Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage

Abstract

The emergence of a simple translation device consisting of an assembler strand (primordial mRNA) and RNA hairpins (primordial tRNA) is presumed to be an important step leading to the origin of life. The assumption of a non-enzymatic interaction of primordial tRNA and mRNA is experimentally approached. DNA hairpins containing five or more adenosine residues in the loop are able to bind to complementary oligonucleotides covalently bound to cellulose. The exact number of base pairs formed between the hairpins and the assembler strand is determined by two methods applied to DNA hairpin/assembler complexes. The melting temperature of a complex is measured and the cleavage pattern by nuclease from mung bean is determined. The loop of the smallest hairpin able to bind consists of five adenosine residues and only three base pairs are formed. This supports the idea of a primordial recognition similar to the contemporary codon-anticodon interaction.The emergence of a simple translation device is a crucial step in the process leading to the origin of life. A proposed translation device [l] consists of interacting oligoribonucleotides. The occurrence of short oligoribonucleotides seems reasonable, since the synthesis of chemically activated ribonucleotides under almost primordial conditions [2], their oligomerisation [3] and their template-directed enzyme-free polymerisation [4, 51 have been demonstrated. The model for self-organisation of matter needs oligoribonucleotides with a hairpin structure acting as primeval tRNA and a singlestranded polynucleotide functioning as primeval mRNA. This single-stranded assembler is thought to bind the hairpin molecules by formation of three base pairs with the loop nucleosides thus arranging the hairpins in a distinct sequence. The base-pairing interactions are thought to be stabilized additionally by lateral forces between the helical parts of the hairpin oligonucleotides occurring at a high Mg2 + concentration. The search for conditions leading to stable binding of hairpins to single strands by base triplets is of interest and a presupposition for intended formation of the peptide bond.In order to investigate the proposed base-pairing ability, two sets of molecules containing either thymidine or deoxyadenosine in the loop region both with an identical helical region as shown in Fig. 1 were synthesized 16 size of the loop was varied with regard to a possible primordial codon-anticodon interaction. The binding ability of the hairpins to complementary homooligonucleotides chemically bound to a solid support was investigated. This method had been originally used for the study of complexes of singlestranded oligonucleotides [8, 91. In order to investigate the steric arrangement of the particular loop nucleosides in free and complexed hairpin oligonucleotides, the single-strandspecific nuclease from mung bean was used as a structural probe [lo, 111. The best known similar nuclease S1 from Aspergillus oryzae had been used as a structural tool to reveal special features of tRNA [12, 131. MAT...

Computer-modeling origin of a simple genetic apparatus

“…1). The compact arrangement of hairpins and their binding to the assembler by triplets are reasonable assumptions, as demonstrated by molecular modeling (9, 10), force-field calculations (13), and experiments (14,15). Basic assumptions of the model are supported by experiments (16)(17)(18)(19) and computer models (20,21).…”

Adding to Hans Kuhn's thesis on the emergence of the genetic apparatus: Of the Darwinian advantage to be neither too soluble, nor too insoluble, neither too solid, nor completely liquid

“…Enriched with Christoph Kuhn's more recent computer simulations [26,27], they qualitatively and semi-quantitatively suggest how supramolecular machines could self-propel into a dynamic 'animate' system. This pioneering work is on the one hand intellectually extremely stimulating and on the other suffered too long a time from a lack of experimental testing, although efforts have been reported that addressed directly or inadvertedly Kuhn's concept [28][29][30][31][32]. The majority of these experiments focused on simple molecular recognition processes, simple in the sense of nonsystemic and non-dynamic.…”

Affinity sorbents containing nucleic acids and their fragments

“…60,61,261 A series of papers devoted to affinity chromatography of poly(A)-mRNA, 214,254,262,263 NA or oligonucleotides containing homogeneous sequences were published in the late 1980's ± early 1990's owing to the development of methods of synthesis of oligonucleotides and the accessibility of novel carriers. 26,264 However, this method was not successful for the isolation of individual oligonucleotides or longer sequences devoid of homogeneous inserts. Present-day studies widely employ commercial supports carrying immobilised homogeneous oligonucleotides, most commonly, oligo(T) supports.…”