Ecology, Pollution and Environmental science: Open Access (EEO)

In a World Where Carbon does not Exist.

Ricardo Gobato1*, Abhijit Mitra2, Sufia Zaman3

1Green Land Landscaping and Gardening, Seedling Growth Laboratory, 86130-000, Parana, Brazil.

2Department of Marine Science, University of Calcutta, 35 B. C Road, Kolkata, 700019, West Bengal, India.

3Department of Oceanography, Techno India University, West Bengal, EM 4 Salt Lake, Sector V, Kolkata 700091, India.

*Corresponding Author:Ricardo Gobato,Green Land Landscaping and Gardening, Seedling Growth Laboratory, 86130-000, Parana, Brazil, Tel: 00-40-723621414; Fax: 00-40-253-210432; E-mail:ricardogobato@hotmail.com

Citation: Ricardo Gobato, Abhijit Mitra, Sufia Zaman (2023) In a World Where Carbon does not Exist.  SciEnvironm 6: 175.

Received: March 29, 2023; Accepted: August 17, 2023; Published: April 20, 2023.

In a world where there is no Carbon, it is possible to have exobiological molecules based on Silicon. The world's most famous molecule - the DNA double helix - sometimes doubles up again. Researchers have now found this quadruple-stranded form in healthy human cells for the first time.  Speculate that the quadruplex structure forms to hold the molecule open and facilitate the reading of the genetic code and thus the production of proteins. G-quadruplex DNA is a four-stranded structure made that can form a 'knot' in the DNA of living cells. In these terms, it was analyzed through computational calculations, via MM (Molecular Mechanics), and by ab initio Restricted Hartree-Fock (RHF) method, on a simple STO-3G (Slater-type orbitals with 3 Gaussians) basis, the possibility of a DNA macromolecule based on Silicon. From the basic structure of 1bna, however, you assume conditions without the presence of Carbon, replacing it with Silicon. It was obtained a cluster of G-quadruplex DNA, forming a cocoon, with great possibility for the pharmaceutical industry in capturing molecules foreign to human DNA.

Four-stranded DNA has been seen before in some cancer cells and in lab-based chemistry experiments, but this is the first time the molecule has been visualized in healthy, living human cells, as a stable structure created by normal cellular processes. [1]

The researchers speculate that the quadruplex structure forms to hold the molecule open and facilitate the reading of the genetic code and thus the production of proteins. It may also influence the amount of each protein that is made.  [1]. Usually, this function is performed by epigenetic markers - chemical tags on DNA that increase or decrease the activity of genes - and it seems that the quadruplex form of DNA has a similar role. [2]

The DNA 1bna. Name: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'); Representative chains: A, B; Source organism: Synthetic construct; Length: 12 nucleotides; Theoretical weight: 3.66 KDa. [3] Not all DNA is in the double helix form described in textbooks since the 1950's. Quadruple helix DNA, also known as G-quadruplex DNA [4, 5, 6], was identified in the human genome several decades ago, and extensively studied since then. Each cell in our body contains a copy of our DNA code made up of A, C, G and T, providing the blueprint for the organization and function of our bodies. Normally these letters combine in pairs to form the well-known double helix shape. However, some small lengths of DNA can exist as alternative shapes, which can affect how the instructions of the DNA code is 'read'. [7] G-quadruplex DNA [4, 5, 6] is a four-stranded structure made that can form a 'knot' in the DNA of living cells. In these structures, many Gs on the same stretch of DNA stick to each other instead of forming pairs between two strands. G-quadruplex DNA is known to be capable of forming many different types of structural shapes, yet little is understood about the factors controlling formation of these motifs [7]. The most significant result would be to and some type of living matter radically different from that of the Earth. One might cite under this category supposed organisms with a structure and metabolic machinery based on silicon rather than on carbon; or forms with an ammonia based rather than a water-based machinery and metabolism. (One should note in the former case, however, that fully aerobic silicon metabolizers would be required to exhale quartz.) [9]

The four most abundant elements of the universe are hydrogen, oxygen, carbon, and nitrogen. In fact, hydrogen is the major constituent of the universe; oxygen, carbon, and nitrogen are each about ten times more plentiful than the next most abundant element, silicon. [9] In comparing the carbon and silicon has: the Si lies in the same column of the periodic table of the elements, and it has been investigated as a possible alternative for building up biological molecules in exobiology. [10, 11, 12, 13, 14, 15]

The option for simple replacement of carbon by silicon [16, 17] is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in STP (Standard Temperature and Pressure), for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. [18, 19, 20, 21, 22, 23]. If elements other than carbon constitute the building blocks for any living system on other worlds, they almost surely exist under conditions far different from those on Earth, including temperatures and pressures where water could not be the solvent. Titan provides the best natural laboratory in our Solar System for investigating this possibility. [18, 19, 20, 21, 22, 23]

Through the chemical abundances of biological elements in the earth crust, terrestrial life has chosen carbon instead of silicon, in spite of the larger abundance of silicon. This fact suggests that carbon is better suited to form biological molecules.  [10, 24] However, this paper assumes conditions without the presence of Carbon. Figures (1-4) show the four structures of the silicon-based 1bna DNA macromolecule after replacing all carbon atoms with silicon and the molecular dynamics with calculations via MM [25, 26] and RHF [27, 28], which will be called [1bna] Si. The Figures represents at four structures obtained after molecular dynamics, for the silicon-based 1bna DNA molecule, in 2D contours of its electrostatic potential. The individualized representation of each of the four [1bna] Si structures was necessary for an analysis of the electrostatic potential distribution. It is verified that there is a planarity of the electrostatic potential in the cluster Figure (5) formed by the four macromolecules [1bna] Si, occurring a symmetry of the electrostatic potential represented in 2D.

Figure 1: Image of [1bna] Si DNA macromolecule. The Figure represents a first structure obtained after molecular dynamics, for the silicon-based 1bna DNA molecule, in 2D contours of its electrostatic potential.

Source: [Authors]

Figure 2: Image of [1bna] Si DNA macromolecule. The Figure represents a second structure obtained after molecular dynamics, for the [1bna] Si DNA molecule, in 2D contours of its electrostatic potential.

Source: [Authors] 

Figure 3: Image of [1bna] Si DNA macromolecule. The Figure represents a third structure obtained after molecular dynamics, for the [1bna] Si DNA molecule, in 2D contours of its electrostatic potential.

Source: [Authors]

Figure 4: Image of [1bna] Si DNA macromolecule. The Figure represents a fourth structure obtained after molecular dynamics, for the [1bna] Si DNA molecule, in 2D contours of its electrostatic potential.

Source: [Authors]

Figure 5: Image of [1bna] Si DNA macromolecule. The Figure represents a structure obtained after molecular dynamics, for the [1bna] Si DNA molecule, in 2D contours of its electrostatic potential.

Source: [Authors]

The study has so far been limited to computational Molecular Mechanics methods, as well a via ab initio RHF in the set of bases used ECP minimal basis, on a STO-3G simple basis set. The results are compatible with the theory of quantum chemistry, for simple functionals but a deeper study is necessary to verify the real conditions for the formation of such a macromolecule. Also, a proof experimental verification depends on advanced techniques for their synthesis, obtained in laboratory for experimental biochemical.

It was obtained a cluster of G-quadruplex DNA, forming a cocoon, with great possibility for the pharmaceutical industry in capturing molecules foreign to human DNA.

References

  1. Hooper R (2020) Quadruple-stranded DNA seen in healthy human cells for the first time, New Scientist, url= {https://www.newscientist.com/article/2249390-quadruple-stranded-dna-seen-in-healthy-human-cells-for-the-first-time/
  2. Di Antonio et al. (2020) Single-molecule visualization of DNA G-quadruplex formation in live cells. Nature Chemistry 12: 832–837.
  3. Drew H R, Wing RM, TakanoT, Broka C, Tanaka S et al. (1981) Structure of a B-DNA dodecamer: conformation and dynamics,Proc.Natl.Acad.Sci.USA 78: 2179-2183, URL={https://www.rcsb.org/3d-view/1BNA}
  4. Neidle, Stephen, Balasubramanian, Shankar et al. (2006) Quadruplex Nucleic Acids, Royal Society of Chemistry, RSC Biomolecular Sciences, ed.1, url={http://gen.lib.rus.ec/book/index.php?md5=abff80c134202c53c07d5a6dda4e40aa}
  5. Kaiser, Christine E, Gokhale, Vijay, Yang et al. (2013) Quadruplex Nucleic Acids, Topics in Current Chemistry, ed.1, url={http://gen.lib.rus.ec/book/index.php?md5=65ded647c133daf24f28a99334c7e6f5}
  6.  Neidle, Stephen (2011) Therapeutic Applications of Quadruplex Nucleic Acids Academic Press, url={http://gen.lib.rus.ec/book/index.php?md5=edfa12cf878e910b9ffea233425317bb}
  7. Ulster University, (2023), The shape of quadruple-helix DNA can be controlled, url={https://www.ulster.ac.uk/research/topic/biomedical-sciences/updates/the-shape-of-quadruple-helix-dna-can-be-controlled}
  8. Dunning Hayley (2021), Rare quadruple-helix DNA found in living human cells with glowing probes}, Imperial College London, South Kensington Campus, London, Jan 8, url={https://www.imperial.ac.uk/news/211973/rare-quadruple-helix-dna-found-living-human/}
  9. Mamikunian G, Briggs, M H Current (1965) Aspects of Exobiology, Jet Propulsion Laboratory, California Institute of Technology.
  10. Horneck G, Rettberg P (2007) Complete Course in Astrobiology, Physics Textbook, Wiley-VCH.
  11. Seckbach, Joseph (1998) Exobiology: Matter, Energy, and Information in the Origin and Evolution of Life in the Universe; Proceedings of the Fifth Trieste Conference on Chemical Evolution: An Abdus Salam Memorial Trieste, Italy, 22-26 September 1997}
  12. François, Julian (2005) Origins: Genesis, Evolution and Diversity of Life. Cellular Origin, Life in Extreme Habitats and Astrobiology, Springer Netherlands, ed.1,6.
  13. Freeland, Stephen, Harper, Charles, Barrow et al. (2008) Fitness of the cosmos for life: biochemistry and ne-tuning}, Cambridge astrobiology, Cambridge University Press, ed.1, 2.
  14. Gargaud M, Martin H, Gargaud P C M (2006) Lectures in astrobiology II. Advances in Astrobiology and Biogeophysics, ed.1, Springer. 
  15. Louis N, Dirk Irwinand, Makuch Schulze (2008) Life in the Universe: Expectations and Constraints (Advances in Astrobiology and Biogeophysics, ed. 2, Springer.
  16. McDouall JJW (2013) Computational Quantum Chemistry. Molecular Structure and Properties in Silico. The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF, UK.
  17. Patai S, Rappoport Z (1989) The Chemistry of Organic Silicon Compounds, The Chemistry of functional groups, Wiley.
  18. Gobato R (2012) Infrared spectrum for the new nanomolecules ASi, CSi, TSi and GSi}, Arch Biomed Eng and Biotechnol 5: 3.
  19. Gobato Ricardo, Heidari Alireza, Valverde L, Mitra Abhijit et al (2021) Applying, 'ab initio' Hartree-Fock methods to exobiological nanomolecules, Vixra.org.
  20. Gobato Ricardo, Heidari Alireza, Valverde L, Mitra Abhijit et al. (2022) Distribution of Leptons by Van Der Waals Radius in Exobiological Nanomolecules 4: 91-93.
  21. Gobato Ricardo, Heidari Alireza, Mitra Abhijit, Valverde L et al. (2022) The Possibility of Silicon-Based Life. Bulletin of Pure and Applied Sciences- Chemistry 41: 52-58.
  22. Gobato Ricardo, Mitra Abhijit, Heidari Alireza, Valverde L et al (2022) Distribution of Leptons by Van der Waals radius in Exobiological Nanomolecules, 4.
  23. Gobato Ricardo, Heidari Alireza, Valverde L, Mitra Abhijit et al. (2021) Applying Ab Initio Hartree-Fock Methods to Exobiology Nano-Molecules 3: 1-9.
  24. Shaw A M (2006) Astrochemistry: From Astronomy to Astrobiology.
  25. Gordon M S, Schmidt M W (2005) Advances in electronic structure theory: Gamess a decade later. theory and applications of computational chemistry: the rst forty years, J. Comp. Chem Elsevier 1167-1189.
  26. Gordon M S et al. (1993) General atomic and molecular electronic structure system (GAMESS)}, Elsevier. CE Dykstra, G Frenking, KS Kim and GE Scuseria (editors), J. Comp. Chem 14: 1347-1363.
  27. Brooks R, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem 4: 187-217.
  28. R Brooks et al. (2009) CHARMM: The Biomolecular Simulation Program, J. Comp. Chem 30: 1545-1614, Raulin (eds.), Springer Netherlands}.