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9 protocols using aunps

1

AuNPs-based Thrombin Aptamer Assay

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AuNPs (40 nm in diameter) were obtained from BBI solutions (Cardiff, UK). Thrombin binding aptamer (Th-apt, 5′-AGT CCG TGG TAG GGC AGG TTG GGG TGA CT-3′) was purchased from Eurofins Genomics (Tokyo, Japan). 22 2-Melcaptethanol (2-ME) and methyl orange were obtained from Wako (Osaka, Japan). 3-Aminopropyltriethoxysilane (APTES) and bovine serum albumin (BSA) were obtained from Tokyo Chemical Industry (Tokyo, Japan) and Bio RAD (Hercules, CA, USA), respectively. Slide glass and cover glass were purchased from Matsunami Glass Industry (Osaka, Japan).
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2

Synthesis and Characterization of AuNP Conjugates

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Neutravidin was purchased from Thermo-Scientific. Peptide 1 with the sequence CALNN and peptide 2 with the sequence CALNN(PEG) 4 SNKTRIDEANQRATKLLGSGDDGDDGDD were purchased from GL Shanghai, China. AuNPs of size 40nm, 60nm and 80nm were purchased from BBI solutions. Hydrogen peroxide 30%wt was purchased from VWR chemicals, Poland. Gold (III) chloride trihydrate (99.9%), sodium citrate tribasic dehydrate (99%), ascorbic acid (99%), silver nitrate (99%), cetyl trimethylammonium bromide (96%) (CTAB), chitosan (low molecular weight), acetic acid (99.7%), 3-Mercaptopropionic acid (99%) (MPA), hydroxylamine hydrochloride (99%), sodium borohydride (98%), sodium chloride (99%) and glycerol (99%) were purchased from Sigma Aldrich. Hydrochloric acid (37%) was purchased from Merck Millipore, Singapore. The synthesis of the polypeptide JR2EC with the sequence (NAADLEKAIEALEKHLEAKGPCDAAQLEKQLEQAFEA FERAG) has been described elsewhere. 28 MMP7 human recombinant, E. Coli was purchased from Merck Chemicals.
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3

Thermally Controlled Plasmonic Nanostructure Fabrication

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A 3 mm–by–3 mm Au film (70 nm) on Si substrate was immersed in 20 mM OS-1 (Fig. 1A) or OS-2 (Fig. 4A)/chloroform solution overnight, followed by rinsing with pure chloroform (99%; Yonghua Chemical Co. Ltd.) and dried quickly. Au NPs (5 μl; 80 nm; BBI Solutions) were drop-casted on the film for 20 min and blow-dried using nitrogen. For solvent treatment, pure chloroform, MeOH (99.8%; Hushi Co. Ltd.) and dichloromethane (99.9%; Aladdin) mixed at the ratio of 1:8 and 1:4, and pure MeOH were used. For temperature-induced disassembly/assembly, the sample was immersed into hot chloroform (60°C) for 30 s and room temperature chloroform for 3 hours, respectively. All the samples were vacuum-dried to remove any residue solvent before taking DF scattering spectra.
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4

Fluorescent Probes Synthesis and Characterization

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AuNPs (5 nm in water, EM.GC5) were purchased from BBI Solutions (Newport, Wales, UK). 3-(3,4- Dihydroxyphenyl) propionic acid (DPA), bPEI (25 kDa), and RITC were purchased from Sigma-Aldrich (St. Louis, MO, USA). Fluorescein-conjugated HP (H7482) was purchased from Invitrogen (Carlsbad, CA, USA).
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5

Colorimetric and Fluorescent AuNP Assays

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AuNPs (20 and 40 nm) were obtained from BBI Solutions (Cardiff, UK). All oligonucleotides (Probe-A, Probe-B, ssDNA-15, ssDNA-20, agDNA-15, agDNA-20, RNA-15, NA, NB, and MB) shown in Figure S1 were purchased from FASMAC (Kanagawa, Japan). T7 RNA polymerase was purchased from Takara Bio Inc. (Shiga, Japan). 96-7 DNA polymerase and RNase inhibitor were purchased from Nippon Gene (Tokyo, Japan). Deoxynucleotide solution mix (dNTPs) and ribonucleotide solution mix (rNTPs) were purchased from New England Biolabs Inc. (Ipswich, ME, USA). Human α-thrombin was purchased from Funakoshi (Tokyo, Japan). Transferrin, human immunoglobulin G (IgG), human serum albumin (HSA), and bovine serum albumin (BSA) were purchased from Merck (Munich, Germany). NAP-5 columns were provided with the oligonucleotides. Absorption spectra and fluorescence intensities were measured using microplate reader (TECAN, Zürich, Switzerland). All photographs were taken using a digital camera (SONY, Tokyo, Japan).
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6

AuNPs-based IgA Immunoassay Protocol

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All reagents used were of guaranteed grade and used without further purification. All inorganic salts, 1-Ethyl-3-(3dimethylaminopropyl) carbodiimide ·HCl (EDC), N-hydroxysuccinimide (NHS), polyethylene glycol (Mw is 20,000), trehalose dihydrate, and pH 7.5 D-PBS (-) were purchased from Fujifilm Wako Pure Chemicals (Osaka, Japan). AuNPs with diameters of 60 nm were purchased from BBI Solutions (Cardiff, UK). Anti-IgA (α), Human, Goat-Poly, A80-102A, and Purified Human IgA, P80-102 were purchased from Bethyl Laboratory (Montgomery, AL, USA). Bovine serum albumin (BSA) was purchased from Jackson Immunoresearch (West Grove, PA, USA). All water used in this study was Milli-Q water (18.3 MΩ cm).
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7

Colloidal Au Nanoparticles Synthesis

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Colloidal suspension of 100 nm diameter AuNPs was purchased from BBI solutions (UK).
Poly(methyl methacrylate) (PMMA) with a nominal molecular weight of 100 kDa, used for creating the replica template from the Si master, was purchased from Polysciences, Inc.
(Warrington, PA, USA). Potassium hexacyanoferrate (II) trihydrate and potassium hexacyanoferrate (III) used for electro-/photoelectro-chemistry and biphenyl-4-thiol used for single particle SERS were all purchased from Sigma-Aldrich (Merck KGaA, Darmstadt, Germany).
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8

Thiol-modified Oligonucleotide Immobilization on Gold

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Thiol-modified custom-designed oligonucleotides (sequences are presented in Table 1), dithiothreitol (DTT), 6-mercapto hexanol (MHOH), and NAP-10 columns were obtained from Sigma-Aldrich (Woodlands, TX, USA). AuNPs(50 nm diameter) were purchased from BBI Solutions (Cardiff, UK). Human serum samples were purchased from Fitzgerald Industries International Inc. (North Acton, MA, USA). SpotReady-16 gold spotted glass microarray chips (spot size 1 mm diameter, SPR-1000-016) were obtained from GWC Technologies (Madison, WI, USA). Gold disc infused quartz crystals (gold diameter 0.2 inch) used for the QCM were purchased from International Crystal Manufacturing Co, Inc.(Oklahoma City, OK, USA). All other chemicals were of high-purity analytical grade. To prepare all solutions, ultrapure distilled water (DNAse and RNAse free) purchased from Life Technologies (Carlsbad, CA, USA) was used.
The hybridization sequences for probe, target, and control are highlighted. Base pair mismatches of the control with respect to the target are highlighted in red. The addition of Poly-T50 segments to the target and control sequences provides stability and flexibility to the strands.29 (link)
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9

Synthesis and Characterization of Halogenated Nucleobases

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Guanine
(Gua), 8-bromoGuanine (BrGua), silver
nitrate (AgNO3), and trisodium citrate were purchased from
Sigma-Aldrich (Germany). 8-Bromoadenine (BrAde) was purchased from
Carbosynth (U.K.). Sodium hydroxide (NaOH) was purchased from Merck.
AuNPs (diameter 40 nm) were purchased from BBI solutions. Si-wafers
were purchased from CrysTec GmbH (100 mm, p-Typ). All chemicals were
used as received without further purification. Milli-Q grade water
was used for synthesis and experimental work.
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