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Author Topic:   How to make a ribozyme (using abiotic starting compounds)
Matt P
Member (Idle past 4804 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 4 of 55 (402551)
05-27-2007 10:51 PM
Reply to: Message 1 by Doddy
05-26-2007 10:18 AM


In the void of space
Hi Doddy,
Formaldehyde has been detected in space at fairly high concentrations, so it's probably not as hard to form as you might expect. It's formed through a number of high-energy processes, most starting with CO (exact chemical pathways aren't clear, but probably ion-molecule or radical reactions). It could be formed naturally at 10^-8 atm under equilibrium in an O2-poor atmosphere (like on the early Earth), and enriched to ~10^-4 through non-equilibrium processes in a CO2 atmosphere with water or H2 (lightning, meteor infall).
Once you get formaldehyde, you can toss it through the formose reaction (which historically has used CaCO3), and get pentoses that way, but it's not quite that selective. Alternatively, you could mix it with borate minerals to select specifically for ribose and associated pentoses (see Steve Benner's work- e.g., Ricardo et al. 2004, 1 page article in Science). You could also mix it with a bit of ammonia and some trimetaphosphate, and get ribose phosphates (a la Krishnamurthy et al. 1999).
Hope this helps!

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 Message 1 by Doddy, posted 05-26-2007 10:18 AM Doddy has replied

Replies to this message:
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Matt P
Member (Idle past 4804 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 9 of 55 (402726)
05-29-2007 4:09 PM
Reply to: Message 7 by Doddy
05-29-2007 7:06 AM


Re: Synthesis of Nucleobases
As Coragyps said, HCN isn't that difficult to make. I've run some quicky atmospheric thermodynamic equilibrium models, and like formaldehyde, it's formed at about 10^-8 atm in a reduced or neutral atmosphere. Raise this to about 10^-4 through non-equilibrium processes.
Also, as kalimero says (and you say as well), adenine is especially easy. It's essentially 5(HCN), and a prebiotic synthesis was shown back in 1960 by Jan Oro. Add some urea, and you've got the rest. This experiment is frequently referred to as second only to the Miller-Urey experiment. Alternatively, you could use formamide (HCONH2) coupled with TiO2 to form nucleobases in pretty good yield (Saladino 2003).
For the next step, heating nucleobases with ribose for a few minutes at 130-160 C will form nucleosides (Reid, Orgel, and Ponnamperuma Nature 1967). This pathway appears less than perfect, but there's a master's thesis from a Ga Tech student that may help:
http://smartech.gatech.edu/...ollins_james_p_200512_mast.pdf
It provides a good background for a few of these other subjects as well.
I'm anxiously awaiting your next step/question, since that's one I did my dissertation on!

This message is a reply to:
 Message 7 by Doddy, posted 05-29-2007 7:06 AM Doddy has replied

Replies to this message:
 Message 10 by Doddy, posted 05-30-2007 7:48 PM Matt P has replied

  
Matt P
Member (Idle past 4804 days)
Posts: 106
From: Tampa FL
Joined: 03-18-2005


Message 11 of 55 (403972)
06-06-2007 5:15 AM
Reply to: Message 10 by Doddy
05-30-2007 7:48 PM


Re: Synthesis of Nucleosides
Hi Doddy,
Sorry for the delay- I'm out of town. I'm going to copy a section from a paper I'm writing for phosphorylation.
The incorporation of phosphate into organics through abiotic processes has been pursued extensively, with the critical step consisting of the removal of water during condensation. Methods employed for the phosphorylation of organics include adding condensing agents to mixtures of orthophosphate and organics (5-7), heating orthophosphate with organics (8-10), adding condensed phosphates to organics (9,11), or a combination of these methods (5, 12, 13). Geochemical environments where these processes may take place include a dry pond with wet/dry cycles (13), hydrothermal vents (3), or under high UV (14).
5. Beck A, Orgel LE (1965) Proc. Natl. Acad. Sci. USA 54:664-667.
6. Steinman G, Kenyon DH, Calvin M (1965) Nature 206:707-708.
7. Keefe AD, Miller SL (1996) Origins Life Evol B 26:15-25.
8. Ponnamperuma C, Mack R (1965) Science 148:1221-1223.
9. Ponnamperuma C, Chang S (1971) in Chemical Evolution and the Origin of Life, eds Buvet R., Ponnamperuma C, (North-Holland, Amsterdam), pp.
10. Terelli E, Wheeler SF (1993) Chem Industry 1993:164-165.
11. Schwartz AW, Ponnamperuma C (1968) Nature 218:443.
12. Ibanez JD, Kimball AP, Oro J (1971) Science 173:444-445.
13. Bishop MJ, Lohrmann R, Orgel LE, 1972, Nature 237:162-164.
14. Simakov M. B., and Kuzicheva E. A. (2005) Adv Space Res 36:190-194.

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Replies to this message:
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