Biochemistry

   

Abiotic Polymerization of Nucleotides

Authors: Alexey I. Balabin

The book concerns itself with a novel process of mononucleotide assembly into double-stranded polymers. This process, which I call stamping, can be organized either as synthesis of a random double-stranded polynucleotide from mononucleotides or as a reaction of copying a polynucleotide (replication of the DNA or RNA, transcription or reverse transcription). Stamping proceeds in five stages; its crucial step takes place on certain prism faces of apatite crystals. Nucleotides insert their phosphate groups into the positions of PO4 tetrahedra of the crystal lattice, and thereupon condensation of adjacent nucleotides takes place. Inherent in stamping is the constraint that certain bond lengths in the synthesized polymer be equal to certain interatomic distances P–P in the crystal, so that the width and length of each nucleotide pair are fixed. Geometric regularity of the synthesized polymer imparts a regularity to its bond structure—all nucleotides are joined with 3’,5’ phosphodiester linkages (and none with 2’,5’), and all base pairs are the same Watson-Crick type. Because of the geometric constraints, double-stranded RNA molecules could emerge via stamping from a primordial soup circumventing the combinatorial explosion issue (the multitude of nucleotide-type molecules present in the soup had different geometries hence could not join into the polymer). Furthermore, involvement of the crystal surface imparts stereoselectivity to stamping. Synthesis of a polynucleotide from a racemic mixture of the four possible types of nucleotides (L- and D- enantiomers, α- and β-anomers) will result in formation of four types of macromolecules, each consisting predominantly of similar nucleotides (α-L, α-D, β-L or β-D). Though stamping is a hypothetical process, its different stages have been carried out in practice separately. Outlining conditions, at which stamping can be implemented as a whole, constitutes the subject of the main part of the monograph. Remarkably, such conditions have been found, and ways to carry out polynucleotide copying (without enzymes) have been outlined, based upon the data available on apatite surface chemistry, apatite crystal chemistry, physical chemistry of nucleic acids along with certain results from enzymology. In a separate chapter a scenario is proposed for the early history of life, built on the assumption that life originated via stamping and that inheritance relied on stamping apatite crystals, first non-biogenic, supplied by hydrothermal vents, then biogenic ones, until the emergence of bona fide polymerases. This hypothesis clarifies the roles played by group I introns in the ancient world, explains how modern polymerases could emerge in the course of miniaturization of the apatite crystals, the ribozymes involved being replaced with enzymes one by one. (The catalytic center of the modern polymerase in its active state, the phosphate group positioned between two metal atoms, is nothing else then a fragment of the apatite structure.) Combining the idea of stamping with the available phylogenetic data, the Archaea come out as descendants of the organisms whose life cycle was based upon RNA replication, whereas the ancestors of Bacteria appear to be the “inventors” of DNA, whose life cycle was based on transcription alternated with reverse transcription. Drawing an analogy between introns and transposons, the latter appear to be likely descendents of single-stranded catalytically active forms of mobile DNA. The origin of translation can be explained next as a spin-off from stamping performed at elevated hydrostatic pressures. A model for the origin of Eukaryotes can also be proposed as further development of these ideas, accounting for their phylogenetic traits, meiosis, spliceosomal introns and inteins, mechanisms of intron mobility (the homing endonuclease, retrohoming), acidocalciosomes, links between transposons and regulatory sequences of genes, domesticated transposases (including convergent domestication), the nuclear membrane, emergence of the double-stranded DNA, mobilization of double-stranded transposons, gene migration from mitochondria, plastids and nucleomorphs into the nucleus, epigenetic regulation of gene expression, multicellularity. Also explained are nuclear dimorphism in the ciliates, genome rearrangements in their macronuclei and some other phenomena.

Comments: 407 Pages. Russian

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[v1] 2016-07-15 08:38:47

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