Synthesis of information-carrying polymers of mixed sequences from double stranded short deoxynucleotides

Abstract

The "RNA World" hypothesis suggests that an early form of life on Earth was based on nucleic acid strands able to store genetic information and catalyze a wide range of reactions including those which lead to self-replication. For this hypothesis to be true there must exist an efficient process for creating RNA or RNA-like polymers of mixed sequences from short precursors, where these polymers have to be long enough to fold into catalytically active structures (at least 40 bases). We report on the polymerization of dimeric to hexameric 5'-amino- oligodeoxynucleotides 3'-phosphates in the presence of the water-soluble carbodiimide EDC. Non-complementary single stranded nucleotides fail to polymerize and yield di- to hexameric cyclooligomers or capped EDC-adducts unable to undergo further 3'-5'-phosphoramidate formation. Complementary building blocks polymerize with a conversion close to 100% when starting from a concentration of typically 20 mM. The reactions proceed within a few hours yielding strands of mixed pyrimidine-purine sequences up to 300 bases long. The maximum length of the products depends on the type of the starting oligonucleotides. Copolymerization of a dimer alphabet consisting of equimolar quantities of all four sequences d(nYRp), where Y are pyrimidines and R are purines, generates a mixed-sequence library of 50-70 mers. Libraries of long oligonucleotides with potentially catalytic activity are formed from short precursors within hours. Reactions occur via blunt end ligation of the double strands, and the reaction rates correlate with stacking interactions at the ligation sites. Circular dichroism measurements, polarized light microscopy and fluorescence microscopy suggest the formation of supramolecular aggregates during chain growth. These aggregates accelerate the reactions by increasing the local concentration of the reactants in a non-sequence-specific templating mode. Aggregation of the double strands into higher order "compartimented" structures might have been the key for the formation of the first inhabitants of the "RNA World".