1. Interface-Driven Hybrid Materials Based on DNA-Functionalized Gold Nanoparticles 
Biwu Liu, Juewen Liu 
Matter 
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3. Figure 1 Optical Properties of AuNPs
(A) Large AuNPs have high extinction coefficients, ε, much higher than organic dyes.
(B) The color of AuNPs changes from red to blue upon aggregation.
(C) AuNPs can also strongly scatter light, and the scattered color is dependent on the aggregation state of AuNPs.
(D) AuNPs can strongly quench fluorescence, and adsorption can also be detected by LSPR.
(E) AuNPs can form hot spots for surface-enhanced Raman spectroscopy (SERS).
(F) AuNPs can catalyze the growth of a silver shell and also act as oxidase or peroxidase mimics.
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4. Figure 2 Interfacing DNA with AuNPs
(A) A DNA oligomer with four bases with a backbone phosphorothioate (PS) and a terminal disulfide modification. The purple circles indicate the possible binding sites with AuNPs.
(B) Binding modes and the ranking of adsorption affinity of thiol, PS, and the four bases adsorbed on gold surface with the structures of the bases and PS shown.
(C) Kinetics of fluorescence quenching by AuNPs as a function of NaCl, indicating the DNA adsorption.
(D) Effect of cations on aggregation of citrate-capped AuNPs, Cs+ being stronger than Li+ for inducing aggregation.
Reprinted with permission from: (C) Zhang et al.,41 copyright 2012, ACS; and (D) Liu et al.,42 copyright 2014, ACS.
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5. Figure 3 Methods for Conjugating DNA on AuNPs
(A) A low density of DNA tends to wrap around the Au surface, and the DNA cannot hybridize with the cDNA.
(B) The typical salt-aging process involving initial DNA adsorption, and gradual increase of NaCl concentration.
(C) Attaching DNA in the presence of stabilizing ligands (e.g., surfactants) to improve the colloidal stability of AuNPs.
(D) Low-pH loading requiring the DNA containing a poly(A) block to assemble into a parallel duplex.
(E) The freezing method does not require additional reagents.
(F) Anchoring poly(A) containing nonthiolated DNA on AuNPs with controlled density; a longer poly(A) block yields a lower DNA density.
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6. Figure 4 DNA-Directed Assembly of AuNPs
(A and B) Scheme (A) and TEM image (B) showing assembly of DNA-AuNPs without crystallization. AuNPs were modified with two different DNAs, and a partial duplex linker.
(C) Scheme of AuNPs modified with partially hybridized DNA with a four-base overhang for hybridization.
(D and E) SAXS pattern of DNA-AuNP single-crystalline domains (D) and the integrated data (E). With this design, DNA-AuNPs formed crystallized structures (FCC).
(F) Different crystal structures formed by DNA-AuNPs.
Reproduced with permission from: (B) Mirkin et al.,5 copyright 1996, Springer Nature; (D and E) Park et al.,6 copyright 2008, Springer Nature; and (F) Macfarlane et al.,79 copyright 2013, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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7. Figure 5 Modification of DNA-AuNP Assemblies
(A) Solidifying DNA-AuNP crystals by a silica layer.
(B–D) Scheme (B) showing that Ag+ can shorten and stabilize DNA-linked AuNP dimers by interacting with the surface BSPP ligands. The TEM micrographs of the dimers before (C) and after (D) adding Ag+ are shown.
(E–I) Enhancing the surface plasmon coupling by cationic polymers. (E) A Scheme showing the assembled core-satellite superstructure. TEM micrographs of the assembly in (F) PBST buffer, (G) with MgCl2, and (H) with a cationic polyelectrolyte (PE) are shown. (I) TEM micrographs and photographs showing the addition of PE to the satellite-to-core with increasing stoichiometry (from 3:1 to 30:1).
Reprinted with permission from: (A) Auyeung et al.,84 copyright 2012, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim; (B–D) Wang et al.,86 copyright 2015, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim; and (E–I) Chou et al.,87 copyright 2016, ACS.
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8. Figure 6 DNA-Directed Growth of AuNPs
(A and B) Schemes (A) and TEM micrographs (B) showing the growth of Au shell on AuNPs functionalized with a dense HS-DNA layer of different sequences.
(C and D) Schemes (C) and scanning electron microscopy micrographs (D) showing the growth on Au nanoprism seeds in the presence of various DNA sequences at different time points.
Reprinted with permission from: (A and B) Oh et al.,99 copyright 2014, ACS; and (C and D) Tan et al.,100 copyright 2015, ACS.
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9. Figure 7 Typical Designs of Colorimetric Assays Using DNA-AuNPs
(A) AuNPs are densely functionalized with HS-DNA, and the target DNA assembles the AuNPs to large aggregates with a color change.
(B) Melting curves of DNA without AuNPs (red) and with AuNPs (black) by monitoring the absorbance at 260 nm. Insets showing the derivative curve of each set.
(C) AuNPs are functionalized with SH-aptamer DNA. The target-aptamer complex can better protect the core particles from salt-induced aggregation.
(D) UV-vis absorbance spectra of Au-aptamer (black) and Au-aptamer with MgCl2 (blue), and Au-aptamer-target with MgCl2. Insets show images of (1) Au-aptamer-target, (2) Au-aptamer, (3) Au-aptamer-nontarget, and (4) Au-nonaptamer-target. All solutions contained MgCl2 (30 mM).
(E) Nonthiolated can adsorb on AuNPs in the absence of targets and prevent salt-induced aggregation.
(F) UV-vis absorbance of AuNPs (diamonds) with ssDNA (circles), with cDNA (triangles), and with duplex (squares). Inset shows the color changes of AuNPs-ssDNA in presence of different amounts of target DNA. The ratio of target-to-probe DNA was 0, 0.2, 0.4, 0.6, and 1 (from left to right).
Reprinted with permission from: (B) Elghanian et al.,105 copyright 1997, American Association for the Advancement of Science; (D) Zhao et al.,107 copyright 2008, ACS; and (F) Li et al.,108 copyright 2004, National Academy of Sciences.
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10. Figure 8 Typical Designs of Fluorescent Assays Using DNA-AuNPs
(A–C) Scheme (A) showing nano-flare for mRNA detection. A reporter DNA is hybridized with DNA-AuNPs and displaced by the target DNA to produce fluorescence. Confocal fluorescent micrographs of HeLa cells incubated with survivin nano-flare (B) and control nano-flare (C).
(D–F) Scheme (D) showing DNAzyme-AuNPs for metal ion detection. The substrate was modified with a fluorophore and optionally also a quencher. Confocal fluorescent microscopic images of HeLa cells treated with (E) or without (F) uranyl ions and DNAzyme-AuNP probes. The DNAzyme signal is in the red channel and the nuclei are stained blue.
(G–I) 3D DNA walkers (G). Target DNA unblocks the walker DNA (in blue), allowing its hybridization with the fluorophore-labeled substrates, which are subsequently cleaved by a nuclease. A walk can induce multiple cleavage events for signal amplification. Kinetics of fluorescence signal from DNA walker (H) and control (only substrate-modified AuNPs) (I) are shown.
Reprinted with permission from: (B and C) Seferos et al.,113 copyright 2009, ACS; (E and F) Wu et al.,115 copyright 2013, ACS; and (H and I) Yang et al.,116 copyright 2016, ACS.
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11. Figure 9 Interaction of SNA with Biological Media
Scheme (A) showing protein adsorption onto two different DNA (T-rich and G-rich) modified AuNPs. Analysis of proteins on SNA after incubating in 10% human serum for 24 h at 37°C by dynamic light scattering (B), BCA assay (C), and PAGE gel (D). Reprinted with permission from Chinen et al.,138 copyright 2015, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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