The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Here we describe a scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments. The apparatus uses a novel fibre-optic slide of individual wells and is able to sequence 25 million bases, at 99% or better accuracy, in one four-hour run. To achieve an approximately 100-fold increase in throughput over current Sanger sequencing technology, we have developed an emulsion method for DNA amplification and an instrument for sequencing by synthesis using a pyrosequencing protocol optimized for solid support and picolitre-scale volumes. Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine.DNA sequencing has markedly changed the nature of biomedical research and medicine. Reductions in the cost, complexity and time required to sequence large amounts of DNA, including improvements in the ability to sequence bacterial and eukaryotic genomes, will have significant scientific, economic and cultural impact. Largescale sequencing projects, including whole-genome sequencing, have usually required the cloning of DNA fragments into bacterial vectors, amplification and purification of individual templates, followed by Sanger sequencing 1 using fluorescent chain-terminating nucleotide analogues 2 and either slab gel or capillary electrophoresis. Current estimates put the cost of sequencing a human genome between $10 million and $25 million 3 . Alternative sequencing methods have been described 4-8 ; however, no technology has displaced the use of bacterial vectors and Sanger sequencing as the main generators of sequence information.Here we describe an integrated system whose throughput routinely enables applications requiring millions of bases of sequence information, including whole-genome sequencing. Our focus has been on the co-development of an emulsion-based method 9-11 to isolate and amplify DNA fragments in vitro, and of a fabricated substrate and instrument that performs pyrophosphate-based sequencing (pyrosequencing 5,12 ) in picolitre-sized wells.In a typical run we generate over 25 million bases with a Phred quality score of 20 or better (predicted to have an accuracy of 99% or higher). Although this Phred 20 quality throughput is significantly higher than that of Sanger sequencing by capillary electrophoresis, it is currently at the cost of substantially shorter reads and lower average individual read accuracy. Sanger-based capillary electrophoresis sequencing systems produce up to 700 bases of sequence information from each of 96 DNA templates at an average read accuracy of 99.4% in 1 h, or 67,000 bases per hour, with substantially all of the bases having Phred 20 or better quality 23 . We further characterize the performance ...

Polymeric membranes that contain a collection of monodisperse gold nanotubules, with inside diameters of molecular dimensions (less than 1 nanometer), were used in a simple membrane-permeation experiment to cleanly separate small molecules on the basis of molecular size. For example, when such a membrane was presented with an aqueous feed solution containing pyridine (molecular weight 79) and quinine (molecular weight 324), only the smaller pyridine molecule was transported through the nanotubules and into a receiver solution on the other side of the membrane.

An electroless gold deposition method was used to deposit Au nanotubules within the pores of a polycarbonate template membrane. Membranes containing Au nanotubules with inside diameters of 2 and 3 nm were prepared for these studies. Thiols were chemisorbed to the inside tubule walls in order to change the chemical environment within the tubules. The effect of the chemical environment within the tubules on the transport properties of the tubule-containing membrane was investigated. Membranes modified with HS-C(16)H(33) preferentially transported hydrophobic permeant molecules. When a homologous series of permeant molecules was used, the most hydrophobic permeant was preferentially partitioned into and transported by the HS-C(16)H(33) derivatized membrane. In addition, the effect of alkyl chain length (R), in a homologous series of thiols R-SH, was investigated. Hydrophobic permeant molecules were preferentially partitioned into and transported by membranes containing the largest alkyl group. In contrast, membranes modified with HS-C(2)H(4)OH preferentially transported the more hydrophilic permeant pyridine. Finally, we show here that the HS-C(16)H(33) derivatized membrane can be used to separate hydrophobic species from hydrophilic species.

We have developed a new class of synthetic membranes that consist of a porous polymeric support. This support contains an ensemble of gold nanotubules that span the complete thickness of the support membrane. The support is a commercially available microporous polycarbonate filter with cylindrical nanoscopic pores. The gold nanotubules are prepared via electroless deposition of Au onto the pore walls, and tubules that have inside diameters of molecular dimensions (<1 nm) can be prepared. Hence, these membranes are a new class of molecular sieves. We review in this paper the ion‐transport properties of these Au nanotubule membranes. We will show that these membranes can be cation‐permselective or anion‐permselective, and that the permselectivity can be reversibly switched between these two states. Ion permselectivity can be introduced by two different routes. The first entails chemisorption of an ionizable thiol, e.g., a carboxylated or ammonium‐containing thiol to the Au tubule walls. If the thiol contains both of these functionalities (e.g., the amino acid cysteine), the permselectivity can be reversibly switched by varying the pH of the contacting solution phase. Ion permselectivity can also be introduced by potentiostatically charging the membrane in an electrolyte solution. By applying excess negative charge, cation permselective membranes are obtained, and excess positive charge yields anion permselective membranes. In this case the permselectivity can be reversibly switched by changing the potential applied to the membrane.