Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer

Abstract

Recent advances suggest that it may be possible to construct simple artificial cells from two subsystems: a self-replicating cell membrane and a self-replicating genetic polymer. Although multiple pathways for the growth and division of model protocell membranes have been characterized, no self-replicating genetic material is yet available. Nonenzymatic template-directed synthesis of RNA with activated ribonucleotide monomers has led to the copying of short RNA templates; however, these reactions are generally slow (taking days to weeks) and highly error prone. N 3′ -P 5′ -linked phosphoramidate DNA (3′-NP-DNA) is similar to RNA in its overall duplex structure, and is attractive as an alternative to RNA because the high reactivity of its corresponding monomers allows rapid and efficient copying of all four nucleobases on homopolymeric RNA and DNA templates. Here we show that both homopolymeric and mixed-sequence 3′-NP-DNA templates can be copied into complementary 3′-NP-DNA sequences. G:T and A:C wobble pairing leads to a high error rate, but the modified nucleoside 2-thiothymidine suppresses wobble pairing. We show that the 2-thiothymidine modification increases both polymerization rate and fidelity in the copying of a 3′-NP-DNA template into a complementary strand of 3′-NP-DNA. Our results suggest that 3′-NP-DNA has the potential to serve as the genetic material of artificial biological systems.origin of life | nonenzymatic primer extension | artificial genetic systems | nucleotide modifications | mismatch T he phosphoramidate nucleic acids are of particular interest as potential genetic materials for artificial life-forms because of their potential for replication by the nonenzymatic polymerization of amino-sugar nucleotides. Because of the greater nucleophilicity of the amino group relative to the 3′-hydroxyl group of ribo-and deoxyribo-nucleotides, amino-sugar nucleotides exhibit more rapid spontaneous polymerization. Obviating the requirement for a polymerase greatly simplifies the task of creating and assembling the components of an artificial cell, and thus of constructing simple living systems from inanimate materials. We and others have therefore explored the synthesis of a variety of phosphoramidatelinked nucleic acids, their corresponding amino-sugar monomers, and the characterization of nonenzymatic template-directed primer extension reactions in these systems (1-11). Among these systems, we have examined 2′-amino versions of the acyclic glycerol nucleic acid (5), 2′-amino-2′,3′-dideoxyribonucleic acid (4, 6), and 3′-amino-2′,3′-dideoxyribonucleic acid (7).The structural simplicity of the acyclic sugar-phosphate nucleic acid backbones has made them attractive targets for study. Indeed, an acyclic nucleotide consisting of a glycerol-phosphate backbone linked to a formylated nucleobase (12) was among the first of such nucleic acids to be chemically synthesized, but incorporation of this nucleotide into oligomers caused a severe loss of duplex stability. Much later, the glycerol nucleic acids, in which...

Physical autocatalysis driven by a bond-forming thiol–ene reaction

“…Given the wide interest in simple autocatalytic molecules 14,15 and the significant influence of the RNA world hypothesis 16 , molecules capable of template-based self-replication have been studied for many years. This field has advanced to the point that there now exist candidate substrates for the genetic material of a protocell 17 , and it has been proposed that non-enzymatic chemical replication of RNA may even be possible 18 .…”

DNA‐Catalyzed Lysine Side Chain Modification

“…We also note that uncatalyzed, DNA-templated polymerization of 5′-ImpDNA monomers by reaction with 3′-NH 2 groups is quite rapid (complete reaction in <1 h; pH 7.5, 4 °C). [20] …”

DNA Oligonucleotide 3′-Phosphorylation by a DNA Enzyme

“…Subsequently, the 3′-MeImp terminus was joined with a 5′-amino-modified DNA oligonucleotide using a DNA splint, forming a phosphoramidate (P–N) linkage. 42–44 This bond formation leads to a shift on polyacrylamide gel elecrophoresis (PAGE), which enables separation of the catalytically active DNA sequences. These sequences were amplified by PCR, and the forward strand was ligated with the DNA substrate bearing a free 3′-OH and taken into the next selection round.…”