Nanotechnologies for biomolecular detection and medical diagnosticsIntroductionNanostructured surfaces for proteomic analyses via MS and reverse-phase protein microarraysThe bio-bar-code assayNanowires: label-free electronic sensors of genes and proteinsCantilevers: nanomechanical detection of biological moleculesConclusionAcknowledgementsReferences and recommended readingNanotechnologies for biomolecular detection and medicaldiagnosticsMark Ming-Cheng Cheng1,*, Giovanni Cuda2,*, Yuri L Bunimovich3,Marco Gaspari2, James R Heath3, Haley D Hill4, Chad A Mirkin4,A Jasper Nijdam1, Rosa Terracciano2, Thomas Thundat5andMauro Ferrari1Nanotechnology-based platforms for the high-throughput,multiplexed detection of proteins and nucleic acids inheretofore unattainable abundance ranges promise to bringsubstantial advances in molecular medicine. The emergingapproaches reviewed in this article, with reference to theirdiagnostic potential, include nanotextured surfaces forproteomics, a two-particle sandwich assay for the biologicalamplification of low-concentration biomolecular signals, andsilicon-based nanostructures for the transduction of molecularbinding into electrical and mechanical signals, respectively.Addresses1Division of Hematology and Oncology, Internal Medicine, The OhioState University, 473 West 12 Avenue, Columbus OH 43210-1002, USA2Universita’ degli Studi Magna Graecia, Campus Universitario diGermaneto, Viale Europa – Germaneto 88100 Catanzaro, Italy3Caltech Chemistry MC 127-72, 1200 East California Blvd, Pasadena,CA 91125, USA4International Institute for Nanotechnology and Chemistry Department,Northwestern University, 2145 Sheridan, Rd., Evanston, IL 60208-3003,USA5Nanoscale Science and Devices Group, Oak Ridge NationalLaboratory, Bethel Valley Road, Mail stop-6123, Rm. H-150, 4500S,Oak Ridge, TN 37831-6123, USA*These authors contributed equally to this work.Corresponding author: Ferrari, Mauro ([email protected])Current Opinion in Chemical Biology 2006, 10:11–19This review comes from a themed issue onProteomics and genomicsEdited by Garry P Nolan and Emanuel F PetricoinAvailable online 18th January 20061367-5931/$ – see front matter# 2005 Elsevier Ltd. All rights reserved.DOI 10.1016/j.cbpa.2006.01.006IntroductionAs medicine steadily progresses toward diagnostics basedon molecular markers, and highly specific therapies aimedat molecular targets, the necessity for high-throughputmethods for the detection of biomolecules, and thei rabundance, concomitantly increases. Technology plat-forms that provide the reliable, rapid, quantitative, low-cost and multi-channel ident ification of biomarkers suchas genes and proteins are de facto the rate-limiting steps forthe clinical deployment of personalized medicine [1], indomains such as the early detection and the treatment ofmalignant disease. Early detection is particular ly impor-tant in the case of cancer and other pathologies, becausethe early stages of disease are typically treated with thegreatest probability of success.The repeated screening of large populations for signs ofprecancerous developments, or the establishment of earlymalignant lesions is only conceivable in the context of theanalysis of biological fluids such as blood, urine andsputum samples. To date, this has been impossible,largely because there are no contemporary approachesfor the reliable, quantitative detection of multiple low-abundance protein markers, comprised within a formid-able complexity of diverse biomolecular species in eachbio-fluid specimen.Nanotechnology offers promise, as a broad spectrum ofhighly innovative approaches emerges for the overco mingof this challenge [2,3,4–11]. Four emerging approachesare reviewed below: nanost ructured surfaces for theenhancement of proteomic analysis via mass spectrome-try (MS) and reverse-phase protein microarrays; thebio-bar code method for the amplification of proteinsignatures via the use of two-particle, sandwich assa y;nanowires as biologically gated transistors, transducingmolecular binding events into real-time electrical signals;and silicon cantilevers for the mechanics-based recogni-tion of biomolecular populatio ns.Nanostructured surfaces for proteomicanalyses via MS and reverse-phase proteinmicroarraysMS is currently the gold standard for the protein expres-sion profiling of biological fluids and tissues [12–14], withmounting evidence that matrix-assisted laser desorpt ion/ionization time-of-flight (MALDI-TOF) MS can beemployed for the early detection of malignant disease.Current limitations of this approach include the complex-ity and reproducibility of the 2-D gel electrophoresis pre-fractionation steps required for its implementation onbiological fluids. It is also recognized that the numberof different biomolecular species in the plasma proteomeprobably exceeds 300 000, and could be as high as 106,with differences of as many as 12 orders of magnitude inwww.sciencedirect.com Current Opinion in Chemical Biology 2006, 10:11–19relative abu ndances. It is hypothesized that the lowmolecular weight proteome (LMWP), comprising proteo-lyic fragments at extremely low concentration, contains awealth of information of diagnostic and prognostic utility[15]. Current MS methodologies do not enable the rou-tine profiling of the LMWP.The physico-chemical modification of nanoscale domains(‘nanotexturing’) on an MS planar or nanoparticle sub-strate has been propose d (Terracciano R et al. and GaspariM et al., unpublished data) with the objective of thesize-exclusion-based, elective capture and enrichmentof selected regions of the LMWP from bo dy fluids. Inproof-of-principle validation experiments, silicon oxideparticles, obtained starti ng from silica gels, and siliconchips coated with a 500 nm-thick nanoporous film werechallenged with a human plasma-diluted sample.MALDI-TOF analysis was then performed, as a meansof detecting and assessing the extracted proteins(Figure 1).Spiking experi ments performed by adding peptide stan-dards to human plasma at different concentrationsshowed that a MALDI-TOF signal can be detected frompeptide amounts down to the ng/ml range (Figure 2).This demonstrates the effectiveness of silica platforms forincreasing the sensitivity of MS analysis (roughly 400-fold). The selective enrichment achieved by the use ofthe different nanostructured surfaces depends on the poresize, the fabrication procedure and the experimentalconditions, and represents a powerful tool to