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WIREs Nanomed Nanobiotechnol
Impact Factor: 6.14

Encoded anisotropic particles for multiplexed bioanalysis

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Abstract Encoded anisotropic nano‐ and microparticles represent an exciting new class of detection and identification strategies for bioanalysis. These particles are synthesized in a number of different ways and can be encoded by shape, composition, topographical features, or optical properties. In this review, we explore synthetic methods for the formation of anisotropic encoded particles and evaluate these systems as multiplexed biosensing platforms. Suspension arrays using anisotropic particles have been used to detect a range of biological species including proteins, nucleic acids, spores, cells, and small molecules. Because in many cases a large number of codes should be obtainable, the potential exists for high levels of multiplexing (thousands or more). The bulk of work in this area to date has focused on initial proof of principle synthesis and identification; however, multiplexed bioassays have been demonstrated for a number of different anisotropic carrier particles and are beginning to be adopted in commercial assays. WIREs Nanomed Nanobiotechnol 2010 2 578–600 This article is categorized under: Diagnostic Tools > In Vitro Nanoparticle-Based Sensing

Schematic of nanoparticle synthetic routes. (A) Solution‐phase synthesis showing the reduction of a metal salt to form a colloidal suspension of metal nanorods. (B) Synthesis of striped, metallic nanowires by the sequential electrodeposition of metal salts within an alumina template and release into solution by dissolution of the membrane. (C) Lithographically fabricated particles formed by deposition of a photoresist onto a subtrate. A mask is used to block certain areas on the photoresist from light exposure. The photoresist is developed and dissolved; the regions exposed to the light remain on the substrate. The particles are then released from the substrate into solution.

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Illustrations of examples of surface‐based bioassays. (A) A DNA microarray relying on a two‐color fluorescent dye system for hybridization elucidation. (B) A planar array with multicolored nanoparticle tags (i.e., quantum dots) for hybridization determination instead of organic fluorophores. (C) A suspension array, where the encoding element, is nanoparticle shape.

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Examples of bioassays that have explored sensitivity as a function of particle number. (A) Immunoassay binding curves as a function of the number of shape‐encoded silica nanotubes employed. (Reprinted with permission from Ref 43. Copyright 2007 American Chemical Society). (B) The dependence of protein assay sensitivity on the number of digitally‐encoded microspheres used. (Reprinted with permission from Ref 93. Copyright 2008 American Chemical Society).

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Systems that have integrated particle synthesis and bioassay readout with microfluidics with microscopy. (A) Shape‐encoded poly(ethylene glycol) hydrogel microparticles are synthesized, exposed to targets, and read out in a single microfluidic device. Enzyme‐embedded particles are first synthesized in the polymerization chamber, then are flushed through to the reaction chamber, where they are reacted with the enzyme substrates, and the results are read out by microscopy. (Adapted with kind permission from Ref 51. Copyright 2008 Springer Science + Business Media). (B) Oblong dot‐coded particles are synthesized by using continuous‐flow lithography to form particles from two polymers that are flowed down a fluidic channel. (Reprinted with permission from Ref 54. Copyright 2007 AAAS.) (C) Oblong dot‐coded particle readout is achieved by flow through and alignment in a microfluidic channel for code determination by microscopy in the detection region. (Reprinted with permission from Ref 54. Copyright 2007 AAAS).

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Examples of anisotropic nano‐ and microparticles prepared (A–C) in solution, (D–J) through template synthesis, (K–Q) lithographically, and (R) through optical fiber draw methods. (A) Transmission electron micrograph (TEM) of colloidal 12.4 nm ± 18% Ag/Au nanoparticles (Reprinted with permission from Ref 32. Copyright 2001 American Chemical Society.); (B) TEM of Au/Ag core/shell nanoprisms with an average edge length of 70 ± 6 nm (Reprinted with permission from Ref 33. Copyright 2009 Wiley‐VCH Verlag GmbH & Co. KGaA.); (C) TEM of gold nanorods that are 50 ± 5 nm long and 15 ± 3 nm wide (Reprinted with permission from Ref 42. Copyright 2004 American Chemical Society.); (D) darkfield optical image of 6.30 ± 0.08 µm shape‐coded silica nanotubes, S4A, S4B, and S4C, with outer diameters of varying lengths with diameters of 96 ± 4, 72 ± 4, 48 ± 4, and 28 ± 4 nm. (Reprinted with permission from Ref 43. Copyright 2007 American Chemical Society.); (E) scanning electron micrograph (SEM) of a Au modulated microwire with a maximum diameter of 1.35 µm and minimum of 1 µm. (Adapted from Ref 44. Copyright Wiley‐VCH Verlag GmbH & Co. KGaA.); (F) optical image of ∼4.3 µm Au/Ag nanowires under 405 nm light with varying striping patterns. (Reprinted with permission from Ref 45. Copyright 2001 AAAS.); (G) TEM image of a nanoparticle chain with ∼80 × 100 nm Au particles separated by ∼380 nm gaps. (Reprinted with permission from Ref 46. Copyright 2005 American Chemical Society.); (H) field emission SEM (FE‐SEM) image of nanodisk array made of 120 ± 10 nm Au disk dimers separated by ∼1 µm with gaps between the pairs of disks of 160 ± 10, 80 ± 10, 30 ± 5, 15 ± 5, and 5 ± 2 nm from left to top right. (Reprinted with permission from Ref 47. Copyright 2006 National Academy of Sciences, USA); (I) FE‐SEM image of “bamboo‐like” nanowires comprised of alternating 40 nm Co and 38 nm Pt sections, with an average diameter of 65 nm. (Reprinted with permission from Ref 48. Copyright 2005 American Chemical Society.); (J) SEM image of Au‐Ni‐Au‐Ni‐Au 300 nm diameter nanotubes showing the tubular structure. (Reproduced with permission from Ref 49. Copyright Wiley‐VCH Verlag GmbH & Co. KGaA.); (K) SEM of lithographically prepared 7 × 4 µm “LithoParticles” comprised of all 26 letters of the Latin alphabet. (Reprinted with permission from Ref 50. Copyright 2007 American Chemical Society.); (L) circular, triangular, and square‐shaped poly(ethylene glycol)‐based hydrogel microparticles within a microfluidic device. (Adapted with kind permission from Ref 51. Copyright 2008 Springer Science + Business Media); (M) Optical image of octagonal graticles with optical gratings etched into the surface and codes cut into the sides for multiplexing. (Reprinted with permission from Ref 52. Copyright 2008 American Chemical Society.); (N) layer‐by‐layer coated green fluorescent polystyrene microparticles with a photobleached barcoding pattern. (Reproduced with permission from Ref 53. Copyright Wiley‐VCH Verlag GmbH & Co. KGaA.); (O) differential interference contrast image of poly(ethylene glycol) dot‐coded particles with distinct encoding and capture regions. (Reprinted with permission from Ref 54. Copyright 2007 AAAS.); (P) bright field microscope image of 2 µm thick, 100 × 200 µm dot‐coded nickel microparticles.55 (Reproduced with permission from The Royal Society of Chemistry); (Q) optical images of 300 × 700 µm SU‐8 photoresist micropallets with nickel barcodes. (Adapted with kind permission from Ref 56. Copyright 2008 Springer Science + Business Media); (R) fluorescent false colored images of 20 × 100 µm encoded rare earth‐doped alkaline earth aluminosilicate glass microparticles. (Reproduced with permission from Ref 57. Copyright 2003 National Academy of Sciences, USA).

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Quantifications of signals during target presence or absence in multiplexed bioassays. (A) A bar graph quantifying fluorescence for a 5‐plex DNA assay using barcoded Au/Ag nanowires. Oligonucleotide targets were added in sets of two. (Adapted with permission from Ref 115. Copyright 2008 American Chemical Society.) (B) Quantification of fluorescence originating from fluorescent polymers that bind only to double‐stranded DNA in a hybridization assay employing glass‐coated Au/Ag nanowires. The fluorescent polymer acted as a tag and negated the need to label the target sequences. (Adapted with permission from Ref 121. Copyright 2009 American Chemical Society). (C) Fluorescence quantification from a 4‐plex direct immunoassay using diffractive micro bar codes. In all three samples (A, B, and C), pink bars represent target presence, whereas green bars represent target absence. (Adapted with permission from Ref 99. Copyright 2008 American Chemical Society).

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Examples of multiplexed bioassays employing encoded anisotropic particles. (A) A 5‐plex DNA assay using barcoded Au/Ag nanowires where only two targets were present. (Adapted with permission from Ref 115. Copyright 2008 American Chemical Society). (B) Shape‐coded diameter‐modulated silica nanotubes employed in a 3‐plex immunoassay where two of the three targets were present. (Adapted with permission from Ref 43. Copyright 2007 American Chemical Society). (C) Lithographically‐defined dot‐coded rectangles used in a 3‐plex immunoassay with another coded particles included for a negative control. (Adapted with permission from Ref 95. Copyright 2003 American Chemical Society). (D) Shape‐encoded hydrogel microparticles used in multi‐enzymatic reactions. (Adapted with kind permission from Ref 90. Copyright 2008 Springer Science + Business Media). (E) Two‐color, two‐plex immunoassay using optically encoded diffractive micro bar code particles. (Adapted with permission from Ref 99. Copyright 2008 American Chemical Society).

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Illustrations of different biomolecule‐surface attachment chemistries. (A) Biotin‐avidin attachment. (B) Thiol‐metal bond formation. (C) Zero‐length cross‐linker EDC, which can attach a carboxylic acid to an amine via amide bond formation. (D) The use of heterobifunctional cross‐linker sulfo‐SMCC to join amine and thiol functionalities.

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