Waterloo Institute for Nanotechnology

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Adsorption of DNA Oligonucleotides by Titanium Dioxide Nanoparticles
(American Chemical Society, 2014-01-28) Zhang, Xu; Wang, Feng; Liu, Biwu; Kelly, Erin Y.; Servos, Mark R.; Liu, Juewen
Titanium dioxide (TiO2) or titania shows great promise in detoxification and drug delivery. To reach its full potential, it is important to interface TiO2 with biomolecules to harness their molecular recognition function. To this end, DNA attachment is an important topic. Previous work has mainly focused on long double-stranded DNA or single nucleotides. For biosensor development and targeted drug delivery, it is more important to use single-stranded oligonucleotides. Herein, the interaction between fluorescently labeled oligonucleotides and TiO2 nanoparticles is reported. The point of zero charge (PZC) of TiO2 is around 6 in water or acetate buffer; therefore, the particles are positively charged at lower pH. However, if in phosphate or citrate buffer, the particles are negatively charged, even at pH ∼2, suggesting strong adsorption of buffer anions. DNA adsorption takes place mainly via the phosphate backbone, although the bases might also have moderate contributions. Peptide nucleic acids (PNAs) with an amide backbone cannot be adsorbed. DNA adsorption is strongly affected by inorganic anions, where phosphate and citrate can strongly inhibit DNA adsorption. DNA adsorption is promoted by adding salt or lowering pH. DNA adsorption is accompanied with fluorescence quenching, and double-stranded DNA showed reduced quenching, allowing for the detection of DNA using TiO2 nanoparticles.
Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications
(Royal Society of Chemistry, 2012-06-28) Liu, Juewen
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.
Attaching DNA to Nanoceria: Regulating Oxidase Activity and Fluorescence Quenching
(American Chemical Society, 2013-08-14) Pautler, Rachel; Kelly, Erin Y.; Huang, Po-Jung Jimmy; Cao, Jing; Liu, Biwu; Liu, Juewen
Cerium oxide nanoparticles (nanoceria) have recently emerged as a nanozyme with oxidase activity. In this work, we present a few important interfacial properties of nanoceria. First, the surface charge of nanoceria can be controlled not only by adjusting pH but also by adsorption of simple inorganic anions. Adsorption of phosphate and citrate gives negatively charged surface over a broad pH range. Second, nanoceria adsorbs DNA via the DNA phosphate backbone in a sequence-independent manner; DNA adsorption inhibits its oxidase activity. Other anionic polymers display much weaker inhibition effects. Adsorption of simple inorganic phosphate does not have the inhibition effect. Third, nanoceria is a quencher for many fluorophores. These discoveries provide an important understanding for further use of nanoceria in biosensor development, materials science, and nanotechnology.
Cation-Size-Dependent DNA Adsorption Kinetics and Packing Density on Gold Nanoparticles: An Opposite Trend
(American Chemical Society, 2014-11-11) Liu, Biwu; Kelly, Erin Y.; Liu, Juewen
The property of DNA is strongly influenced by counterions. Packing a dense layer of DNA onto a gold nanoparticle (AuNP) generates an interesting colloidal system with many novel physical properties such as a sharp melting transition, protection of DNA against nucleases, and enhanced complementary DNA binding affinity. In this work, the effect of monovalent cation size is studied. First, for free AuNPs without DNA, larger group 1A cations are more efficient in inducing their aggregation. The same trend is observed with group 2A metals using AuNPs capped by various self-assembled monolayers. After establishing the salt range to maintain AuNP stability, the DNA adsorption kinetics is also found to be faster with the larger Cs+ compared to the smaller Li+. This is attributed to the easier dehydration of Cs+, and dehydrated Cs+ might condense on the AuNP surface to reduce the electrostatic repulsion effectively. However, after a long incubation time with a high salt concentration, Li+ allows ∼30% more DNA packing compared to Cs+. Therefore, Li+ is more effective in reducing the charge repulsion among DNA, and Cs+ is more effective in screening the AuNP surface charge. This work suggests that physicochemical information at the bio/nanointerface can be obtained by using counterions as probes.
DNA Adsorption by Indium Tin Oxide (ITO) Nanoparticles
(American Chemical Society, 2015-01-13) Liu, Biwu; Liu, Juewen
The 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.
DNA adsorption by magnetic iron oxide nanoparticles and its application for arsenate detection
(Royal Society of Chemistry, 2014-05-01) Liu, Biwu; Liu, Juewen
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.
Mechanisms of DNA Sensing on Graphene Oxide
(American Chemical Society, 2013-08-20) Liu, Biwu; Sun, Ziyi; Zhang, Xu; Liu, Juewen
Adsorption of a fluorophore-labeled DNA probe by graphene oxide (GO) produces a sensor that gives fluorescence enhancement in the presence of its complementary DNA (cDNA). While many important analytical applications have been demonstrated, it remains unclear how DNA hybridization takes place in the presence of GO, hindering further rational improvement of sensor design. For the first time, we report a set of experimental evidence to reveal a new mechanism involving nonspecific probe displacement followed by hybridization in the solution phase. In addition, we show quantitatively that only a small portion of the added cDNA molecules undergo hybridization while most are adsorbed by GO to play the displacement role. Therefore, it is possible to improve signaling by raising the hybridization efficiency. A key innovation herein is using probes and cDNA with a significant difference in their adsorption energy by GO. This study offers important mechanistic insights into the GO/DNA system. At the same time, it provides simple experimental methods to study the biomolecular reaction dynamics and mechanism on a surface, which may be applied for many other biosensor systems.
Orthogonal Adsorption Onto Nano-Graphene Oxide Using Different Intermolecular Forces for Multiplexed Delivery
(Wiley, 2013-05-31) Wang, Feng; Liu, Biwu; Ip, Alexander C-F.; Liu, Juewen
Nano-graphene oxide can adsorb both doxorubicin and zwitterionic dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes in an orthogonal and non-competing manner with high capacities based on different surface and intermolecular forces taking place on the heterogeneous surface of the graphene oxide. The system forms stable colloids, allowing co-delivery of both cargos to cancer cells.
Oxidation Level-Dependent Zwitterionic Liposome Adsorption and Rupture by Graphene-based Materials and Light-Induced Content Release
(Wiley, 2013-04-08) Ip, Alexander C-F.; Liu, Biwu; Huang, Po-Jung Jimmy; Liu, Juewen
Liposomes may be stably adsorbed or ruptured on graphene-based materials, depending on the oxidation state of graphene. IR-induced liposome leakage is achieved, since graphene oxide does not induce liposome leakage spontaneously.
Photocatalytic performances of ZnO nanoparticle film and vertically aligned nanorods in chamber-based microfluidic reactors: Reaction kinetics and flow effects
(Elsevier BV, 2017-07-15) Zhao, Pei; Qin, Ning; Wen, John Z.; Ren, Carolyn L.
The nanoparticle seed layer (a film) and vertically aligned nanorods of zinc oxide (ZnO) with different lengths were fabricated within a novel chamber-based microfluidic (microchamber) reactor with a varying height of 0.127-5 mm and characterized with their microstructures, photocatalytic performances as well as qualitative reaction kinetics. The ZnO seed layer was produced by a sol-gel procedure and the nanorods were hydrothermally grown on seed layer coated glass substrates. These ZnO samples were integrated into the microchamber reactor through a seven-layer sandwiched configuration. The aqueous methyl orange (MO) solution was chosen as a model polluted water. By comparing the ultraviolet-visible (UV-vis) absorbance of the original MO solution and the post-treatment sample, the reaction constants were calculated, representing the efficiencies of the reactors. The ZnO samples, usually possessing a large amount of defects, with a higher crystal quality showed an enhanced activity. The reaction constant was featured of a plateau with accelerating flow rates, exhibited an exponentially decreasing function of the chamber height, and declined with increasing the initial concentration of the MO solution. The efficiency of the microchamber reactor was found to be one to two orders of magnitude higher than that of a batch reactor. The rate determining step was suggested to be the mass transport related adsorption of MO on ZnO. The measured reaction properties and the reactor design should be of considerable significance to the scaling-up and optimization of microchamber catalytic reactors dedicated to water purification and other applications. (C) 2017 Elsevier B.V. All rights reserved.
A platinum shell for ultraslow ligand exchange: unmodified DNA adsorbing more stably on platinum than thiol and dithiol on gold
(Royal Society of Chemistry, 2015-08-04) Zhou, Wenhu; Ding, Jinsong; Liu, Juewen
Due to the ultraslow ligand exchange rate on Pt, non-thiolated DNA is adsorbed on platinum nanoparticles (PtNPs) more stably than thiolated and even dithiolated DNA on AuNPs. Adsorption kinetics, capacity and stability are systematically compared as a function of DNA sequence. The Pt conjugates can tolerate extreme pH, salt, and thiol molecules. Taking advantage of the optical properties of AuNPs and the extreme stability of DNA on PtNPs, DNA-functionalized Au@Pt NPs are prepared using a cost-effective and more stable bioconjugation method. The DNA-directed assembly of non-thiolated DNA conjugates is also demonstrated.
Polarity Control for Nonthiolated DNA Adsorption onto Gold Nanoparticles
(American Chemical Society, 2013-05-21) Zhang, Xu; Liu, Biwu; Servos, Mark R.; Liu, Juewen
Gold nanoparticles (AuNPs) functionalized with thiolated DNA have enabled many studies in nanoscience. The strong thiol/gold affinity and the nanoscale curvature of AuNPs allow the attached DNA to adapt an upright conformation favorable for hybridization. Recently, it has been shown that nonthiolated DNA can also be attached via DNA base adsorption. Without a thiol label, both ends of the DNA and even internal bases could be adsorbed, decreasing the specificity of subsequent molecular recognition reactions. In this work, we employed a modular sequence design approach to systematically study the effect of DNA sequence on adsorption polarity. A block of poly adenine (poly-A) could be used to achieve a high density of DNA attachment. When the poly-A block length is short (e.g., below 5–7), the loading was independent of the block length, and the conjugate cannot hybridize to its cDNA effectively, suggesting a random attachment controlled by adsorption kinetics. Increasing the block length leads to reduced capacity but improved hybridization, suggesting that more DNA with the desired conformation was adsorbed due to the thermodynamic effects of poly-A binding. The design can be further improved by including capping sequences rich in T or G. Finally, a more general double-stranded DNA approach was described to be suitable for DNA that cannot satisfy the above-mentioned design requirements.
Rationally Designed Nucleobase and Nucleotide Coordinated Nanoparticles for Selective DNA Adsorption and Detection
(American Chemical Society, 2013-12-17) Wang, Feng; Liu, Biwu; Huang, Po-Jung Jimmy; Liu, Juewen
Nanomaterials for DNA adsorption are useful for sequence-specific DNA detection. Current materials for DNA adsorption employ electrostatic attraction, hydrophobic interaction, or π–π stacking, none of which can achieve sequence specificity. Specificity might be improved by involving hydrogen bonding and metal coordination. In this work, a diverse range of nucleobase/nucleotide (adenine, adenosine, adenosine 5′-triphosphate (ATP), adenosine 5′-monophosphate (AMP), and guanosine 5′-triphosphate (GTP)) coordinated materials containing various metal ions (Au(III), Ag(I), Ce(III), Gd(III), and Tb(III)) are prepared. In most cases, nanoparticles are formed. These materials have different surface charges, and positively charged particles only show nonspecific DNA adsorption. Negatively charged materials give different adsorption kinetics for different DNA sequences, where complementary DNA homopolymers are adsorbed faster than other sequences. Therefore, the bases in the coordinated materials can still form base pairs with the DNA. The adsorption strength is mainly controlled by the metal ions, where Au shows the strongest adsorption while lanthanides are weaker. These materials can be used as sensors for DNA detection and can also deliver DNA into cells with no detectable toxicity. By tuning the nanoparticle formulation, enhanced detection can be achieved. This study is an important step toward rational design of materials to achieve specific interactions between biomolecules and synthetic nanoparticle surfaces.
Self-healable and reversible liposome leakage by citrate-capped gold nanoparticles probing initial adsorption/desorption induced lipid phase transition
(Royal Society of Chemistry, 2015-10-14) Wang, Feng; Liu, Juewen
We herein report that the adsorption/desorption of citrate-capped gold nanoparticles (AuNPs) transiently causes leakage in fluid phase DOPC liposomes, while the liposomes do not leak with AuNPs capped with mercaptopropionic acid (MPA). Leakage also fails to occur for gel phase DPPC liposomes. Citrate-capped (but not MPA-capped) AuNPs raise the phase transition temperature of DPPC. We conclude that citrate-capped AuNPs interact with the PC liposomes very strongly, inducing a local fluid-to-gel lipid phase transition for DOPC. Leakage takes place during this transition, and the membrane integrity is resumed after the transition. Citrate-capped AuNPs allow stronger van der Waals forces than MPA-capped AuNPs with PC liposomes, since the latter are separated from the liposome surface by the ∼0.3 nm MPA layer.
Surface Science of DNA Adsorption onto Citrate-Capped Gold Nanoparticles
(American Chemical Society, 2012-02-28) Zhang, Xu; Servos, Mark R.; Liu, Juewen
Single-stranded DNA can be adsorbed by citrate capped gold nanoparticles (AuNPs), resulting in increased AuNP stability, which forms the basis of a number of biochemical and analytical applications, but the fundamental interaction of this adsorption reaction remains unclear. In this study, we measured DNA adsorption kinetics, capacity, and isotherms, demonstrating that the adsorption process is governed by electrostatic forces. The charge repulsion among DNA strands and between DNA and AuNPs can be reduced by adding salt, reducing pH or by using noncharged peptide nucleic acid (PNA). Langmuir adsorption isotherms are obtained, indicating the presence of both adsorption and desorption of DNA from AuNPs. While increasing salt concentration facilitates DNA adsorption, the desorption rate is also enhanced in higher salt due to DNA compaction. DNA adsorption capacity is determined by DNA oligomer length, DNA concentration, and salt. Previous studies indicated faster adsorption of short DNA oligomers by AuNPs, we find that once adsorbed, longer DNAs are much more effective in protecting AuNPs from aggregation. DNA adsorption is also facilitated by using low pH buffers and high alcohol concentrations. A model based on electrostatic repulsion on AuNPs is proposed to rationalize the DNA adsorption/desorption behavior.
Tandem Phosphorothioate Modifications for DNA Adsorption Strength and Polarity Control on Gold Nanoparticles
(American Chemical Society, 2014-09-10) Zhou, Wenhu; Wang, Feng; Ding, Jinsong; Liu, Juewen
Unmodified DNA was recently used to functionalize gold nanoparticles via DNA base adsorption. Compared to thiolated DNA, however, the application of unmodified DNA is limited by the lack of sequence generality, adsorption polarity control and poor adsorption stability. We report that these problems can be solved using phosphorothioate (PS) DNA. PS DNA binds to gold mainly via the sulfur atom and is thus less sequence dependent. The adsorption affinity is ranked to be thiol > PS > adenine > thymine. Tandem PS improves adsorption strength, allows tunable DNA density, and the resulting conjugates are functional at a low cost.
Toward Fast and Quantitative Modification of Large Gold Nanoparticles by Thiolated DNA: Scaling of Nanoscale Forces, Kinetics, and the Need for Thiol Reduction
(American Chemical Society, 2013-08-01) Zhang, Xu; Gouriye, Tony; Göeken, Kristian; Servos, Mark R.; Gill, Ron; Liu, Juewen
We have recently reported on the fast and quantitative adsorption of DNA to 13 nm gold nanoparticles (AuNPs) at pH 3. This is in contrast to most traditional methods at neutral pH, where the adsorption is both slow and requires high excess of DNA. Direct application of our protocol to large particles in many cases did not result in particles that are stable at high (0.3 M) salt, and high excess of DNA was still required for the formation of stable particles. In this work, we investigate the reasons for this limitation on the basis of kinetics and colloidal stability. On the basis of our investigation, fast and quantitative modification of large AuNPs is still possible, either by working at high particle concentration, or by using sonication. As we have shown that fast quantitative modification of large particles is possible, the preparation step of reduction and purification of the thiolated DNA becomes the rate limiting step in the whole AuNP-DNA conjugate protocol. However, we show that this step is unnecessary when using our current protocol.

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