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Extreme accumulation of nucleotides in simulated hydrothermal pore systems

Baaske, Philipp and Weinert, Franz M. and Duhr, Stefan and Lemke, Kono H. and Russell, Michael J. and Braun, Dieter (2007) Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proceedings of the National Academy of Sciences of the United States of America, 104 (22). pp. 9346-9351. ISSN 0027-8424. https://resolver.caltech.edu/CaltechAUTHORS:BAApnas07

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Abstract

We simulate molecular transport in elongated hydrothermal pore systems influenced by a thermal gradient. We find extreme accumulation of molecules in a wide variety of plugged pores. The mechanism is able to provide highly concentrated single nucleotides, suitable for operations of an RNA world at the origin of life. It is driven solely by the thermal gradient across a pore. On the one hand, the fluid is shuttled by thermal convection along the pore, whereas on the other hand, the molecules drift across the pore, driven by thermodiffusion. As a result, millimeter-sized pores accumulate even single nucleotides more than 108-fold into micrometer-sized regions. The enhanced concentration of molecules is found in the bulk water near the closed bottom end of the pore. Because the accumulation depends exponentially on the pore length and temperature difference, it is considerably robust with respect to changes in the cleft geometry and the molecular dimensions. Whereas thin pores can concentrate only long polynucleotides, thicker pores accumulate short and long polynucleotides equally well and allow various molecular compositions. This setting also provides a temperature oscillation, shown previously to exponentially replicate DNA in the protein-assisted PCR. Our results indicate that, for life to evolve, complicated active membrane transport is not required for the initial steps. We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life.


Item Type:Article
Additional Information:© 2007 by The National Academy of Sciences of the USA. Edited by Howard Brenner, Massachusetts Institute of Technology, Cambridge, MA, and approved March 9, 2007 (received for review October 28, 2006). Published online on May 9, 2007, 10.1073/pnas.0609592104. We thank Ludmilla Mendelevitch for initial simulations and Hermann Gaub for hosting D.B.'s Emmy–Noether Nachwuchsgruppe, which was funded by the Deutsche Forschungsgemeinschaft. M.J.R.'s work was conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. Author contributions: D.B. designed research; P.B., F.M.W., and S.D. performed research; P.B., F.M.W., S.D., K.H.L., M.J.R., and D.B. analyzed data; and P.B., K.H.L., M.J.R., and D.B. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. See Commentary on page 9105. http://dx.doi.org/10.1073/pnas.0702699104
Subject Keywords:concentration problem; hydrothermal vents; molecular evolution; origin of life problem; RNA world
Issue or Number:22
Record Number:CaltechAUTHORS:BAApnas07
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:BAApnas07
Alternative URL:http://dx.doi.org/10.1073/pnas.0609592104
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9855
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:24 Mar 2008
Last Modified:03 Oct 2019 00:04

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