Zhicheng Huang

Poly-cytosine DNA as a High-Affinity Ligand for Inorganic Nanomaterials

Attaching DNA to nanomaterials is the basis for DNA-directed assembly, sensing, and drug delivery using such hybrid materials. Poly-cytosine (poly-C) DNA is a high affinity ligand for four types of commonly used nanomaterials, including nanocarbons (graphene oxide and single-walled carbon nanotubes), transition metal dichalcogenides (MoS2 and WS2 ), metal oxides (Fe3 O4 and ZnO), and metal nanoparticles (Au and Ag). Compared to other homo-DNA sequences, poly-C DNA has the highest affinity for the first three types of materials. Using a diblock DNA containing a poly-C block to attach to surfaces, the target DNA was successfully hybridized to the other block on graphene oxide more efficiently than that containing a typical poly-A block, especially in the presence of non-specific background DNA, proteins, or surfactants. This work provides a simple solution for functionalizing nanomaterials with non-modified DNA and offers new insights into DNA biointerfaces.

Janus DNA orthogonal adsorption of graphene oxide and metal oxide nanoparticles enabling stable sensing in serum

While DNA/graphene oxide (GO) conjugates have been widely used for DNA detection, they suffer from non-specific DNA displacement by proteins, making their application in biological samples difficult. To find new materials tightly adsorbing DNA but not proteins, we screened seven metal oxide nanoparticles, all interacting with the phosphate backbone of DNA, while DNA uses its nucleobases to interact with GO. In this regard, DNA is a Janus polymer orthogonally adsorbing GO and metal oxides. The DNA adsorption affinity ranks CoO > NiO > Cr2O3 > Fe2O3 > Fe3O4 > TiO2 > CeO2 based on a phosphate displacement assay. Among them, CoO is nearly fully resistant to protein displacement, while NiO has the best limit of detection of 0.24 nM DNA. This study provides fundamental insights into the biointerface chemistry of DNA, and reveals new materials useful for bioanalytical chemistry, DNA separation, and DNA-directed assembly.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈1014 random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

Bromide as a Robust Backfiller on Gold for Precise Control of DNA Conformation and High Stability of Spherical Nucleic Acids

Functionalization of a gold surface with DNA is often complicated by kinetic traps from unintended DNA base adsorption. Herein, we communicate that Br- serves as a robust backfilling agent displacing selected DNA bases on gold. Traditional thiol backfillers are too strong, while even 300 mM Br- is well tolerated. Conjugates prepared with Br- hybridize 10-fold faster and resist DNA release with better colloidal stability yielding highly sensitive probes. From colorimetric and Raman assays, adsorption affinity ranks as F- < T ≈ Cl- < C < G ≈ Br- < A < I-, allowing Br- to displace nonpoly-A sequences from gold. This well-controlled biointerface will impact biosensing, drug delivery, and directed assembly of nanomaterials.

Polyvalent Spherical Nucleic Acids for Universal Display of Functional DNA with Ultrahigh Stability

For nanomaterials that are difficult to functionalize by covalent attachment of DNA, we herein communicate a general method taking advantage of the high avidity of polyvalent binding and the 3D structure of densely functionalized spherical nucleic acids (SNAs). Using DNA-functionalized gold nanoparticles, simple mixing leads to the formation of highly stable conjugates on 11 different materials including metals, metal oxides, metal-organic frameworks, transition-metal dichalcogenides, nanocarbons, and polymers. The adsorption affinity of SNAs can be over thousand-fold higher than that of free DNA of the same sequence, and practically irreversible conjugates are formed withstanding various denaturing agents. The surface attachment and molecular recognition functions of DNA are spatially separated, showing a key advantage of SNAs. The functionalized materials possess the properties of both the substrate and the SNA, allowing specific DNA hybridization in buffer and in serum.

Etching silver nanoparticles by DNA

While DNA has been widely used for directing the growth and assembly of nanomaterials, the reverse reaction, etching nanoparticles using DNA, has yet to be demonstrated. We herein communicate that poly-cytosine (poly-C) DNA can efficiently etch silver nanoparticles (AgNPs) followed by Ostwald ripening at higher DNA concentrations. The etching process was precisely controlled by varying the length, sequence, and concentration of DNA, and the number of consecutive cytosines is particularly important for the efficacy of etching. In addition to spherical AgNPs, etching also occurred for silver nanoplates displaying interesting color changes. Compared to other chemical etching agents such as H2O2 and ferricyanide, DNA is highly biocompatible, allowing biological applications. Poly-C etching enhanced the cytotoxicity of AgNPs against cancer cells, and Gram-positive and Gram-negative bacterial cells. This study will stimulate many related studies in DNA nanotechnology, bioanalytical sensors and nanomedicine.

Fluorescent DNA Probing Nanoscale MnO2: Adsorption, Dissolution by Thiol, and Nanozyme Activity

Manganese dioxide (MnO2) is an interesting material due to its excellent biocompatibility and magnetic properties. Adsorption of DNA to MnO2 is potentially of interest for drug delivery and sensing applications. However, little fundamental understanding is known about their interactions. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were used to explore the effect of salt concentration, pH, and DNA sequence and length for adsorption by MnO2, and comparisons were made with graphene oxide (GO). The DNA desorbs from MnO2 by free inorganic phosphate, while it desorbs from GO by adenosine and urea. Therefore, DNA is mainly adsorbed on MnO2 through its phosphate backbone, and DNA has a stronger affinity on MnO2 than on GO based on a salt-shock assay. At the same time, DNA was used to study the effect of thiol containing compounds on the dissolution of MnO2. Adsorbed DNA was released from MnO2 after its dissolution by thiol, but not from other metal oxides with lower solubility such as CeO2, TiO2, and Fe3O4. DNA-functionalized MnO2 was then used for detecting glutathione (GSH) with a detection limit of 383 nM. Finally, DNA was found to inhibit the peroxidase-like activity of MnO2. This study has offered many fundamental insights into the interaction between MnO2 and two important biomolecules: DNA and thiol-containing compounds.

Sub-Angstrom Gold Nanoparticle/Liposome Interfaces Controlled by Halides

A hallmark of nanoscience is size-dependent and distance-dependent physical properties. Although most previous studies focused on optical properties, which are often tuned at nanometer scale, we herein report on the interaction between halide-capped gold nanoparticles (AuNPs) and phosphocholine (PC) liposomes at the sub-Angstrom level. Halide-capped AuNPs are adsorbed by PC liposomes attributable to van der Waals force. Iodide-capped AuNPs interact much more weakly with the liposomes compared with bromide- and chloride-capped AuNPs, as indicated by a liposome leakage assay and differential scanning calorimetry. This is explained by the slightly larger size of iodide separating the AuNP core more from the liposome surface. Cryo-transmission electron microscopy indicates that the liposomes remain intact when mixed with these halide-capped AuNPs of 13 or 70 nm in diameter. Other even larger ligands, including small thiol compounds, DNA oligonucleotides, proteins, and polymers, fully blocked the interaction, whereas AuNPs dispersed in noninteracting ions, including fluoride, phosphate, perchlorate, nitrate, sulfate, and bicarbonate, are still adsorbed strongly by 1,2-dioleoyl- sn-glycero-3-phosphocholine liposomes. Taken together, halides can be used to control interparticle distances at an extremely small scale with remarkable effects on materials properties, allowing surface probing, biosensor development, and fundamental surface science studies.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS2), and tungsten disulfide (WS2) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS2 and WS2 nearly fully retained the fluorescence of the positive samples. The mechanism for MoS2 and WS2 to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS2 can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS2 could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.