The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.DNA sequencing and, more recently, massively parallel DNA sequencing 1-4 has had a profound impact on research and medicine. The reductions in cost and time for generating DNA sequence have resulted in a range of new sequencing applications in cancer 5,6 , human genetics 7 , infectious diseases 8 and the study of personal genomes 9-11 , as well as in fields as diverse as ecology 12,13 and the study of ancient DNA 14,15 . Although de novo sequencing costs have dropped substantially, there is a desire to continue to drop the cost of sequencing at an exponential rate consistent with the semiconductor industry's Moore's Law 16 as well as to provide lower cost, faster and more portable devices. This has been operationalized by the desire to reach the $1,000 genome 17 .To date, DNA sequencing has been limited by its requirement for imaging technology, electromagnetic intermediates (either X-rays 18 , or light 19 ) and specialized nucleotides or other reagents 20 . To overcome these limitations and further democratize the practice of sequencing, a paradigm shift based on non-optical sequencing on newly developed integrated circuits was pursued. Owing to its scalability and its low power requirement, CMOS processes are dominant in modern integrated circuit manufacturing 21 . The ubiquitous nature of computers, digital cameras and mobile phones has been made possible by the low-cost production of integrated circuits in CMOS.Leveraging advances in the imaging field-which has produced large, fast arrays for photonic imaging 22 -we sought a suitable electronic sensor for the construction of an integrated circuit to detect the hydrogen ions that would be released by DNA polymerase 23 during sequencing by synthesis, as opposed to a sensor designed for the detection of photons. Although a variety ...

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We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50-mer agree with theoretical predictions, and the DNA diffusion constant agrees with previous experiments. This type of micromachine could provide a generic pump or separation component for DNA or other charged species as part of a microscale lab-on-a-chip. A device with reduced feature size could produce a size-based separation of DNA molecules, with applications including the detection of single-nucleotide polymorphisms. The Human Genome Project aims to provide the complete sequence of the 3 billion base pairs of the human genome. While the dominant method for analyzing DNA fragments remains gel electrophoresis, new technologies that have the potential to increase the rate and decrease the cost of DNA sequencing and analysis, such as mass spectrometry and hybridization arrays, are critical to the project's success (1).Here we describe a method of DNA transport and separation based on a Brownian ratchet. As described originally by Smoluchowski (2) and noted by Feynman (3), a Brownian particle can undergo net transport on a potential energy surface that is externally driven to fluctuate between several distinct states. Brownian ratchets have attracted theoretical attention (4-12) because of their description of molecular motors (13-15) and their similarity with phenomena termed stochastic resonance and resonance activation (16,17).Brownian ratchets have been demonstrated to transport micrometer-to millimeter-sized particles in experiments with ratchets generated by dielectrophoresis (18), optical tweezers (19), and electrocapillary forces (20,21). Other devices based on entropic ratchets (22) or physical barriers (23, 24) have been proposed as well. More recently, a geometrical sieve device has been used to separate phospholipids (25).Despite these successes, the Brownian ratchet mechanism has not before proved capable of transporting DNA fragments in the size ranges applicable to DNA sequencing (Ͻ1000 nt) because the interactions used to establish the ratchet potential were too weak. In contrast to previous devices using polarization interactions to generate ratchets (18,19), the device that we have fabricated uses charge-charge interactions to generate the ratchet potential. As seen below, the charge-charge interactions have sufficient strength to establish ratchets that can trap small DNA fragments.The ratchet-like wells that trap DNA are generated by charging a series of patterned electrodes. When the electrodes are discharged, the traps vanish and the molecules undergo Brownian motion. Next the potential is reapplied, and the particles again collect in the traps. A spatial asymmetry in the shape of each ratchet-shaped well rectifies the Brownian motion and produces net transport as the on-off cycle is repeated. Each molecule's transport rate depends on its diffusion constant, allowing the possibility of size-based separations. We...

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