Waterloo Institute for Nanotechnology

Permanent URI for this collectionhttps://uwspace.uwaterloo.ca/handle/10012/11339

This is the collection for Waterloo Institute for Nanotechnology.

Waterloo faculty, students, and staff can contact us or visit the UWSpace guide to learn more about depositing their research.

Browse

Now showing 1 - 20 of 193

Self-Assembly of Amphiphilic Nanoparticle-Coil “Tadpole” Macromolecules
(American Chemical Society, 2004) Lee, Jae Youn; Balazs, Anna C.; Thompson, Russell B.; Hill, Randall M.
There has been considerable fascination with the self-assembling behavior of amphiphilic chainlike molecules that range from short-chain surfactants to high molecular weight block copolymers. The self-assembly of simple amphiphiles into membranes may have played an important role in the origin of life. The self-organization of amphiphiles with more complex architectures can lead to a stunning variety of complex morphologies. In the case of short-chain surfactants, the equilibrium morphology of the self-assembled sys- tem depends on geometric factors, such as the ratio of the “head” to “tail” sizes. Here, the headgroups are small molecules and the tails are coillike. In the case of block copolymers, the structure of the melt depends on the relative composition of the chains, the degree of polymerization, and the incompatibility between the different blocks.
Self-Assembly of Amphiphilic Nanoparticle-Coil “Tadpole” Macromolecules
(American Chemical Society, 2004) Lee, Jae Youn; Balazs, Anna C.; Thompson, Russell B.; Hill, Randall M.
None.
Origins of Elastic Properties in Ordered Block Copolymer/Nanoparticle Composites
(American Chemical Society, 2004) Thompson, Russell B.; Rasmussen, Kim O.; Lookman, Turab
We predict a diblock copolymer melt in the lamellar phase with added spherical nanoparticles that have an affinity for one block to have a lower tensile modulus than a pure diblock copolymer system. This weakening is due to the swelling of the lamellar domain by nanoparticles and the displacement of polymer by elastically inert fillers. Despite the overall decrease in the tensile modulus of a polydomain sample, the shear modulus for a single domain is unaffected by fillers.
Ordering mechanisms in triblock copolymers
(American Physical Society, 2004) Maniadis, P.; Thompson, Russell B.; Rasmussen, Kim O.; Lookman, Turab
The ordering mechanisms for an ABC triblock copolymer system are studied using self-consistent field theory. We find a two-phase mechanism, similar to what has been suggested experimentally 􏰖two-step mecha- nism􏰌. Analysis of free energy components shows that the two-phase process comes about through a compe- tition between stretching energy and interfacial energy. The mechanism is found to be sufficiently robust so as to make it potentially useful for device applications.
Assembly of DNA-Functionalized Nanoparticles in Alcoholic Solvents Reveals Opposite Thermodynamic and Kinetic Trends for DNA Hybridization
(American Chemical Society, 2010-05-12) Smith, Brendan D.; Liu, Juewen
DNA has been a key molecule in biotechnology and nanotechnology. To date, the majority of the experiments involving DNA have been performed in aqueous solutions, which may be related to the perception that DNA hybridization is slower and less stable in organic solvents. All studies on the effect of organic solvents have focused on thermodynamic properties such as DNA melting temperature and the B-to-A form transition for very long DNAs, but not on the hybridization kinetics of short synthetic DNAs. We employed DNA-functionalized gold nanoparticles (AuNPs) as a model system and found that if the alcohol content is less than ∼30%, more alcohol leads to a faster DNA hybridization, although with a decreased melting temperature. The generality of this observation was independently verified with two molecular beacon systems (in the absence of AuNPs) using fluorophore and quencher-labeled DNAs. With 25% ethanol, the hybridization rates are three to four times faster than in the case with water. This discovery will extend the application of DNA bio- and nanotechnology to organic solvents with improved performance.
Flow Cytometry-Assisted Detection of Adenosine in Serum with an Immobilized Aptamer Sensor
(American Chemical Society, 2010-05-15) Huang, Po-Jung Jimmy; Liu, Juewen
Aptamers are single-stranded nucleic acids that can selectively bind to essentially any molecule of choice. Because of their high stability, low cost, ease of modification, and availability through selection, aptamers hold great promise in addressing key challenges in bioanalytical chemistry. In the past 15 years, many highly sensitive fluorescent aptamer sensors have been reported. However, few such sensors showed high performance in serum samples. Further challenges related to practical applications include detection in a very small sample volume and a low dependence of sensor performance on ionic strength. We report the immobilization of an aptamer sensor on a magnetic microparticle and the use of flow cytometry for detection. Flow cytometry allows the detection of individual particles in a capillary and can effectively reduce the light scattering effect of serum. Since DNA immobilization generated a highly negatively charged surface and caused an enrichment of counterions, the sensor performance showed a lower salt dependence. The detection limits for adenosine are determined to be 178 μM in buffer and 167 μM in 30% serum. Finally, we demonstrated that the detection can be carried out in 10 μL of 90% human blood serum.
Regenerable DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II) Detection and Removal in Water
(American Chemical Society, 2010-09-15) Dave, Neeshma; Chan, Michelle Y.; Huang, Po-Jung Jimmy; Smith, Brendan D.; Liu, Juewen
Mercury is a highly toxic environmental pollutant with bioaccumulative properties. Therefore, new materials are required to not only detect but also effectively remove mercury from environmental sources such as water. We herein describe a polyacrylamide hydrogel-based sensor functionalized with a thymine-rich DNA that can simultaneously detect and remove mercury from water. Detection is achieved by selective binding of Hg2+ between two thymine bases, inducing a hairpin structure where, upon addition of SYBR Green I dye, green fluorescence is observed. In the absence of Hg2+, however, addition of the dye results in yellow fluorescence. Using the naked eye, the detection limit in a 50 mL water sample is 10 nM Hg2+. This sensor can be regenerated using a simple acid treatment and can remove Hg2+ from water at a rate of ∼1 h−1. This sensor was also used to detect and remove Hg2+ from samples of Lake Ontario water spiked with mercury. In addition, these hydrogel-based sensors are resistant to nuclease and can be rehydrated from dried gels for storage and DNA protection. Similar methods can be used to functionalize hydrogels with other nucleic acids, proteins, and small molecules for environmental and biomedical applications.
Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity
(American Chemical Society, 2010-12-02) Dave, Neeshma; Liu, Juewen
DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.
DNA-Functionalized Monolithic Hydrogels and Gold Nanoparticles for Colorimetric DNA Detection
(American Chemical Society, 2010-12-22) Baeissa, Aifan; Dave, Neeshma; Smith, Brendan D.; Liu, Juewen
Highly sensitive and selective DNA detection plays a central role in many fields of research, and various assay platforms have been developed. Compared to homogeneous DNA detection, surface-immobilized probes allow washing steps and signal amplification to give higher sensitivity. Previously research was focused on developing glass or gold-based surfaces for DNA immobilization; we herein report hydrogel-immobilized DNA. Specifically, acrydite-modified DNA was covalently functionalized to the polyacrylamide hydrogel during gel formation. There are several advantages of these DNA-functionalized monolithic hydrogels. First, they can be easily handled in a way similar to that in homogeneous assays. Second, they have a low optical background where, in combination with DNA-functionalized gold nanoparticles, even ∼0.1 nM target DNA can be visually detected. By using the attached gold nanoparticles to catalyze the reduction of Ag+, as low as 1 pM target DNA can be detected. The gels can be regenerated by a simple thermal treatment, and the regenerated gels perform similarly to freshly prepared ones. The amount of gold nanoparticles adsorbed through DNA hybridization decreases with increasing gel percentage. Other parameters including the DNA concentration, DNA sequence, ionic strength of the solution, and temperature have also been systematically characterized in this study.
Programmable Assembly of DNA-Functionalized Liposomes by DNA
(American Chemical Society, 2011-02-22) Dave, Neeshma; Liu, Juewen
Bionanotechnology involves the use of biomolecules to control both the structure and property of nanomaterials. One of the most studied examples is DNA-directed assembly of inorganic nanoparticles such as gold nanoparticles (AuNPs). However, systematic studies on DNA-linked soft nanoparticles, such as liposomes, are still lacking. We herein report the programmable assembly and systematic characterization of DNA-linked liposomes as a function of liposome size, charge, fluidity, composition, DNA spacer, linker DNA sequence, and salt concentration for direct comparison to DNA-directed assembly of AuNPs. Similar to the assemblies of AuNPs, sharp melting transitions were observed for liposomes where the first derivative of the melting curve full width at half-maximum (fwhm) is equal to or less than 1 °C for all of the tested liposomes, allowing sequence specific DNA detection. We found that parameters such as liposome size, charge, and fluidity have little effect on the DNA melting temperature. Cryo-TEM studies showed that programmable assemblies can be obtained and that the majority of the liposomes maintained a spherical shape in the assembled state. While liposome and AuNP systems are similar in many aspects, there are also important differences that can be explained by their respective physical properties.
Adsorption and Desorption of DNA on Graphene Oxide Studied by Fluorescently Labeled Oligonucleotides
(American Chemical Society, 2011-03-15) Wu, Marissa; Kempaiah, Ravindra; Huang, Po-Jung Jimmy; Maheshwari, Vivek; Liu, Juewen
Being the newest member of the carbon materials family, graphene possesses many unique physical properties resulting is a wide range of applications. Recently, it was discovered that graphene oxide can effectively adsorb DNA, and at the same time, it can completely quench adsorbed fluorophores. These properties make it possible to prepare DNA-based optical sensors using graphene oxide. While practical analytical applications are being demonstrated, the fundamental understanding of binding between graphene oxide and DNA in solution received relatively less attention. In this work, we report that the adsorption of 12-, 18-, 24-, and 36-mer single-stranded DNA on graphene oxide is affected by several factors. For example, shorter DNAs are adsorbed more rapidly and bind more tightly to the surface of graphene. The adsorption is favored by a lower pH and a higher ionic strength. The presence of organic solvents such as ethanol can either increase or decrease adsorption depending on the ionic strength of the solution. By adding the cDNA, close to 100% desorption of the absorbed DNA on graphene can be achieved. On the other hand, if temperature is increased, only a small percentage of DNA is desorbed. Further, the adsorbed DNA can also be exchanged by free DNA in solution. These findings are important for further understanding of the interactions between DNA and graphene and for the optimization of DNA and graphene-based devices and sensors.
Electrostatically Directed Visual Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly Sensitive Hg2+ Detection
(American Chemical Society, 2011-03-23) Dave, Neeshma; Liu, Juewen; Joseph, Kevin A.
Hydrogels are cross-linked hydrophilic polymer networks with low optical background and high loading capacity for immobilization of biomolecules. Importantly, the property of hydrogel can be precisely controlled by changing the monomer composition. This feature, however, has not been investigated in the rational design of hydrogel-based optical sensors. We herein explore electrostatic interactions between an immobilized mercury binding DNA, a DNA staining dye (SYBR Green I), and the hydrogel backbone. A thymine-rich DNA was covalently functionalized within monolithic hydrogels containing a positive, neutral, or negative backbone. These hydrogels can be used as sensors for mercury detection since the DNA can selectively bind Hg2+ between thymine bases inducing a hairpin structure. SYBR Green I can then bind to the hairpin to emit green fluorescence. For the neutral or negatively charged gels, addition of the dye in the absence of Hg2+ resulted in intense yellow background fluorescence, which was attributed to SYBR Green I binding to the unfolded DNA. We found that, by introducing 20% positively charged allylamine monomer, the background fluorescence was significantly reduced. This was attributed to the repulsion between positively charged SYBR Green I by the gel matrix as well as the strong binding between the DNA and the gel backbone. The signal-to-background ratio and detection limit was, respectively, improved by 6- and 9-fold using the cationic gel instead of neutral polyacrylamide gel. This study helps understand the electrostatic interaction within hydrogels, showing that hydrogels can not only serve as a high capacity matrix for sensor immobilization but also can actively influence the interaction between involved molecules.
Immobilization of DNA on Magnetic Microparticles for Mercury Enrichment and Detection with Flow Cytometry
(Wiley, 2011-04-26) Huang, Po-Jung Jimmy; Liu, Juewen
Mercury detection in water has attracted a lot of research interest due to its highly toxic nature and adverse environmental impact. In particular, the recent discovery of specific binding of HgII to thymine-rich (T-rich) DNA resulting in T-HgII-T base pairs has led to the development of a number of sensors with different signaling mechanisms. However, the majority of such sensors were non-immobilized. Immobilization, on the other hand, allows active mercury adsorption, signal amplification, and sensor regeneration. In this work, we immobilized a thymine-rich DNA on a magnetic microparticle (MMP) surface through biotin–streptavidin interactions. In the presence of HgII, the DNA changes from a random coil structure into a hairpin, upon which SYBR Green I binds to emit green fluorescence. Detection was carried out by using flow cytometry where the fluorescence intensity increased ≈9-fold in the presence of mercury and the binding of mercury reached equilibrium in less than 2 min. The sensor showed a unique sample-volume-dependent fluorescence signal change where a higher fluorescence was obtained with a larger sample volume, suggesting that the particles can actively adsorb HgII. Detection limits of 5 nM (1 ppb) and 14 nM (2.8 ppb) were achieved in pure buffer and in mercury-spiked Lake Ontario water samples, respectively.
Assembly of DNA-Functionalized Gold Nanoparticles with Gaps and Overhangs in Linker DNA
(American Chemical Society, 2011-04-28) Smith, Brendan D.; Dave, Neeshma; Huang, Po-Jung Jimmy; Liu, Juewen
DNA-directed assembly of gold nanoparticles (AuNPs) has been extensively studied because of its important applications in analytical chemistry, materials science, and nanomedicine. In a typical system, two DNA-functionalized AuNPs are assembled via a linker DNA to form large aggregates. In the majority of the previous reports, the linker DNA is fully base paired with no gaps or overhangs present. Introducing such nonbase-paired regions in the linker DNA has been recently shown to be important for making stimuli-responsive materials and in crystallization of such AuNPs. In this work, we systematically studied the effect of introducing gaps and overhangs in the linker DNA to understand the kinetics of assembly and the melting transition of these aggregates. We found that the assembly kinetics decreased with increasing linker DNA length. The melting temperature decreased with the loss of base stacking by introducing gaps as well as the steric effect of overhangs. Additional insights were obtained by measuring the melting curves of the free DNAs in the absence of AuNPs. For example, it appeared that DNA base stacking at the nick site was favored in assembled nanoparticles compared to that in free DNA. Our results indicate that, while it is possible to form AuNP assemblies with linker DNAs containing various types of unpaired regions, these kinetic and thermodynamic factors need to be considered when designing related sensors and materials.
Dissociation and Degradation of Thiol-Modified DNA on Gold Nanoparticles in Aqueous and Organic Solvents
(American Chemical Society, 2011-05-17) Bhatt, Nishi; Huang, Po-Jung Jimmy; Dave, Neeshma; Liu, Juewen
Gold nanoparticles functionalized with thiol-modified DNA have been widely used in making various nanostructures, colorimetric biosensors, and drug delivery vehicles. Over the past 15 years, significant progress has been made to improve the stability of such functionalized nanoparticles. The stability of the gold–thiol bond in this system, however, has not been studied in a systematic manner. Most information on the gold–thiol bond was obtained from the study of self-assembled monolayers (SAMs). In this study, we employed two fluorophore-labeled and thiol-modified DNAs. The long-term stability of the thiol–gold bond as a function of time, salt, temperature, pH, and organic solvent has been studied. We found that the bond spontaneously dissociated under all tested conditions. The dissociation was favored at high salt, high pH, and high temperature, and little DNA degradation was observed in our system. Most organic solvents showed a moderate protection effect on the gold–thiol bond. The stability of the gold–thiol bond in the DNA system was also compared with that in SAMs. While there are many similarities, we also observed opposite trends for the salt and ethanol effect. This study suggests that the purified DNA-functionalized gold nanoparticles should be freshly prepared and used in a day or two. Long-term storage should be carried out at relatively low temperature in low salt and slightly acidic buffers.
Synergistic pH effect for reversible shuttling aptamer-based biosensors between graphene oxide and target molecules
(Royal Society of Chemistry, 2011-06-07) Huang, Po-Jung Jimmy; Kempaiah, Ravindra; Liu, Juewen
DNA aptamers are known to desorb from graphene oxide (GO) surface in the presence of target molecules. We demonstrate herein that the binding equilibrium can be shifted by simply tuning the solution pH. At lower pH, the aptamer/GO binding is enhanced while aptamer/target binding is weakened, making this system a regenerable biosensor without covalent conjugation.
Protection and Promotion of UV Radiation-Induced Liposome Leakage via DNA-Directed Assembly with Gold Nanoparticles
(Wiley, 2011-07-26) Dave, Neeshma; Liu, Juewen
DNA-functionalized gold nanoparticles and liposomes are assembled by a linker DNA. The gold nanoparticles can either protect the liposome from UV radiation induced leakage or can promote the leakage, depending on the DNA sequence and the alignment of the particles.
Oligonucleotide-functionalized hydrogels as stimuli responsive materials and biosensors
(Royal Society of Chemistry, 2011-08-07) Liu, Juewen
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.
Stimuli-responsive releasing of gold nanoparticles and liposomes from aptamer-functionalized hydrogels
(Institute of Physics, 2011-11-21) El-Hamed, Firas; Dave, Neeshma; Liu, Juewen
Controlled release of therapeutic agents is important for improving drug efficacy and reducing toxicity. Recently, hydrogels have been used for controlled release applications. While the majority of the previous work focused on releasing the cargo in response to physical stimuli such as temperature, light, electric field, and pH, we aim to trigger cargo release in the presence of small metabolites. In our system a DNA aptamer that can bind to adenosine, AMP, and ATP was used as a linker to attach either DNA-functionalized gold nanoparticles or liposomes to DNA-functionalized hydrogels. In the presence of the metabolite, both the nanoparticle and liposome cargos were released. The effect of salt, temperature, target concentration, and drying has been systematically studied. Interestingly, we found that the gel can be completely dried while retaining the DNA linkages and adenosine induced release was still achieved after rehydration. Our work demonstrates that aptamers can be used to control the release of drugs and other materials attached to hydrogels.
Amplifying the Macromolecular Crowding Effect Using Nanoparticles
(American Chemical Society, 2012-01-11) Zaki, Ahmed; Liu, Juewen; Dave, Neeshma
The melting temperature (Tm) of DNA is affected not only by salt but also by the presence of high molecular weight (MW) solutes, such as polyethylene glycol (PEG), acting as a crowding agent. For short DNAs in a solution of low MW PEGs, however, the change of excluded volume upon melting is very small, leading to no increase in Tm. We demonstrate herein that by attaching 12-mer DNAs to gold nanoparticles, the excluded volume change was significantly increased upon melting, leading to increased Tm even with PEG 200. Larger AuNPs, higher MW PEGs, and higher PEG concentrations show even larger effects in stabilizing the DNA. This study reveals a unique and fundamental feature at nanoscale due to geometric effects. It also suggests that weak interactions can be stabilized by a combination of polyvalent binding and the enhanced macromolecular crowding effect using nanoparticles.

Browse

Browsing Waterloo Institute for Nanotechnology by Issue Date