DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction can decipher many sequences in parallel. We report here a DNA sequencing method that is a hybrid between the Sanger dideoxynucleotide terminating reaction and SBS. In this approach, four nucleotides, modified as reversible terminators by capping the 3-OH with a small reversible moiety so that they are still recognized by DNA polymerase as substrates, are combined with four cleavable fluorescent dideoxynucleotides to perform SBS. The ratio of the two sets of nucleotides is adjusted as the extension cycles proceed. Sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs. On removing the 3-OH capping group from the DNA products generated by incorporating the 3-O-modified dNTPs and the fluorophore from the DNA products terminated with the ddNTPs, the polymerase reaction reinitiates to continue the sequence determination. By using an azidomethyl group as a chemically reversible capping moiety in the 3-O-modified dNTPs, and an azido-based cleavable linker to attach the fluorophores to the ddNTPs, we synthesized four 3-O-azidomethyl-dNTPs and four ddNTP-azidolinker-fluorophores for the hybrid SBS. After sequence determination by fluorescence imaging, the 3-O-azidomethyl group and the fluorophore attached to the DNA extension product via the azidolinker are efficiently removed by using Tris(2-carboxyethyl)phosphine in aqueous solution that is compatible with DNA. Various DNA templates, including those with homopolymer regions, were accurately sequenced with a read length of >30 bases by using this hybrid SBS method on a chip and a four-color fluorescence scanner.sequencing by synthesis ͉ DNA chip T he completion of the Human Genome Project (1) was a monumental achievement in biological science. The engine behind this project was the Sanger sequencing method (2), which is still the gold standard in genome research. The prolonged success of the Sanger sequencing method is because of its efficiency and fidelity in producing dideoxy-terminated DNA products that can be separated electrophoretically and detected by fluorescence (3-5). However, a challenge in the use of electrophoresis for DNA separation is the difficulty in achieving high throughput and the complexity involved in the automation, although some level of increased parallelization may be achieved by using miniaturization (6).To overcome the limitations of the Sanger sequencing technology, a variety of new methods have been investigated. Such approaches include sequencing by hybridization (7), mass spectrometry sequencing (8, 9), sequencing by nanopores (10), and sequencing by ligation (11). More recently, DNA sequencing by synthesis (SBS) approaches such as pyrosequencing (12), sequencing of single DNA molecules (13,14), and polymerase colonies (15) have been widely explored. Previously, we reported the development of a general strategy to rationally design cleavable fluorescent nucleotide reversible terminators (NRTs) ...

A fast and accurate pathway for nonenzymatic RNA replication would simplify models for the emergence of the RNA world from the prebiotic chemistry of the early earth. However, numerous difficulties stand in the way of an experimental demonstration of effective nonenzymatic RNA replication. To gain insight into the necessary properties of potentially self-replicating informational polymers, we have studied several model systems based on amino–sugar nucleotides. Here we describe the synthesis of N3′–P5′-linked phosphoramidate DNA (3′-NP-DNA) by the template-directed polymerization of activated 3′-amino-2′,3′-dideoxyribonucleotides. 3′-NP-DNA is an interesting model because of its very RNA-like A-type duplex conformation and because activated 3′-amino-2′,3′-dideoxyribonucleotides are much more reactive than the corresponding activated ribonucleotides. In contrast to our previous studies with 2′-amino-2′,3′-dideoxyribonucleotides (for which G and C but not A and T exhibit efficient template copying), we have found that all four canonical 3′-amino-2′,3′-dideoxyribonucleotides (G, C, A, and T) polymerize efficiently on RNA templates. RNA templates are generally superior to DNA templates, and oligo-ribo-T templates are superior to oligo-ribo-U templates, which are the least efficient of the RNA homopolymer templates. We have also found that activation of 3′-aminonucleotides with 2-methylimidazole results in a ca. 10-fold higher polymerization rate relative to activation with imidazole, an observation that parallels earlier findings with ribonucleotides. We discuss the implications of our experiments for the possibility of self-replication in the 3′-NP-DNA and RNA systems.

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...