Did nature also choose arsenic?

2009 ◽  
Vol 8 (2) ◽  
pp. 69-74 ◽  
Author(s):  
Felisa Wolfe-Simon ◽  
Paul C.W. Davies ◽  
Ariel D. Anbar
Keyword(s):  
Nucleic Acids ◽  
Periodic Table ◽  
Inorganic Phosphate ◽  
Organic Molecules ◽  
Genetic Material ◽  
Chemical Properties ◽  
Biochemical Pathways ◽  
Evolution Of Life ◽  
Biochemical Systems ◽  
Life On Earth

AbstractAll known life requires phosphorus (P) in the form of inorganic phosphate (PO43−or Pi) and phosphate-containing organic molecules. Piserves as the backbone of the nucleic acids that constitute genetic material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic because As and P are similar enough that organisms attempt this substitution. We hypothesize that ancient biochemical systems, analogous to but distinct from those known today, could have utilized arsenate in the equivalent biological role as phosphate. Organisms utilizing such ‘weird life’ biochemical pathways may have supported a ‘shadow biosphere’ at the time of the origin and early evolution of life on Earth or on other planets. Such organisms may even persist on Earth today, undetected, in unusual niches.

Template-directed nonenzymatic oligonucleotide synthesis: lessons from synthetic chemistry

2015 ◽  
Vol 87 (2) ◽  
pp. 205-218 ◽  
Author(s):  
Albert C. Fahrenbach
Keyword(s):  
Nucleic Acids ◽  
Organic Molecules ◽  
Rna World ◽  
Significant Development ◽  
Directed Synthesis ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Life On Earth ◽  
And Storage ◽  
Rna World Hypothesis

AbstractThe nonenzymatic synthesis of nucleic acids, in particular, RNA, and the template-directed synthesis of artificial organic molecules, such as macrocycles, catenanes and rotaxanes, have both undergone significant development since the last half of the 20th century. The intersection of these two fields affords insights into how template effects can lead to information copying and storage at the molecular level. Mechanistic examples of model template-directed RNA replication experiments as well as those for totally artificial organic template-directed syntheses will be discussed. The fact that templates typically bind to their reacted products more tightly than their unreacted substrates may be a mechanistic feature necessary to store information in the form of nucleic acids. Understanding the mechanisms of nonenzymatic RNA synthesis is not only essential for testing the RNA world hypothesis in the context of the origin of life on Earth and other planetary bodies, but may one day afford chemists the insights to construct their own artificial molecular replicators.

scholarly journals Who is the “Matchmaker” between Proteins and Nucleic Acids?

2021 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Photochemical Reactions ◽  
Host Cells ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Life On Earth

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthetic system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remain largely unknown thus far. Based on the ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.

scholarly journals The ATP Hypothesis Discovers the Missing “Matchmaker” between Proteins and Nucleic Acids

2020 ◽  
Author(s):  
Ping Xie
Keyword(s):  
Nucleic Acids ◽  
Genetic Code ◽  
Photochemical Reactions ◽  
Host Cells ◽  
Darwinian Evolution ◽  
Lipid Vesicle ◽  
Biochemical System ◽  
Cellular Life ◽  
Biochemical Systems ◽  
Life On Earth

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored the energetic driving force, its relation to the biochemical system, and most importantly, the missing “matchmaker” between proteins and nucleic acids. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by driving the coevolution of the genetic code with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced e.g. by photochemical reactions in a protocell that derived from a lipid vesicle enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically form and elongate chains of both polynucleotides and polypeptides, thus acting a “matchmaker” between these two bio-polymers and eventually mediating precellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of permanently recording the genetic information by DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis assumes or supports the photochemical origin of life, shedding light on the origins of both photosynthetic and biochemical systems, which remains largely unknown thus far. Based on ATP hypothesis, virus (like the new coronavirus) could not be the earliest life on Earth, as it has neither biochemical systems nor lipid bilayer membrane that provided relatively isolated environment for the development of protobiochemical reactions, although it owns the genetic code of a cellular life. Virus could not be a bridge between life and non-life, but is an anti-life substance, as it depletes cellular material for its own replication, and then spreads by destroying the host cells. It can be imagined that if cellular life are completely wiped out by the virus, the complete destruction of life on Earth would be inevitable.

scholarly journals Low-Digit and High-Digit Polymers in the Origin of Life

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 17 ◽  
Author(s):  
Peter Strazewski
Keyword(s):  
Nucleic Acids ◽  
Information Transfer ◽  
Test Tube ◽  
Linear Polymers ◽  
Fine Grained ◽  
Catalytic Potential ◽  
Cellular Life ◽  
Evolution Of Life ◽  
Compositional Diversity ◽  
Life On Earth

Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential. The fine-grained diversity of proteins makes an unambiguous information transfer from protein templates too error-prone, so they need to be resynthesized in every generation. But proteins can catalyse both their own reproduction as well as the efficient and faithful replication of nucleic acids, which resolves in a most straightforward way an issue termed “Eigen’s paradox”. Here the importance of the existence of both kinds of linear biopolymers is discussed in the context of the emergence of cellular life, be it for the historic orgin of life on Earth, on some other habitable planet, or in the test tube. An immediate consequence of this analysis is the necessity for translation to appear early during the evolution of life.

scholarly journals Theoretical methods for measuring chemo-physical properties of nucleic acids during the radicalization of dna and the incidence of cancer

2019 ◽  
Vol 32 (01) ◽  
pp. 01-12
Author(s):  
Mehdi Imanzadeh ◽  
Karim Zare ◽  
Majid Monajjemi ◽  
Ali Shamel
Keyword(s):  
Nucleic Acids ◽  
Genetic Material ◽  
Chemical Properties ◽  
Relevant Information ◽  
Dna Damages ◽  
Theoretical Methods ◽  
Chemical Agents ◽  
Incidence Of Cancer ◽  
Comprehensive Survey ◽  
Physical And Chemical

One of cases considered for diagnosing DNA damages is diagnosing DNA probable damages against oxidizing agents, including oxidizing chemicals and various incident rays which cause the bases in the DNA to be oxidized and especially bases G in the DNA sequence which is more easily oxidized than the other bases. Therefore, the main objective of this comprehensive survey is to provide relevant information on measure physical chemical properties of nucleic acids during DNA radicalization and incidence of cancer using theoretical methods. The aim of the present study is to examine the single-stranded NBO with sequences of GG, CG, AA AG AC: AT CT GT TT followed by the levels of energy and form of orbital LUMO and HOMO obtained from Gaussian computations for above double-stranded sequences. Our results showed that form B genetic material is the most stable structure against physical and chemical agents. Only the number of molecular population and the levels of molecular dynamic vibration and molecular thermochemistry such as enthalpie and entropie are temperature independent. In addition to this, the gap between the layers and the potential and energy needed to oxidize the components in the two strands of DNA and its optimum structure will not change with temperature. Optimum conditions on DNA and its bonds are the temperature of 37 ° C and pH is 7 to 8.7. DNA has form B and the rate of physical protection is the highest.

scholarly journals Transcription of 4′-thioDNA templates to natural RNA in vitro and in mammalian cells

2015 ◽  
Vol 51 (37) ◽  
pp. 7887-7890 ◽  
Author(s):  
Hideto Maruyama ◽  
Kazuhiro Furukawa ◽  
Hiroyuki Kamiya ◽  
Noriaki Minakawa ◽  
Akira Matsuda
Keyword(s):  
Nucleic Acids ◽  
Mammalian Cells ◽  
Genetic Material ◽  
Rna Polymerases ◽  
Chemically Modified ◽  
Biological Studies ◽  
Modified Nucleic Acids

Synthetic chemically modified nucleic acids, which are compatible with DNA/RNA polymerases, have great potential as a genetic material for synthetic biological studies.

scholarly journals ‘Whole Organism’, Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 690
Author(s):  
Clifford F. Brunk ◽  
Charles R. Marshall
Keyword(s):  
Origin Of Life ◽  
Top Down ◽  
Chemical Systems ◽  
Biochemical Pathways ◽  
The Origin Of Life ◽  
Energy And Material Flows ◽  
Complex Scenario ◽  
Life On Earth ◽  
Physical Laws ◽  
Equilibrium Chemical

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

Structural Insights into the Recognition of DNA Defects by Small Molecules

2021 ◽  
Author(s):  
David Dayanidhi Paul Elisa Sundar ◽  
Vaidyanathan Ganesan
Keyword(s):  
Nucleic Acids ◽  
Metal Complexes ◽  
Small Molecules ◽  
Chemical Properties ◽  
Biological Applications ◽  
Binding Interaction ◽  
Structural Insights

Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural...

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