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."

Re:So if they figure out..

[cobaltnova]

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.

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:Possibility for alternative method of DNA testi

[mattb112885]

They already do this, it's called hybridization [wikipedia.org].

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?

[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.

Suspicious

[digitalderbs]

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.

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 [slashdot.org] that elaborates on this.

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[Anonymous Coward]

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