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The theory of the emergence of the matrix mechanism in protocells on complexes of minerals (apatite, carbonate-apatite, calcite, and quartz) with the reciprocal proportions and with the participation of the gas phase radicals (NH3, CH4, and CO) is considered. The structure of apatite and carbonate-apatite predetermined the formation of a double helix of DNA with the complementary pairs of purine-pyrimidine bases, as well as RNA strands complementary to DNA, and helical protein chains combined into supramolecular structures with RNA. It is proposed that during the Archean Eon, a gradual replacement of the mineral matrix with organic matter took place. The site of the origin of the matrix mechanism is the defect-free and growing defective zone of apatite and carbonate-apatite. The size and specificity of DNA, complementary-bound RNA and protein molecules in supramolecular protein-RNA complexes increased as defects accumulated in the structure of minerals. An increase in the size of RNA transcripts was accompanied by an increase in the number of protein molecules in supramolecular protein-RNA complexes. At the first, anhydrous, stage, the formation of a transcriptional-translational apparatus in the form of a crystalline organic-mineral complex -DNA, RNA and protein, based on the “spiral into spiral” principle of gas phase elements. The appearance of water determined the launch of the transcriptional-translational apparatus and the transformation of the organo-mineral crystalline complex into a liquid-crystalline state. A detailed description of the preparation and launch of the matrix mechanism is given. The following problems are discussed: the origin of ribosomal proteins and the role of super-specific aminoacyl-tRNA synthetase as a true carrier of genetic information; properties of the genetic code and synthesis of protocells without violating the second law of thermodynamics; the origin of biological asymmetry; the appearance of nanobacteria and dark genetic matter of eukaryotic systems. Communicated by Ramaswamy H. Sarma

On the origin of matrix mechanism in protocells and key problems of molecular biology