molecules with identical sequences are more likely to stay next to each other.

      it IS due to the same SORT of thing, but the molecules are not base pairing with each other. each base has a particular charge, which allows them to bas
  • by istartedi (132515) on Sunday January 27, 2008 @02:47PM (#22201328) Journal

    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.

    • Re: (Score:2, Informative)

      you might also make an analogy to crystallization, but it is surprising because dna strands in solution are flexible, and the charge density differences are not that great, and, most importantly, in any reasonable solution (water, salt, pH...) the DNA is either heavily charged (and therfore intrinsically self repulsive) or coated with proteins, which give the association property naturally
      this paper is like a lot of biophysics: completely irrelevant to any property of dna in the real world
    • If I had two strands of magnets, arranged with random orders of polarity, identical strands would be able to stick together ... Dissimilar strands ... [if] you wiggled them, ... [would] be more likely to come aparts.

      Well, the article says:

      Genes have the ability to recognise similarities in each other from a distance, without any proteins or other biological molecules aiding the process

      And who knows if the writer of the article has a proper understanding or is being suitably precise. However, by

      • The first thing that occurred to me was that similar structures will tend to cluster together simply because all the various minute forces will tend to act similarly on similar strands. This is somewhat different from your oak tree example, in that the acorn indeed "senses" its environment; I'm suggesting that perhaps the strands are merely passively tending to pool together due to the prevailing eddy currents, electromagnetic forces, or whatever might act to push like strands in like directions. It seems
    • by cosmicaug (150534)
      Individual strands recognize each other by hydrogen bonds called Watson-Crick base pairing (forming the well known C-G & A-T base pairs). The sequence recognition between two double helices is something else which has been known to happen for a long time. The assumption would have been that it is mediated by various proteins such as recA in E. coli. It seems to be the case that non-Watson-Crick base pairing might be involved. Finding out that this is the case and that it need not be mediated by some rec
    • by novakyu (636495)

      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.

      Forgive my ignorance, but don't they repel? When you have two magnets where their "north" pole points in the same direction, those two poles repel each other. And since the arrangement is random, unless each individual corresponding magnets attract each other, getting an overall attractive configuration seems hopeless. In nature (well, at least electromagnetism), like things repel each other and unlike things attract.

      Even from that perspective, this seems a very different phenomenon.

    • Re: (Score:1, Informative)

      by Anonymous Coward
      It _is_ surprising, because a dna strand is folded.
      That makes the charge/magnetic matching hypotheses very unlikely, because the strands will _not_ align "parallel" to each other in general.
      Secondly even if the strands aligned parallel, the forces from the "electrostatic pattern" would be much too small on the relevant scale.
    • by digitalderbs (718388) on Sunday January 27, 2008 @05:26PM (#22202416)
      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 [slashdot.org] that elaborates on this.
      • Re: (Score:1, Interesting)

        by Anonymous Coward
        I thank the previous poster for clearing up what the authors are claiming. Hybridization between complementary single stranded DNA strands are highly specific and are used in a variety of assays like Northern blots, and PCR. These techniques can pick out the complementary molecule in a sea of other non-related DNA fragments. It is highly specific and has a huge dynamic range, in the sense that your target molecule can be an exceedingly minor species in a whole gamish of other DNA species and still be spec
  • by sohp (22984)
    Two bosons walk into a bar. The first one orders a beer. The second one says, "I'll have what he's having."
    • http://www.irregularwebcomic.net/1525.html [irregularwebcomic.net] has a similar joke, but about fermions.
      • by sohp (22984)
        Hee. The fermion version of the bar joke goes: Two fermions walk into a bar. The first one orders a beer. The second ways, "Damn, that's what I wanted!"

        Or:
        The first one orders the stiffest, biggest drink on the menu and proceeds to get roaring drunk. The second one just sips water.
  • Is it just me... (Score:2, Insightful)

    by vajaradakini (1209944)
    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.
    • by EnsilZah (575600)
      I very much doubt that elimination of these 'errors' in a significant part of the earth's population would be financially feasible, and even if it was, there would be large groups of people that would avoid it due to theological and other reasons.
    • Eliminating this gene from the entire species could wind up killing us all off in the end.
      Since when has the entire species ever been reached by anything?
  • From TFS:

    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

    Hey it's great that some interesting study is being done, but really there's no need to make far reaching wild guesses as to why it's important. Let the achievement stand on it's own merits.

  • Suspicious (Score:5, Informative)

    by digitalderbs (718388) on Sunday January 27, 2008 @05:05PM (#22202210)
    I was quite suspicious of their claim, so I read the original article [acs.org].

    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.
    • If these molecules really did recognize each other over a long distance, with no intermediary molecules, that would be spooky. I'd call it spooky action at a distance [wikipedia.org], but that's already taken, and this would be even spookier!
    • Yeah they really have to show that no single strand is forming transiently before they can come up with such a unlikely mechanism.

      Resistance to nucleases would be a test for example.

      It wouldn't have made it into a decent biology journal, that's for sure...
  • Maybe I have a one track mind, but it seems like there are a lot of applications of this in terms of algorithms.
  • Well... (Score:2, Funny)

    by costela (198904)
    ...so much for Opposites Attract.
    Take that Paula Abdul!

    --
    nü!
  • We need to immediately pass legislation banning and criminalizing this blatant discriminatory behavior. DNA strands should be forced by law to associate with all different kinds of DNA strands, regardless of the biological, chemical, and social consequences!

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