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January 28, 2011
Arsenic in DNA: The Kinetic Argument.
Posted by Derek
Here's the first response in the chemical literature to the arsenic-in-DNA controversy, from three authors in ACS Chemical Biology. They detail the argument, familiar to readers of the comment section here, that arsenate esters just would not be expected to have the hydrolytic stability needed for arseno-DNA to function usefully.
How far off is it? By, well, about 13 (make that 17) orders of magnitude, which is much worse than I'd thought. As the authors put it, "Overcoming such dramatic kinetic instability in its genetic material would present serious challenges to Halomonadacea GFAJ-1." Indeed it would.
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1. Curious Wavefunction on January 28, 2011 1:33 PM writes...
More accurately by about 17 orders of magnitude, as I blogged about a few days ago.
Permalink to Comment2. Rhenium on January 28, 2011 2:38 PM writes...
Ok, I read this paper as well as the classic "why nature chose phosphates" and the understanding that phosphate esters hydrolyze is clear. My question is why?
The above paper discusses how similar the phosphorous and arsenic atoms are, so why the big difference? Size perhaps, access to higher coordination numbers similar to the "Why life exists" paper which explains carbon versus silicon for life?
Permalink to Comment3. John Gramophon on January 28, 2011 2:42 PM writes...
Could not it be a "blinking" DNA, teleporting its parts being attacked by hydrolysis/enzymes temporarily into other realms? Or using the immaterial copy of DNA "out there" as a template for reparation of damage caused by O-As-O bond instability? I believe similar properties of nucleic acids have been demonstrated recently.
Permalink to Comment4. daen on January 28, 2011 2:51 PM writes...
Yeah, I wondered about that magnitude too ... :-) Beat me too it, CW!
Permalink to Comment5. partial agonist on January 28, 2011 3:26 PM writes...
The arsenic DNA didn't exist very long, but it left its signature magnetic imprint on the water it was in. That imprint lasted much longer, I am told. The tooth fairy wanted it that way.
Permalink to Comment6. MoMo on January 28, 2011 5:52 PM writes...
Don't forget about magnesium chelating to the phosphoanhydride group. Adds much more energy when hydrolyzed and is not coordinated planting As. Which is why the original paper is specious at best.
Permalink to Comment7. anon on January 28, 2011 8:45 PM writes...
Yes, I'd also like to know why, since As(V) and P(V) are so chemically similar, does the rate of hydrolysis differ by 17 orders of magnitude?
Permalink to Comment8. pondering on January 29, 2011 10:08 AM writes...
doesn't the fact the the rate of hydrolysis is 17 orders of magnitude different suggest that the two are not all the similar chemically? its like saying fluoride and chloride are really similar chemically...except for size, electronegativity, bond strengths...
Permalink to Comment9. Dane on January 30, 2011 11:20 AM writes...
One of my friends joked that all we'd need to make arsenic-DNA stable is to make a corresponding change of water to hydrogen sulfide. Of course, with S being so much more nucleophilic than O, the feasibility of arsenic-DNA would be even more pathetic in such an environment :)
Permalink to Comment10. Anthony Bishop on January 31, 2011 12:57 AM writes...
Only problem is how to explain to my 10 & 11 year olds how that cool discovery of a new chemical biology I was telling them about was bogus. Maybe I should have a 6-month embargo on telling them anything new.
Permalink to Comment11. LiqC on February 9, 2011 5:32 PM writes...
The reason for increased lability of arsenoesters is the ease with which arsenic goes pentacoordinate. The most dramatic difference between P and As is atomic radii (31 vs 48 pm). The bigger you are, the easier it is to pick up that nucleophile en route to the transition state.
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