Catalyzing Inquiry at the Interface of Computing and Biology

238 CATALYZING INQUIRY

troscopy today allow 1,000 proteins per day to be analyzed in an automated fashion, and there is hope
that a next-generation facility will be able to analyze up to 1 million proteins per day.^16

• Cell sorters. Cell sorters separate different cell types at high speed on the basis of multiple param-
  eters. While microarray experiments provide information on average levels of mRNA or protein within
  a cell population, the reality is that these levels vary from cell to cell. Knowing the distribution of
  expression levels across cell types provides important information about the underlying control mecha-
  nisms and regulatory network structure. A state-of-the-art cell sorter can separate 30,000 elements per
  second according to 32 different parameters.^17

Box 7.4

Microarrays: A Close-up

A “classical” microarray typically consists of single-stranded pieces of DNA from virtually an entire genome

placed physically in tiny dots on a flat surface and labeled with a fluorescent dye. (Lithographic techniques

used to develop semiconductor chips are now used to deposit the DNA on a silicon chip that can later be read

optically.) In a microarray experiment, messenger RNA (mRNA) from a cell of interest is extracted and placed

in contact with the prepared surface. If the sample contains mRNA corresponding to the DNA on one or more

of the dots on the surface, the molecules will bind and the dye will fluoresce. Because the mRNA represents

the fraction of genes from the sample that have been transcribed from DNA into mRNA, the resulting fluores-

cent dots on the surface are a visual indicator of gene expression (or transcription) in the cell’s genome.

Different intensities of the dots reflect greater or lesser levels of transcription of particular genes.

Obtaining the maximum value from a microarray experiment depends on the ability to correlate the data from

a microarray experiment per se with extensive data that identify or classify the genes by other characteristics.

In the absence of such data, any given microarray experiment merely points out the fact that some genes are

expressed to a greater extent than others in a particular experimental situation.

Protein microarrays can identify protein-protein (and protein-drug) interactions among some 10,000 proteins

at once.^1 As described by Templin,^2

[protein] microarray technology allows the simultaneous analysis of thousands of parameters within a single exper-

iment. Microspots of capture molecules are immobilized in rows and columns onto a solid support and exposed to

samples containing the corresponding binding molecules. Readout systems based on fluorescence, chemilumines-

cence, mass spectrometry, radioactivity or electrochemistry can be used to detect complex formation within each

microspot. Such miniaturized and parallelized binding assays can be highly sensitive, and the extraordinary power

of the method is exemplified by array-based gene expression analysis. In these systems, arrays containing immobi-

lized DNA probes are exposed to complementary targets and the degree of hybridization is measured. Recent

developments in the field of protein microarrays show applications for enzyme-substrate, DNA-protein and different

types of protein-protein interactions. Here, we discuss theoretical advantages and limitations of any miniaturized

capture-molecule-ligand assay system and discuss how the use of protein microarrays will change diagnostic meth-

ods and genome and proteome research.

(^1) See G. MacBeath and S.L. Schreiber, “Printing Proteins as Microarrays for High-Throughput Function Determination,” Science 289(5485):
1760-1763, 2000.
(^2) Reprinted by permission from M.F. Templin, D. Stoll, M. Schrenk, P.C. Traub, C.F. Vohringer, and T.O. Joos, “Protein Microarray
Technology,” Trends in Biotechnology 20(4):160-166, 2002. Copyright 2002 Elsevier.
NOTE: An overview of microarray technology is available on a private Web site created by Leming Shi: http://www.gene-chips.com/. See
also http://www.genome.gov/10000533 and P. Gwynne and G. Page, “Microarray Analysis: The Next Revolution in Molecular Biology,”
special advertising supplement, Science 285, August 6, 1999, available at http://www.sciencemag.org/feature/e-market/benchtop/micro.shl.
(^16) S.P. Gygi, B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold, “Quantitative Analysis of Complex Protein Mixtures
Using Isotope-coded Affinity Tags,” Nature Biotechnology 17(10):994-999, 1999. (Cited in Ideker et al., 2001.)
(^17) See, for example, http://www.systemsbiology.org/Default.aspx?pagename=cellsorting.