Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Microfabrication Technologies for Integrated Nucleic Acid Analysis David T. Burke, 3'4's Mark A. Burns, 2,4 and Carlos Mastrangelo 1Department of Human Genetics, 2Department of Chemical Engineering, 3Department of Electrical Engineering and Computer Science, and 4Bioengineering Program, University of Michigan, Ann Arbor, Michigan 48109 In any field, the prediction of future technology is a sey et al. 1995; McIntyre 1996). Although an at- risky venture. One need only skim through a pile of tempt to cover the range of published research ef- popular scientific magazines from 20 years ago to forts has been made, this is not a comprehensive resurrect a long list of beautiful, but unimple- review. mented, technologies, ranging from helium-filled sky cranes to weeds that exude high-grade motor The Demand for Nucleic Acid Analysis is Essentially oil. In the face of uncertainty, technology predic- Unlimited tion relies on three basic ideas. New technologies are (1) driven by demand, (2) in competition with The biological and biomedical sciences, from agri- the economics of established methods, and (3) lim- culture to epidemiology to taxonomy, have enthu- ited by the available materials and systems for de- siastically incorporated DNA and RNA analysis into signing and fabricating tools. their experimental domains. Extraction of nucleic In basic science, few areas have witnessed tech- acid-based information from biological samples has nical changes of the magnitude observed recently in become accessible worldwide, even for laboratories DNA and RNA analysis. To continue this advance, with limited resources and basic technical knowl- future analytical devices must balance cost and ac- edge. Rather than satisfying demand, this initial curacy with the rapidly increasing demand for ge- burst of information has stimulated scientific appe- netic information. The long-term potential of any tites for an even greater breadth and depth of data proposed nucleic acid analysis system will be linked (Olson 1993). For example, in genetics, variations in to the efficiency of its construction methods. Pho- DNA sequence provide an enormous resource for tolithographic rnicrofabrication is a mature tech- the analysis of inheritance, mutation, and disease nology developed and optimized by the computer (Botstein et al. 1980; Cooper and Clayton 1988; microprocessor industry. The modern silicon-based Bowcock et al. 1991; Tanksley 1993). Similarly, in microprocessor is an example of a monolithic inte- developmental biology, the dynamic expression of grated system, with each device containing large RNAs across tissue types and over time can address numbers of compatible components formed on a fundamental questions of pattern formation and or- single substrate. Uniform replicate devices are pro- ganogenesis (Ringwald et al. 1994; Schena et al. duced economically in large batches using photo- 1995). Within any experimental program, analyti- graphic templates. In a similar manner, photolitho- cal demand is constantly extended by the need graphic microfabrication may provide a candidate for contiguous information, broader surveys of technology to build integrated nucleic acid analysis individuals, multiple-tissue analyses, or replicate systems having improved sample throughput, accu- samples. racy, and cost efficiency. In the field of medicine, analytical demand con- This paper presents a perspective of nucleic acid tinues to increase as new knowledge is gained by analysis, its compatibility with silicon microfabrica- research scientists. Because clinical science is con- tion strategies, and future prospects for merging the cerned with what is wrong with a "particular" hu- two. Microfabricated devices for biochemical and man, knowledge of individual variation is essential fluidic manipulation are undergoing rapid develop- to clinic-level diagnosis. As a consequence, human ment in many laboratories around the world (Ram- genetic analysis is rapidly developing into the study of hundreds to thousands of individuals in popula- tions (Davies et al. 1994; Lander and Schork 1994). SCorresponding author. E-MAIL [email protected]; FAX (313) 763-3784. Pathogen isolate analysis also will be increasingly 7:189-197 ©1997 by Cold Spring Harbor Laboratory Press ISSN 1054-9803/97 $5.00 GENOME RESEARCH~ 189 Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press BURKE ET AL. important for accurate clinical diagnosis and treat- Not surprisingly, high-throughput sample ment (Seillier-Moiseiwitsch et al. 1994). At some analysis based on linking robotic liquid handling point in the future, clinical applications of genetic equipment and automated electrophoresis has been knowledge may impact the majority of individuals successful in reducing costs (Fraser et al. 1995). The worldwide. incremental advances based on these technologies, If made sufficiently inexpensive, clinical, envi- however, may be approaching their limit. As an ex- ronmental, and agricultural nucleic acid analyses ample, although clearly an improvement over indi- may easily increase to hundreds of millions of indi- vidual reaction tubes, molded plastic tube arrays vidual reactions per year. have a lower size limit and packing density. The factors limiting conventional microtube sample handling include (1) surface evaporation in open Nucleic Acid Analysis is Consistent and Amenable to vessels, (2) fabrication precision of plasticware, and Automation (3) three-dimensional location accuracy of robotic The biochemistries for extracting nucleic acid infor- pipetting equipment. Additionally, the sample pro- mation are relatively uniform. Samples are aqueous cessing and sample analysis instruments have been and within a defined range of volume (1 ml-0.1 lJl), designed to stand alone, resulting in distinct steps temperature (0°C-100°C), and pH (6-10). Process- in a processing stream rather than a fully integrated ing mechanics involve volume measurement, liquid system. mixing, temperature control, molecular weight The capital investment in specialized auto- separation, and molecular detection. Throughout mated equipment, especially dedicated robotic de- the processing chain, samples must remain distinct vices, can be significant (Adams et al. 1994; Hall et and free of external contaminants. Most reactions al. 1996). As a result, the implementation of these are defined by the mixing of nucleic acid samples technologies, although effective, may remain re- with substrate-specific enzymes under controlled stricted to well-funded research laboratories or cen- temperature. Often, enzymatic and thermal process- ters. ing reactions are linked in series. Alternatively, a sample may be divided into subsamples, with each Monolithic Integrated Devices division undergoing a unique set of process steps. The end products of the reactions are characterized Ideally, new systems for nucleic acid analysis will either by hybridization to known nucleic acid se- address several of the limitations in current technol- quences or electrophoretic determination of poly- ogy, including cost inefficiencies. Large-scale mer length. Although generally uniform, some nucleic acid testing will demand instruments with variation occurs among the specific analysis meth- technical simplicity, assay reproducibility, and in- ods-for example, in complementary-strand bind- herent quality control, as well as high sample ing parameters, polymer size range, electrophoretic throughput. Many of these desired functions are resolution, and product detection sensitivity. consistent with fabrication technologies for "mono- The consistent processing characteristics of lithic integrated" devices. nucleic acids allow for "industrial-style" sample Systems that use interchangeable units to per- handling. Such effort is often economically favor- form diverse processing steps on a single, unified able, as the reduced cost per unit of data can out- platform can be described as monolithic and inte- weigh the capital investment in complex, high- grated. Integrated systems use modular components throughput machines. The most significant recent having standardized connections and a consistent improvements in sample handling result from bun- format. Each component performs a unique, funda- dling groups of reaction tubes into standardized mental function and meets preset criteria for con- rectangular arrays (8 × 12 or 16 × 24 places). The struction. Consequently, during the design stage in- tube arrays are matched with robotic handling and dividual components are assumed to be compatible pipetting equipment having the same format (Uber in the final device. et al. 1991; Watson et al. 1993). A second major From the design and testing standpoint, inte- advance has occurred in electrophoretic analysis. grated systems are extremely powerful. Once each The introduction of automated gel readers and load- component is established, the units can be linked in ers has reduced labor costs for electrophoresis as a logical pattern to accomplish a specific task. Inte- well as improving data detection, handling, and er- grated systems are remarkably adaptable to chang- ror rates (Hunkapillar et al. 1991; Ansorge et al. ing demand, as complex devices can be modified 1992; Wilson et al. 1994). rapidly by rearranging existing components. Design 1 90 ~ GENOME RESEARCH Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring