DNA stabilized fluorescent metal nanoclusters for biosensor development

The final publication is available at Elsevier via https://doi.org/10.1016/j.trac.2013.12.014." © 2014. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Fluorescent silver, gold and copper nanoclusters (NCs) have emerged for biosensor development. Compared to semiconductor quantum dots, there is less concern about the toxicity of metal NCs, which can be more easily conjugated to biopolymers. These NCs need a stabilizing ligand. Many polymers, proteins and nucleic acids stabilize NCs, and many DNA sequences produce highly-fluorescent NCs. Coupling these DNA stabilizers with other sequences, such as aptamers, has generated a large number of biosensors. We summarize the synthesis of DNA and nucleotide-templated NCs; and, we discuss their chemical interactions. We briefly review properties of NCs, such as fluorescence quantum yield, emission wavelength and lifetime, structure and photostability. We categorize sensor-design strategies using these NCs into: (1) fluorescence de-quenching; (2) generation of templating DNA sequences to produce NCs; (3) change of nearby environment; and, (4) reacting with heavy metal ions or other quenchers. Finally, we discuss future trends.University of Waterloo || Canadian Foundation for Innovation || Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |

Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications

The interaction between DNA and inorganic surfaces has attracted intense research interest, as a detailed understanding of adsorption and desorption is required for DNA microarray optimization, biosensor development, and nanoparticle functionalization. One of the most commonly studied surfaces is gold due to its unique optical and electric properties. Through various surface science tools, it was found that thiolated DNA can interact with gold not only via the thiol group but also through the DNA bases. Most of the previous work has been performed with planar gold surfaces. However, knowledge gained from planar gold may not be directly applicable to gold nanoparticles (AuNPs) for several reasons. First, DNA adsorption affinity is a function of AuNP size. Second, DNA may interact with AuNPs differently due to the high curvature. Finally, the colloidal stability of AuNPs confines salt concentration, whereas there is no such limit for planar gold. In addition to gold, graphene oxide (GO) has emerged as a new material for interfacing with DNA. GO and AuNPs share many similar properties for DNA adsorption; both have negatively charged surfaces but can still strongly adsorb DNA, and both are excellent fluorescence quenchers. Similar analytical and biomedical applications have been demonstrated with these two surfaces. The nature of the attractive force however, is different for each of these. DNA adsorption on AuNPs occurs via specific chemical interactions but adsorption on GO occurs via aromatic stacking and hydrophobic interactions. Herein, we summarize the recent developments in studying non-thiolated DNA adsorption and desorption as a function of salt, pH, temperature and DNA secondary structures. Potential future directions and applications are also discussed.University of Waterloo || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation || Canadian Institutes of Health Research || Canadian Foundation for Innovation |

Oligonucleotide-functionalized hydrogels as stimuli responsive materials and biosensors

Hydrogels are crosslinked hydrophilic polymers that undergo swelling in water. The gel volume is affected by many environmental parameters including temperature, pH, ionic strength, and solvent composition. Therefore, these factors have been traditionally used for making smart hydrogels. DNA, on the other hand, is a special block copolymer. Incorporation of DNA within a hydrogel network can have several important effects. For example, DNA can serve as a reversible crosslinker modulating the mechanical and rheological properties of a hydrogel. Second, DNA can selectively bind to a variety of different molecules. Attaching these binding DNAs (aptamers) to hydrogel makes it possible to expand the range of stimuli to chemical and biological molecules. At the same time, the gel matrix can also improve DNA-based sensors and materials. For example, the hydrogel can be dried for storage and rehydrated prior to use and the immobilized DNAs are protected from nuclease cleavage. The gel backbone property can also be tuned to affect the interaction between DNA and other molecules. The rational functionalization of DNA in hydrogels has generated a diverse range of smart materials and biosensors. In the last 15 years, the field has made tremendous progress and some of the recent developments are summarized in this review. Challenges and possible future directions are also discussed.University of Waterloo || Natural Sciences and Engineering Research Council |

Lipid/inorganic hybrids: biointerfaces and drug delivery applications

Zwitterionic phosphocholine (PC) lipids are the major component of the outer membrane of mammalian cells. While PC lipids are anti-fouling (resistant to protein adsorption), they adsorb all tested inorganic nanoparticles. It is well-established that PC liposomes adsorb silica nanoparticles followed by membrane fusion onto the particle surface. However, PC liposomes are only adsorbed by titania and other metal oxides (e.g. iron oxide) without fusion. We found that the lipid phosphate group is mainly responsible for bonding to these non-silica oxides, while the choline in the headgroup poses a steric effect, preventing subsequent liposome fusion. By flipping the PC headgroup to choline phosphate (CP), where the phosphate is fully exposed, liposome fusion on titania was achieved. The second class of material we studied was metal, and gold nanoparticles (AuNPs) are used as an example here. Citrate-capped AuNPs are adsorbed very strongly via van der Waals force by PC liposomes, inducing a phase transition temperature increase and local lipid gelation. The consequence of this gelation is a transient liposome leakage upon AuNP adsorption or desorption. Finally, all the carbon-based nanomaterials (graphene oxides, carbon nanotubes, and nanodiamond) are adsorbed by PC liposomes mainly via hydrogen bonding. The above three types of nanoparticles (metals, metal oxides, and carbon) have covered the most important and representative inorganic materials. While they all interact strongly with PC liposomes, each type has its own interaction mechanism. These inorganic/lipid hybrids are useful for analytical and biomedical applications. For example, we have also demonstrated that all these conjugates can be internalized by cancer cells while the free PC liposomes cannot. Controlled content release from liposomes was also achieved based on our fundamental understandings

A Comprehensive Screen of Metal Oxide Nanoparticles for DNA Adsorption, Fluorescence Quenching, and Anion Discrimination

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Applied Materials & Interfaces, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acsami.5b08004Although DNA has been quite successful in metal cation detection, anion detectioin remains challenging because of the charge repulsion. Metal oxides represent a very important class of materials, and different oxides might interact with anions differently. In this work, a comprehensive screen of common metal oxide nanoparticles (MONPs) was carried out for their ability to adsorb DNA, quench fluorescence, and release adsorbed DNA in the presence of target anions. A total of 19 MONPs were studied, including Al2O3, CeO2, CoO, Co3O4, Cr2O3, Fe2O3, Fe3O4, In2O3, ITO, Mn2O3, NiO, SiO2, SnO2, a-TiO2 (anatase), r-TiO2 (rutile), WO3, Y2O3, ZnO, ZrO2. These MONPs have different DNA adsorption affinity. Some adsorb DNA without quenching the fluorescence, while others strongly quench adsorbed fluorophores. They also display different affinity toward anions probed by DNA desorption. Finally, CeO2, Fe3O4, and ZnO were used to form a sensor array to discriminate phosphate, arsenate, and arsenite from the rest using linear discriminant analysis. This study not only provides a solution for anion discrimination using DNA as a signaling molecule but also provides insights into the interface of metal oxides and DNA.Natural Sciences and Engineering Research Council || Discovery and Strategic Project Grant: STPGP-447472-2013 05576

Accelerating peroxidase mimicking nanozymes using DNA

DNA-capped iron oxide nanoparticles are nearly 10-fold more active as a peroxidase mimic for TMB oxidation than naked nanoparticles. To understand the mechanism, the effect of DNA length and sequence is systematically studied, and other types of polymers are also compared. This rate enhancement is more obvious with longer DNA and, in particular, poly-cytosine. Among the various polymer coatings tested, DNA offers the highest rate enhancement. A similar acceleration is also observed for nanoceria. On the other hand, when the positively charged TMB substrate is replaced by the negatively charged ABTS, DNA inhibits oxidation. Therefore, the negatively charged phosphate backbone and bases of DNA can increase TMB binding by the iron oxide nanoparticles, thus facilitating the oxidation reaction in the presence of hydrogen peroxide.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation |

DNA Adsorption by Indium Tin Oxide (ITO) Nanoparticles

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/la503917jThe high conductivity and optical transparency of indium tin oxide (ITO) has made it a popular material in the electronic industry. Recently, its application in biosensors is also explored. To understand its biointerface chemistry, we herein investigate its interaction with fluorescently labeled single-stranded oligonucleotides using ITO nanoparticles (NPs). The fluorescence of DNA is efficiently quenched after adsorption, and the interaction between DNA and ITO NPs is strongly dependent on the surface charge of ITO. At low pH, the ITO surface is positively charged to afford a high DNA adsorption capacity. Adsorption is also influenced by the sequence and length of DNA. For its components, In2O3 adsorbs DNA more strongly while SnO2 repels DNA at neutral pH. The DNA adsorption property of ITO is an averaging result from both components. DNA adsorption is confirmed to be mainly by the phosphate backbone via displacement experiments using free phosphate or DNA bases. Last, DNA-induced DNA desorption by forming duplex DNA is demonstrated on ITO, while the same reaction is more difficult to achieve on other metal oxides including CeO2, TiO2, and Fe3O4 because these particles adsorb DNA more tightly.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation |

DNA adsorption by magnetic iron oxide nanoparticles and its application for arsenate detection

Iron oxide nanoparticles adsorb fluorescently labeled DNA oligonucleotides via the backbone phosphate and quench fluorescence. Arsenate displaces adsorbed DNA to increase fluorescence, allowing detection of arsenate down to 300 nM. This is a new way of using DNA: analyte recognition relies on its phosphate instead of the bases

DNA templated fluorescent gold nanoclusters reduced by Good’s buffer: from blue emitting seeds to red and near infrared emitters

The final published version is available at NRC Research Press via https://doi.org/10.1139/cjc-2014-0600DNA-templated fluorescent gold nanoclusters (AuNCs) have been recently prepared showing higher photostability than the silver counterpart. In this work, we examined the effect of pH, DNA length, DNA sequence, and reducing agent. Citrate, HEPES, and MES produce blue emitters, glucose and NaBH4 cannot produce fluorescent AuNCs, while ascorbate shows blue emission even in the absence of DNA. This is the first report of using Good’s buffer for making fluorescent AuNCs. Dimethylamine borane (DMAB) produces red emitters. Poly-C DNA produces AuNCs only at low pH and each DNA chain can only bind to a few gold atoms, regardless of the DNA length. Otherwise, large nonfluorescent gold nanoparticles (AuNPs) are formed. Each poly-A DNA might template a few independent AuNCs. The blue emitters can be further reduced to form red emitters by adding DMAB. The emission color is mainly determined by the type of reducing agent instead of DNA sequence.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research and Innovation |

Liposome Supported Metal Oxide Nanoparticles: Interaction Mechanism, Light Controlled Content Release and Intracellular Delivery

This is the peer reviewed version of the following article: Wang, F. and Liu, J. (2014), Liposome Supported Metal Oxide Nanoparticles: Interaction Mechanism, Light Controlled Content Release, and Intracellular Delivery. Small, 10: 3927–3931. doi:10.1002/smll.201400850, which has been published in final form at http://dx.doi.org/10.1002/smll.201400850. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Zwitterionic phosphotydylcholine lipo­somes stably adsorb a number of metal oxide nanoparticles via its phosphate group. This is different from physisorption and fusion with SiO2. The hybrid materials can be internalized by cancer cells and TiO2 allows light controlled liposome content release.University of Waterloo || Canada Foundation for Innovation || Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |