Dna And Silicification

Mechanism: Entombment or covalent bonding are possible. Organics were observed in IR spectra. Si-O-C IR bands were observed in some cases.

Gel formation and appearance: Immediately formed hard, white gels. Needed a very small volume to form gel compared to an alcohol of similar molecular weights. Gels were partially water-soluble. Dried gels consist of hard, rubbery, opaque chunks. Sol-gel-sol transformation: Some transformations were seen related to water-solubility.

Other: One of the rare cases (in addition to acid halides) where Si-O-C bond formation was observed in the IR. Mechanism: Varies. Catalysis was observed in some cases, while the strong presence of organics and the Si-O-C IR band indicates covalent bond formation in others.

Gel formation and appearance: The length of time required to form a gel varies from seconds to days depending on the compounds tested. Gels are yellowish, and partially water-soluble in some cases, depending on the nature of the acid halide. Dried gels consisted of small white chunks.

Sol-gel-sol transformation: Some transformations were seen. Other: These and amino alcohols are the only compounds that gave the IR evidence for the formation of Si-O-C covalent bonds. Mechanisms: Not yet determined. For ATP and DNA soluble phospho-silicates are possibly formed. Gel formation and appearance: No gel formation. Gel formation and appearance: Soft, whitish gels form quickly within seconds. Gels highly water-soluble. In some cases, gel entirely dissolved within a 24-48 hours of forming. Sol-gel-sol transformation: Dramatic transformations were seen related to water-solubility, preventing analysis at this point in time Gel formation and appearance: No gel formation. Gel formation and appearance: No gel formation.

to the other alcohols we had already studied. Some notable amino alcohols, such as ethanolamine, have long been known to be important metabolic precursors (Weissbach and Sprinson, 1952).

Additionally, polyamines assist condensation of silica in diatoms (Pohnert, 2002), which make great biomarkers. Amines alone effect condensation of silica in model systems in which the naturally occurring silica was replaced by tetraethoxysi-lane under circum-neutral pH values (Delak and Sahai, 2005, 2006). The latter studies suggest the nucleophile-driven reaction mechanism, of an SN2 type.

We have found that the amino alcohols behaved strikingly different from the alcohols we studied (Liesch and Kolb, 2007a). In some ways, the amino alcohols reacted more like amino acids than alcohols. For example, the sodium silicate polymerized nearly instantly upon addition to form hard white gels. These gels were unexpectedly the hardest produced in our laboratory to date. In fact, on at least one occasion, an experiment needed repetition because the vial had broken while trying to scrape the gel from the inner surface. Furthermore, the amino alcohols did not demonstrate the volume-dependent trend seen in the alcohols. Interestingly, alcohols required the addition of up to ten times the volume of an amino alcohol of comparable molecular weight to form a firm gel (Liesch and Kolb, 2007a).

As in the case of alcohols, the gels from amino alcohols were somewhat water-soluble and dissolved partially while being processed. After processing and drying these samples, the resulting gels consisted of hard, rubbery, opaque chunks. These dried gels were quite similar to the alcohol gels in appearance. However, a key difference from the alcohol gels was the confirmed presence of organics in the IR spectra. Not only was this one of the few cases where organics were observed in the IR spectra, but Si-O-C bond formation was also observed in the case of ethanolamine. Thus, for the amino alcohols, entombment and covalent bond forming mechanisms may be at work in addition to merely catalyzing the polymerization of the sodium silicate (Liesch and Kolb, 2007a).


Acid halides are reactive organic compounds, which we have used as model compounds in order to effect a rapid Si-O-C bond formation. This model was successful, at least in some cases, as we were able to observe high levels of organics in the gels, as well as the formation of Si-O-C bonds (Kolb and Liesch, 2007a).

The gels resulting from different acid halides vary greatly in the length of time required for polymerization to occur. In some cases polymerization occurred nearly instantly, in others it took days (Kolb and Liesch, 2007a). The gels resulting from acid halides were hard, somewhat brittle, and pale yellow in appearance. Like the alcohols, some of these gels were found to have water-soluble properties, and sol-gel-sol transformations were observed.

Like the highly variable temporal aspects of gel formation, the mechanisms responsible for interaction with sodium silicate seem equally as variable. In the case of 2,4-dinitrobenzoyl chloride, organics were clearly seen in the IR spectra as well as Si-O-C bonds - suggesting a mechanism of covalent bond formation. In some other cases, no organics were seen in the IR spectra, and it appears that acid catalysis may cause polymerization of the highly basic sodium silicate solution in some cases, as the formation of the corresponding organic acids was observed in some cases (Kolb and Liesch, 2007a). At this point, we believe that the miscibility of the individual acid halides may play the greatest role upon determining which mechanism is involved in gel formation.


This last section briefly discusses some of the most peculiar and least understood cases examined in our laboratory. These biomolecules serve key roles in metabolic pathways, and the storage of genetic information (Lehninger et al., 2004). While some of these experiments may be considered "failures" on the grounds that polymerization did not occur under our experimental conditions, vital information can still be gained from the study of these compounds. Take DNA for example: using <50 bp oligonucleotides extracted from Herring sperm, we found that polymerization and subsequent gel formation did not occur (Kolb and Liesch, 2007a). The solubility of DNA-silicate complex remains a possibility. An intriguing possibility is a formation of the soluble DNA-phospho-silicate complex, such as the proposed phospho-silicate gel of the phytic acid, a compound that is derived from myo-inositol (an isomer of the hexa-hydroxy cyclohexane in which all six hydroxyl groups are phosphorylated) (Samba-Fouala et al., 2000). The solubility of the DNA complex may be a plus, since the precipitated or bound polymer could no longer function as an effective template for replication (Liesch and Kolb, 2007c).

As in the case of DNA oligonucleotides, we did not observe any gel formation with either urea or ATP. These substances resulted only in clear, colorless solutions. Urea may make soluble silicates, and the ATP may form soluble phospho-sili-cates. Unlike the DNA, ATP, and urea, AMP did result in the polymerization of the sodium silicate solution and led to the formation of soft, whitish gels. Dramatic sol-gel-sol transformations were also observed in the AMP gels. In some cases, transformations were so dramatic that the gels completely transformed back to the sol phase and processing could not be conducted. When we finally managed to extract a gel from AMP, we found that these gels were highly water-soluble (Kolb and Liesch, 2007a). In fact, these gels completely dissolved during processing, which prevented the final isolation and drying of the gel, and ultimately prevented the analysis of the gel via infra-red spectroscopy. The inability to study the solid gels therefore leaves the mechanisms of interaction as an open question at this point in time.

In conclusion of this section, our initial results show that the silicification of the biologically relevant molecules that are associated with the genetic material (ATP, AMP, and DNA) do not yield solid gels, and are thus not expected to be preserved via the entombment mechanism, at least not in our experimental model. The same is true for urea, which is also found in biological systems.

5. Conclusions and Summary

Our lab has made great advances in the study of the silicification process over the past few years. The determination of the exact range of the Si-O-C IR band, and the ability to determine and distinguish between the mechanisms of silicification may provide crucial insight in helping achieve the goals set forth by NASA's astro-biology strategy (Morison, 2001; NASA, 2007a). We have gained a great deal of knowledge on the aspects of cataloging biosignatures, determining what characteristics of the Martian landscape may be due to non-biological processes, and showing that certain biosignatures may actually be inorganic in nature (such as the highly dramatic Si-O-Si band shift seen with alcohols). Perhaps our greatest achievement has been to survey a broad spectrum of organic compounds, identifying key characteristics of each, and summarizing our findings for the advancement of the study of biosignatures. Our key findings are summarized in Table 2.

6. Acknowledgments

Thanks are expressed to the Wisconsin Space Grant Consortium/NASA for research grants to V. M. K. and P. J. L., and to the University of Wisconsin-Parkside Dean's research funds (URAP) to P. J. L.

7. References

Azrak, R. G. and Angell, C. L. (1973) Study of alcohol-silica surface reactions via infrared spectroscopy. J. Phys. Chem. 77, 3048-3052.

Bellamy, L. J. (1975) The Infrared Spectra of Complex Molecules, Vol. I, Third Edition. Chapman and Hall, London, England, pp. 374-385.

Benning, L. G., Phoenix, V. G., Yee, N. and Kornhauser, K. O. (2004).The dynamics of cyanobacterial silicification: An infrared micro-spectroscopic investigation. Geochim. Cosmochim. Acta 68, 743-757.

Cooper, G., Kimmich, N., Belisle, W., Sarinana, J., Brabham, K. and Garrel, L. (2001) Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth. Nature 414, 879-883.

Coradin, T. and Livage, J. (2001) Effect of some amino acids and peptides on silicic acid polymerization. Colloid Surface B 21, 329-336.

Coradin, T., Durupthy, O. and Livage, J. (2002) Interaction of amino-containing peptides with sodium silicate and colloidal silica: A biomimetric approach of silicification. Langmuir 18, 2331-2336.

Cronin, J. R. (1998) Clues from the origin of the solar system: Meteorites. In: A. Brack (ed.) Molecular Origins of Life. Cambridge University Press, Cambridge, England, pp. 119-146.

Cronin, J. R. and Chang, S. (1993) Organic Matter in Meteorites: Molecular and Isotopic Analysis of the Murchison Meteorite. In: J. M. Greenberg, C. X. Mendoza-Gomez and V. Pirronello (eds.) The Chemistry of Life's Origins., Kluwer, Dordrecht, The Netherlands, pp. 209-258.

Cronin, J. R., Cooper, G. W. and S. Pizzarello, S. (1995) Characteristics and formation of amino acids and hydroxyl acids of the Murchison meteorite. Adv. Space Res. 15, 91-97.

Delak, K. M. and Sahai, N. (2005) Amine-catalyzed biomimetics hydrolysis and condensation of organosilicate. Chem. Mater. 17, 3221-3227.

Delak, K. M. and Sahai, N. (2006) Mechanisms of amine-catalyzed organosilicate hydrolysis at circum-neutral pH. J. Phys. Chem. B 110, 17819-17829.

Hino, M. and Sato, T. (1971) Infrared absorption spectra of silica gel-water, water-d2, and water-18O systems. Bull. Chem. Soc. Jpn. 44, 33-37.

Iler, R. K. (1979) The Chemistry of Silica, Solubility, Polymerization, Colloid and Surface Properties, and Biochemistry. Wiley, New York, pp. 150-157, 174-177, 239, 288-304, 730, 761-766.

Kastele, X., Klufers, P., Kopp, F., Schuhmacher, J. and Vogt, M. (2005) Silicon chelation in aqueous and nonaqueous media: The furanoidic diol approach. Chem-Eur. J. 11, 6326-6346.

Kolb, V. M. and Liesch, P. J. (2006) Role of amino acids and their Maillard mixtures with ribose in the biosilicification process. In: R. B. Hoover, G. Y. Levin and A. Y. Rozanov (eds.) Instruments, Methods, and Missions for Astrobiology IX. SPIE, 6309, pp. 63090T 1-8.

Kolb, V. M. and Liesch, P. J. (2007) Role of Organic Silicates in the Biomineralization Process. In: R. A. Yingst, S. D. Brandt, M. Rudd, and N. Kaltcheva (eds.) Internalization of Space, Proceedings of the 17thAnnual Wisconsin Space Conference, Wisconsin Space Grant Consortium Publ., Part Seven (Chemistry), pp. 1-5, Green Bay, WI, 2007.

Kolb, V. M., Philip, A. I. and Perry, R. S. (2004) Testing the role of silicic acid and bioorganic materials in the formation of rock coatings. In: R. B. Hoover, G. L. Levin and A. Y. Rozanov (eds.) Instruments, Methods, and Missions for Astrobiology VIII. SPIE, 5555, pp. 116-125.

Kolb, V. M., Bajagic, M., Zhu, W. and Cody, C. D. (2005) Prebiotic Significance of the Maillard Reaction. In: R. B. Hoover, G. V. Levin, A. Y. Rozanov and G. R. Gladstone (eds.) Astrobiology and Planetary Missions. SPIE, 5906, pp. 59060T 1-11.

Kolb, V. M., Bajagic, M., Liesch, P. J., Philip, A. and Cody, G. D. (2006) On the Maillard reaction of meteoritic amino acids. In: R. B. Hoover, G. Y. Levin and A. Y. Rozanov (eds.) Instruments, Methods, and Missions for Astrobiology IX. SPIE, 6309, pp. 63090B 1-13 and the references cited therein.

Kubicki, J. D. and Heaney, P. J. (2002) Structures of Si-Carbohydrate Aqueous Complexes: Comparison of NMR Spectra and Molecular Orbital Results. American Geophysical Union, Fall Meeting 2002, abstract #B11A-0700.

Lambert, J. B., Lu, G., Singer, S. R. and Kolb, V. M. (2004) Silicate complexes of sugars in aqueous solution. J. Am. Chem. Soc. 126, 9611-9625.

Lehninger, A. L., Nelson, D. L. and Cox, M. M. (2004) Principles of Biochemistry, Fourth Edition. W. H. Freeman, New York, pp. 76-81, 251-261.

Liesch, P. J. and Kolb, V. M. (2007a) Importance of the interaction between sodium silicate and organic materials to astrobiology: Alcohol-based organo-silicates as potential biosignatures. In: R. B. Hoover, G. Y. Levin, A. Y. Rozanov and P. C. W. Davies (eds.) Instruments, Methods, and Missions for Astrobiology X. SPIE, 6694, pp. 669405 1-10.

Liesch, P. J. and Kolb, V. M. (2007b) The importance of the Maillard-metal complexes and their silicates in astrobiology. In: R. B. Hoover, G. Y. Levin, A. Y. Rozanov and P. C. W. Davies (eds.) Instruments, Methods, and Missions for Astrobiology X. SPIE, 6694, pp. 66941G 1-8.

Liesch, P. J. and Kolb, V. M. (2007c) Living strategies of unusual life forms on Earth and the relevance to astrobiology. In: R. B. Hoover, G. Y. Levin, A. Y. Rozanov and P. C. W. Davies (eds.) Instruments, Methods, and Missions for Astrobiology X. SPIE, 6694, pp. 66941F 1-9.

Lodish, H., Berk, A, Matsudaria, P., Kaiser, C. A., Krieger, M., Scott, M. P., Zipursky, S. L. and Darnell. J. (2004) Molecular Cell Biology, Fifth Edition. W. H. Freeman, New York, pp. 59-86, 301-315.

Mann, S. (2001) Biomineralization. Oxford University Press, Oxford, pp. 13-15, 106-108, 134-136, 168, 176.

Morison, D. (2001) The NASA astrobiology program. Astrobiology 1, 3-13.

NASA (2007a) Astrobiology Roadmap, Goal 7, http://astrobiology.arc.nasa.gov/roadmap/g7.html, Final version, September 2003, site visited December 12, 2007.

NASA (2007b) Jet Propulsion Laboratory News Releases May 21, 2007, http://www.jpl.nasa.gov/ news/news.cfm?release = 2007-061, site visited December 12, 2007.

National Academies Report (2007) Committee on an astrobiology strategy for the exploration of Mars. An Astrobiology Strategy for the Exploration of Mars. The National Academies Press, Washington, DC, pp. 3, 4, 51, 58, 118.

Perry, R. S. and Kolb, V. M. (2004) From Darwin to Mars: Desert varnish as a model for preservation of complex (bio) chemical systems. In: R. B. Hoover and A. Y. Rozanov (eds.) Instruments, Methods, and Missions to Astrobiology VII. SPIE, 5163, pp. 136-144.

Perry, C. C., Belton, D. and Shafran, K. (2003) Studies in biosilicas; structural aspects, chemical principles, model studies, and the future. In: W. E. G. Müller (ed.) Silicon Biomineralization. Springer, New York, pp. 269-299.

Perry, R. S., Kolb, V. M., Philip, A. I., Lynne, B. Y., McLoughlin, N., Sephton, M., Wacey, D. and Green, O. R. (2005) Making silica rock coatings in the lab: synthetic desert varnish. In: R. B. Hoover, G. V. Levin, A. Y. Rozanov and G. R. Gladstone (eds.) Astrobiology and Planetary Missions, SPIE 5906, pp. 5906U 1-11.

Perry, R. S., Lynne, B. Y., Sephton, M. A., Kolb, V. M., Perry, C. C. and Staley, J. T. (2006) Baking black opal in the desert sun: The importance of silica in desert varnish. Geology 34, 537-540.

Pizzarello, S. and Cronin, J. R. (2000) Non-racemic amino acids in the Murray and Murchison meteorites. Geochim. Cosmochim. Acta, 64, 329-338.

Pohnert, G. (2002) Biomineralization of diatoms mediated through peptide- and polyamine-assisted condensation of silica. Angew. Chem. Int. Ed. 41, 3167-3169.

Samadi-Maybodi, A., Harris, R. K., Azizi, S. N. and Kenwright, A. M. (2001) Silicon-29 NMR study of the formation of monomethoxysilicic acid in methanolic alkaline silicate solutions. Magn. Reson. Chem. 39, 443-446.

Samba-Fouala, C., Mossoyan, J.-C., Mossoyan-Deneux, M., Benlian, D., Chaneac, C. and Babonneau, F. (2000) Preparation and properties of silica hybrid gels containing phytic acid. J. Mater. Chem. 10, 387-393.

Sullivan, C. W. (1986) Silicification by diatoms. In: D. Evered and M. O'Connor (eds.) Silicon Biochemistry. Wiley, Chichester, England (Ciba Foundation Symposium 121), pp. 59-89.

Sweryda-Krawiec, B., Cassagneau, T. and Fendler, J. H. (1999) Surface modification of silicon nano-crystallites by alcohols. J. Phys. Chem. B 103, 9524-9529.

Trusovs, S. (2006) Metal complexes produced by Maillard reaction products, US Patent 10605987, January 31, 2006.

Vrieling, E. G., Hazelaar, S., Gieskes, W. W. C., Sun, Q., Beelen, T. P. M. and van Santen, R. A. (2003) Silicon biomineralization: Towards mimicking biogenic silica formation in diatoms. In: W. E. G. Müller (ed.) Silicon Biomineralization. Springer, New York, pp. 301-334.

Weissbach, A. and Sprinson, D. B. (1952) The metabolism of 2-Carbon compounds related to glycine. J. Biol. Chem. 203, 1031-1037.

Williams, R. J. P. (1986) Introduction to silicon chemistry and biochemistry. In: D. Evered and M. O'Connor (eds.) Silicon Biochemistry. Wiley, Chichester, England (Ciba Foundation Symposium 121), pp. 24-39.

Zubay, Z. (2000) Origins of Life on the Earth and in the Cosmos, Second Edition. Academic, San Diego, pp. 283-308, 380-381, 390-392.

Zwitter definition, dict.cc, English-German Dictionary, http://www.dict.cc/german-english/Zwitter. html, copyright 2003-2007, site visited December 12, 2007.

Biodata of Shuhai Xiao and James D. Schiffbauer authors of the chapter "Microfossil Phosphatization and Its Astrobiological Implications"

Dr. Shuhai Xiao is currently full Professor of Geobiology at the Department of Geosciences, Virginia Polytechnic Institute and State University. He received his B.Sc. degree from Beijing University (Beijing, China, 1988) and Ph.D. from Harvard University (Cambridge, Massachusetts, USA, 1998). In the past 10 years, he has been working on the biological and environmental evolution in Earth's early history.

E-mail: [email protected]

James D. Schiffbauer is currently a Ph.D. candidate at Virginia Polytechnic Institute and State University. He received his B.A. (Honors) in Biology from West Virginia University (Morgantown, West Virginia, USA, 2000), and a dual M.S. in Marine Biology and Coastal Ecosystem Mgmt. from Nova Southeastern University (Fort Lauderdale, Florida, USA, 2004). His scientific interests consist of the origin and early evolution of life, prokaryotic diversity through time, microfossil ultrastructure, taphonomic processes of microfossil preservation, modern marine ecological interactions, and the origins of Eukarya, Metazoa, and biomineralization.

E-mail: [email protected]

Dr. Shuhai Xiao James D, Schiffbauer
0 0

Post a comment