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."

Comments

Don't anthropomorphize chemical compounds.

[FooAtWFU]

(They hate it when you do that.)

Re:Don't anthropomorphize chemical compounds.

[B3ryllium]

But in this case, the chemical compounds do that to themselves ...

Re:Don't anthropomorphize chemical compounds.

[Lord Ender]

This post is either profoundly deep or really dumb.

Re:Don't anthropomorphize chemical compounds.

[B3ryllium]

I think you'll find, upon re-reading it, that it is actually profoundly dumb.

Re:Don't anthropomorphize chemical compounds.

[Anonymous Coward]

DNA-dar

Wha?

[Zephurus]

So is this the good type of incest?

Re:Wha?

[djtachyon]

Is there a bad?

So if they figure out..

[MacarooMac]

..how to eliminate errors during the 'homologous recombination' process we get to stay forever young?

Re:So if they figure out..

[cobaltnova]

No. Homologous recombination occurs for two purposes [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.

Re:So if they figure out..

[MacarooMac]

Ah. Close, but no cryogenic freeze mode as default (or even as an optional extra).

Re:So if they figure out..

[asCii88]

Either that, or they can find the way to Neverland.

Re:So if they figure out..

[csoto]

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).

Re:So if they figure out..

[Anonymous Coward]

The textbook examples of homologous recombination is that it is involved in two things:

      a) To create chromosome shuffling during meiosis
      b) To repair of double strand breaks in the DNA back bone

However, this is a simplified view. First of all, in mammals double strand breaks are primarily repaired through an entirely unrelated pathway termed non-homologous end-joining. Homologous recombination functions mostly during the S-phase of the cell cycle, where the cell is generating two copies of a genome before it divides. It is becoming increasingly clear that the role of homologous recombination during replication is very important. It is involved in restarting replication machinery that has stalled for various reasons and is something that happens many times in any mammalian cell trying to duplicate its genome. Organisms with small genomes, like yeast, can be survive with out homologous recombination (although grow slowly and have unstable genomes), but cells with large genomes, like mammalian cells, can not survive. Given that the inability to complete genome replication is fatal to a cell, one could argue that replication restart is a more significant process than recombination mediated sexual diversification.

Homologous recombination is supposed to be error free, however, it is the main source of loss of heterozygosity, which is linked to the development of cancer. Homologous recombination is also linked to the aging process, but the link is not well understood. Patients with increased levels of homologous recombination are prone to rapid aging, probably due to mutations. Where as, patients with low levels of homologous recombination are very sensitive to UV light and often develop skin cancer. This is why cells have very elaborate systems for regulating homologous recombination.

Here's another question ...

[ScrewMaster]

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.

Re:Here's another question ...

[wizardforce]

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.

Re:Here's another question ...

[cpricejones]

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/educated guess.

If you are interested, there is a great book on the RNA world hypothesis called The RNA World, 2nd edition edited by Cech, Atkins, and Gesteland. It contains best guesses on what the early conditions would have been for selfr-replicating RNAs to evolve.

Re:Here's another question ...

[glitch23]

All those characteristics of RNA still don't help evolution explain how DNA and RNA both came into existence from more fundamental chemicals and then were somehow encapsulated into the same first cell (along w/ other things like mitochondria) and for that cell to somehow learn to divide for, at the time, no apparent reason and for the DNA to magically divide correctly the first time in order to obtain replication ability (of course that had to be done prior to the cell itself replicating if I remember my biology correctly) and then for that cell, with the help of others, to somehow turn into an organism. I'm sure there are many other aspects of this area of biology I'm leaving out but I'm sure people get the point.

Re:Here's another question ...

[Anonymous Coward]

except that the origin of life is abiogenesis not biological evolution. biological evolution starts the very instant life started to divide and replicate not before that.

and for that cell to somehow learn to divide for, at the time, no apparent reason and for the DNA to magically divide correctly the first time in order to obtain replication ability

quit anthropomorphizing biological compounds they *hate* it when you do that... you need to understand that RNA can form under reducing conditions like those that would be found on early Earth, it doesn't need to catalyze its own synthesis but some of them can catalyze their replication once they have formed. experiments with a randomized "soup" of RNA strands produced ribozymes which catalyze their own replication. every replication event introduces "mutations" in the new strands which either confer an advantage [faster/more accurate replication] or lead to a dead end [strand hydrolyzes without replicating its self] that's the first example of a replicating system. it can not yet synthesize its precursors or produce proteins yet but it is an example of a self replicating system. there are other RNA strands which can string amino acids together, together with simple polypeptide chains these can form the first ribosomes and "proteins". membrane phospholipids self assemble into protocell enclosures called micelles which resemble little bubbles of phospholipid. these can protect the RNA and "proteins" from damage and localize any metabolites. each step in the evolution beyond a replicating system does so each time giving the system an advantage. once the system had developed enough, it evolved the ability to synthesize DNA [RNA missing the hydroxyl group at position 2] which took over as the genetic information carrier due to its greater stability. RNA remained a large part of the process that synthesizes proteins even 3.5 billion years later. all of the complexity you see is the result of millions and billions of iterations, each a simple step from the last building up until you get something like the immune system, the eye, flagella, ribosomes, nylonase [http://en.wikipedia.org/wiki/Nylonase] and everything else that exists in biology.

I assume what you were suggesting is that intelligent design could better explain life as we know it and frankly there's a reason ID has been dead in any serious scientific resarch for over a hundred years. the reasons being that by definition explains *nothing* in biology. that's the point, to argue that there isn't an explanation for anything in biology by any materialistic [evidence based] explanation therefore God did it... and there's the end of intelligent design, no evidence, no predictions, no explanation, nothing at all. It fails to explain *anything* at all that we already know let alone predict anything which makes it pretty useless other than being a God of the gaps argument.

Re:Here's another question ...

[glitch23]

except that the origin of life is abiogenesis not biological evolution. biological evolution starts the very instant life started to divide and replicate not before that.

I don't care what you call it. The problem of explaining it still exists whatever name you care to give it.

quit anthropomorphizing biological compounds they *hate* it when you do that...

Fine. Tell me how I should say it and I'll say it that way. Should I word it such that evolution is doing the learning? Anyway you say it makes it sound stupid because all the things that had to happen for us to exist using evolutionary theory had to be done in the right order, through several very small stages that were built upon each other with dependent parts of the microscopic human body all working towards the end goal of a single living cell which don't exactly live well outside the body today. And yet they did in the supposed extreme conditions back when this whole story started. Makes you wonder why 2 different cells didn't start up if one could do so using evolutionary logic such that the end result would be 2 independent animal kingdoms instead of just 1.

RNA remained a large part of the process that synthesizes proteins even 3.5 billion years later. all of the complexity you see is the result of millions and billions of iterations, each a simple step from the last building up until you get something like the immune system, the eye, flagella, ribosomes, nylonase [http://en.wikipedia.org/wiki/Nylonase] and everything else that exists in biology.

I'm still waiting for a timeline and a model to be published which shows when and how all that happened with interspersed explanations of how biological dependencies (i.e. chicken and egg type issues in animal biology) that we know exist today were solved using the idea that this all happened by accident.

that's the point, to argue that there isn't an explanation for anything in biology by any materialistic [evidence based] explanation therefore God did it... and there's the end of intelligent design, no evidence, no predictions, no explanation, nothing at all. It fails to explain *anything* at all that we already know let alone predict anything which makes it pretty useless other than being a God of the gaps argument.

I've yet to see a prediction by scientists of when, where, and what the next species will be, care of evolution. And I already mentioned the lack of many explanations in my text above. As far as evidence is concerned, I haven't seen much of that either, at least none that was interpreted correctly and without prejudice. Occam's razor, Creation makes the existence of this world simpler and yet scientists choose to make explanations harder by trying to figure out every single transition that evolution caused for us to exist. Creation does explain the universe in many areas, if you choose to have an open enough mind about it. Astronomers already have proven there was a point of Creation with the universe. Oddly enough the Holy Bible had that fact recorded long ago but no one (well, anyone w/o faith) cared to pay attention to it including Fred Hoyle who believed in the steady-state theory even up to his deathbed.

By the way, why doesn't evolution explain plant life or does it and it just isn't discussed very much?

Re:Here's another question ...

[BigBlueOx]

1) Science is a process. It is a way of doing things. Some people find that process to be a very good way of figuring things out. However, a process cannot provide you with the answers you require.

2) If you choose not to use that particular process, don't. You are free to believe that Shiva danced the universe into existence if you wish.

The universe is not constrained by our beliefs or theories. Deal.

Re:Here's another question ...

[omris]

you don't have a very good grasp of what science has to tell us about the origin of life. abiogenesis (the origin of life) is actually a relatively well researched topic. the premise, in the most basic of terms, is that the normally occuring chemical features of certain molecules cause them to behave in pretty amazing ways. for example, you can generate RNA from simple chemical compounds in the right conditions, and coincidentally, those conditions are almost identical to the conidtion of the earth billions of years ago. some RNA molecules can make copies of themselves. if you randomly generate enough RNA molecules, you're bound to randomly generate one that can replicate itself. there are proteins that can do similar things.

no one is suggesting that wholly formed cells as we know them today spontaneously generated. Yes, all of the biological molecules formed at some point. yes, they all eventually fit together. it is not reasonable to claim that life could not have occured in a random fashion because you don't grasp how it happened. it would have taken hundreds of billions of tries, but eventually, random chance will ALWAYS reach one specific instance.

besides this, where on earth do you get the idea that cells cannot survive outside of a multicellular animal body? not only is that blatantly false, multicellular life is FAR less diverse than single cellular life. by orders of magnitude.

the chicken or the egg issue is only as issue for someone not versed in evolutionary biology. for anyone educated in this manner, the answer is easy. the egg came first. something very-similar-to-but-not-quite-a-chicken laid an egg that hatched into what was indeed a chicken. this is a vast oversimplification. usually, the lines are not as clear cut as we'd like them to be to make it easy to delineate between one species and another, but that is the general trend. there is no biological dependancy, as you describe it.

and i will point out to you, as i point out ot so many others, that evolution is very well documented and researched. the evidence you claim is lacking is there, in relatively black and white terms. evolution is not simple enough to make very specific predictions that will bear out well in the natural world. this is not due to evolution being a poor explanation. it is due to the vast number of different factors that all play in, and the inherant unpredictability in many of the factors, as well as our own inability to quantify many of those same factors. how often is your weatherman spot on? is it because the things science tells us cause the weather are a load of crap? no. it's because it's a complicated system.

Occam's razor cannot apply to creationism, since creationism is not an explanation. creationism is only a justificiation for a lack of explanation, but it is NOT true that the simplest explanation for a phenomenon is that there cannot be an explanation. the issue is that there ISN'T a lack of explanation, if you care to open your eyes.

Re:Here's another question ...

[wizardforce]

or us to exist using evolutionary theory had to be done in the right order,

not really, experiments with pseudomonas bacteria had shown that these bacteria like others, can and do evolve enzymes to metabolize newly introduced chemicals, most importantly each bacterium evolved new enzymes in different ways. none were alike, none were done in "the right order" in a sense. we later sequenced the gene(s) encoding for these enzymes and showed what set of mutations lead to the formation of these genes. all of them simple steps that occur from time to time in bacterial genomes from deletions to recombination to point mutations and duplications.

that were built upon each other with dependent parts of the microscopic human body all working towards the end goal of a single living cell which don't exactly live well outside the body today.

that's very incoherent but it seems like you're trying to imply that the human body couldn't have evolved from ancestors that lived in a very different environment. bacteria [similar to archea] => eucaryotes => multicellular => evolution of hoc genes, increase in O2 in atmosphere supporting collagen synthesis increasing body size and complexity of available reactions=> vertebrates [stronger body form, some could burrow] => first land animals => [plants with roots evolve] => first mammals => [KT boundary marks mass extinction] => "primitive monkeys" => primate species split off leading to pan and homo genera=> Australopithecus => Homo erectus => two separate species in Homo, one the neanderthals, one humans => neanderthals die out ~30kya recently sequenced neanderthal DNA differs significantly from modern human DNA putting it in its own species separate from ours [fossils suggested this as well] http://www.astro.psu.edu/users/niel/scales/geohist1.ascii it's rather abbreviated although a lot more details can be found in science journals, nature in particular is a good source as is sciencedirect which actually has sections devoted specifically to human evolution, PLOS is a much better source as it is an open access journal [libraries and universities usually have nuch greater access to nature/sciencedirect]

I've yet to see a prediction by scientists of when, where, and what the next species will be, care of evolution.

the timing of species evolution depends on several factors that you would at the least need to take into account. 1) rate of mutation 2) generation time 3) environmental conditions such as predation, toxins, food availability, population size, and/or whether the populations are separated or not. in one specific case two species of wasp like insects were found to have been reproductively isolated because of symbiotic bacteria which occured like this: species A had a certain bacteria that kills the gametes of species B and vice versa, attempts at interbreeding would result in the gametes being destroyed before fertilization. when these bacteria were artificially killed, the two could again interbreed. in another instance, a single gene is responsible for shell shape of certain mollusks which prevents the two groups from interbreeding. chromosomes line up and share/exchange/recombine genetic material in what is called chromosomal crossover. if chromosomes can not pair it can result in sterility. chromosome suplication can cause speciation as was likely the case with human chromosome 2. humans have 46 chromosomes, primates have 48, two primate chromosomes fused to form chromosome 2 [so sayeth the human genome project] in any case, any prediction would need to be done knowing the conditions in which it is to occur. much like I wouldn't ask you to figure out precisely where and when an arrow fired from some random bow would hit the ground without knowing the relative gravity, shape/mass of the arrow, density of air it is flying through, air cur

Re:Where's Zoku Sayonara Zetsubou Sensei?

[schnikies79]

You do realize that all forms of anime suck, right?

GATTACA

[Bananatree3]

I doubt it will get to that, but I really am concerned. If you have not seen the movie Gattaca, check out the trailer.

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

[FooAtWFU]

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.

Re:GATTACA

[MacarooMac]

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:GATTACA

[Beavertank]

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 movie, I think.

Re:GATTACA

[thrillseeker]

get yer posts in now ... it's gonna get mighty quiet around here ...

Re:GATTACA

[thanatos_x]

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 individual as a good reason why a less organic approach will be taken and we will choose to augment with machines over biology.

Re:GATTACA

[Scrameustache]

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.

Re:GATTACA

[krakround]

There may be more than astronauts and janitors in the future. There may be alphas, betas, deltas and gammas too.

So do the jockish DNA molecules

[Anonymous Coward]

gang up to throw the nerdy molecules into their lockers?

Re:So do the jockish DNA molecules

[Anonymous Coward]

Where's the stereotypical love for the 6'2" geek who never got beat up as a kid?

I wear glasses. Doesn't that count for anything? :-(

Re:So do the jockish DNA molecules

[Eddi3]

Next thing you're gonna tell us is that you get laid as well.

Possibility for alternative method of DNA testing

[monoqlith]

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?

Good News, Bad News or No News?

[methano]

I think this is No News.

base pairing

[mattb112885]

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?

Re:base pairing

[mOdQuArK!]

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.

Re:base pairing

[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.

Re:base pairing

[omris]

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 base pair correctly with each other. and they think that this phenomena is because the pattern of those particular charges along the strands will make similar molecules more likely to be near each other.

Re:Possibility for alternative method of DNA testi

[mattb112885]

They already do this, it's called hybridization .

Why is this surprising?

[istartedi]

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:Why is this surprising?

[cinnamon colbert]

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

Re:Why is this surprising?

[NetSettler]

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 "at a distance" I must assume it means "with others intervening". So yes, one avenue is what you're perhaps intimating, which is that maybe they come close and then fail to separate because they are similar before they are measured, rather gravitating as a result of being similar. Depending on the experiment, it wouldn't distinguish. But if they have determined that the things just know from a distance where to go, the explanation you suggest might not stand up.

Someone once told me a story about how oak trees separate themselves out. (I don't know if this story is true, but I don't tell it for its truth anyway, I tell it because it seems a good paradigm that could be true and useful.) They said that the leaves are acidic and that the acorns don't like to grow in acidic soil. So they drop acorns everywhere, but the ones that come up are not near the tree. So they don't grow too close together. This could be misinterpreted as "An oak tree sees another oak nearby and tries not to grow too close." and one could puzzle about how they "recognize each other". But if the recognition is just "wow, this is kind of acidic for me" then it could just as well stay clear of non-oak-trees and for no good reason. I wonder if perhaps there is some subtle effect on the electrical charge, on the chemical composition, or something else that is more low-grade than what they're looking for but creates a local gradient of plausibility such that other items nearby look for a metaphorical slope to slide down (a gradient that seems plausible). This wouldn't have to be a high reliability truth, just enough to bias the odds in a way that made it more likely to succeed. In computer science terms, all it needs is to emit a "hash bucket key" that can be read at a distance, but not necessarily an "equality test". It wouldn't have to be biological molecules. It could just be some simpler chemical marker that they aren't testing for.

Or not. I'm neither a chemist nor a biologist.

Re:Why is this surprising?

[Anonymous Coward]

Charge shielding occurs in a salt solution, thereby allowing the molecules to not 'repel' eachother. For instance, 2mM MgCl works well for micromolar ~30 base-pair single-strand DNA. When located in such a solution, the molecules easily approach within distances allowing classical interactions to occur. I didn't read TFA, but this is standard procedure for laboratory-based DNA chemistry.

Re:Why is this surprising?

[cosmicaug]

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 recombination protein is kind of cool. I'm sure that, as a matter of course, various proteins are always going to be involved to optimize this in living cells nowadays but showing that it can happen without accessory proteins does kind of show how such a process might have evolved.

Note: I have not read the journal article.

Re:Why is this surprising?

[novakyu]

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:Why is this surprising?

[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.

Re:Why is this surprising?

[Anonymous Coward]

it's the DNA being 'racist'

quantum state joke

[sohp]

Two bosons walk into a bar. The first one orders a beer. The second one says, "I'll have what he's having."

Re:quantum state joke

[WilliamSChips]

http://www.irregularwebcomic.net/1525.html has a similar joke, but about fermions.

Re:quantum state joke

[sohp]

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.

Re:quantum state joke

[Carpe PM]

Boson buddies?

Is it just me...

[vajaradakini]

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.

Re:Is it just me...

[Anonymous Coward]

No, it's not just you.

Biodiversity is important, even -within- a species. IIRC, the same genetic defect that results in Cystic Fibrosis also (can) result in resistance to (certain strains of) TBC. If you happen to have the right genetic markers, you might not get either condition. CF is a horrible condition, but it might work out for the species as a whole if it allows you to survive a potentially fatal disease at an early age and live at least long enough to procreate.

In addition to the above, although I'm fascinated by the possibilities of gene research, I'm also very ambivalent about where we are headed with this. It only takes one "genetically enhanced" virus or plant to do something unexpected and we could have a major problem. Just keeping my fingers crossed...

Re:Is it just me...

[EnsilZah]

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.

Re:Is it just me...

[Scrameustache]

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?

Re:Is it just me...

[vajaradakini]

We didn't used to have the whole global village thing going on like we do now.

Always looking for the next grant

[7-Vodka]

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.

Re:Always looking for the next grant

[Anonymous Coward]

I just want to know if this can explain how a human, with 46 chromosomes, allegedly came from an ape with 48, and how their offspring went on to mate with another 'mutant' to form the human race.

Re:Always looking for the next grant

[cp.tar]

<troll_fodder>Nah. That's just genetic code optimization.</troll_fodder>

Re:Where's Zoku Sayonara Zetsubou Sensei?

[schnikies79]

Emo sucks worse than all of them.

My sig is a joke, what I replied with is the truth.

duh.

[Anonymous Coward]

just fucking duh!

Basically... In Situ Hybridization

so a guy is sitting there bored while his hybridization cylinders are rotating in the lab... hmm... maybe if I look at first principles I will get published.

There are so many areas of the natural sciences that are starving due to the vast suck factor that is grabbing funding for molecular work.

argh!

who gives these people money?
It's like giving Paris Hilton food stamps.

Suspicious

[digitalderbs]

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.

Re:Suspicious

[hung_himself]

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...

Algorithms

[EchoNiner]

Maybe I have a one track mind, but it seems like there are a lot of applications of this in terms of algorithms.

Re:Possibility for alternative method of DNA testi

[Anonymous Coward]

with the exception that hybridization works on single-stranded DNA, yes. the grandparent's idea likely would be too inexact.

Summary is wrong. Controversial conclusions.

[digitalderbs]

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.

Re:Summary is wrong. Controversial conclusions.

[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 specifically detected.

The claim that identical double stranded fragments have a mere 2x increased chance of association over an unrelated DNA strand, even if it pans out, seems to me to be of little practical consequence to the life cycle of a cell. The background of the whole genome would swamp out the effect of such a weak difference in free energy; i.e. the dynamic range of the interaction would not be sufficient.

Similar thoughs

[dereference]

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 more like acorns of a certain shape being influenced similarly by a constant wind, simply because of their natural aerodynamic profile. Similarly-shaped acorns may tend to cluster, but not because they sense each other, or their environment, in any way.

But hey, it sure does sound a lot more funding-worthy to just call them "telepathic" (as in TFA)!

Mod Parent Up!

[Ken_g6]

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, but that's already taken, and this would be even spookier!

Well...

[costela]

...so much for Opposites Attract.
Take that Paula Abdul!

--
nü!

Re:Where's Zoku Sayonara Zetsubou Sensei?

[Anonymous Coward]

Only an emo would say that! Get him! [There, aren't you happy? You're being persecuted, you fucking emo?]

GOTHS rule!

hehehehehe

[Anonymous Coward]

hehehehehe, you said strands :)

OMGosh

[Anonymous Coward]

Wut about a MULTI-stranded blonde airhead lyk meeee ??

Re:Where's Zoku Sayonara Zetsubou Sensei?

[Anonymous Coward]

Anime is a medium, not a genre. Saying that it all sucks is like saying all CGI sucks, or all live action sucks. It simply does not make sense. Yes, I know that there is more crap anime than good anime, but good anime does exist. Personally, I like Death Note.

Emo, on the other hand...

I can see another new big government program

[EmagGeek]

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!

Why not?

[Roadkills-R-Us]

Maybe it applies. Maybe they're just showing off because they know they're being watched.

The act of observation, and all that.

Re:Where's Zoku Sayonara Zetsubou Sensei?

[schnikies79]

I don't like the animation style. The big eyes, tiny faces, etc. It's not the content, it's the look.

It just bugs me.

Not that surprising

[Anonymous Coward]

The arrangement of similar, so-called 'homologous', coils of dsDNA occurs on a humongous scale every day in every human. It is one of the first steps of cell division and is essential for the growth and development of all organisms. Without it development would stop with the single celled zygote of any multicellular organism and recombination of DNA in any organism would be impossible or at least extremely unlikely. It would have been nice if they could have focused a little more on developing the mechanism for the attraction instead of merely verify an already well-documented and essential process.