Donald M. Cropek

A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity

Here, we report a catalytic beacon sensor for uranyl (UO22+) based on an in vitro-selected UO22+-specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3′ quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5′ and 3′ ends, respectively. The presence of UO22+ causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of ≈230 μM. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.

A cell-based biosensor for real-time detection of cardiotoxicity using lensfree imaging

A portable and cost-effective real-time cardiotoxicity biosensor was developed using a CMOS imaging module extracted from a commercially available webcam. The detection system consists of a CMOS imaging module, a white LED and a pinhole. Real-time image processing was conducted by comparing reference and live frame images. To evaluate the engineered system, the effects of two different drugs, isoprenaline and doxorubicin, on the beating rate and beat-to-beat variations of ESC-derived cardiomyocytes were measured. The detection system was used to conclude that the beat-to-beat variability increased under treatment with both isoprenaline and doxorubicin. However, the beating rates increased upon the addition of isoprenaline but decreased for cultures supplemented with doxorubicin. Moreover, the response time for both the beating rates and the beat-to-beat variability of ESC-derived cardiomyocytes under treatment of isoprenaline was shorter than for doxorubicin, although the amount of isoprenaline used in the measurement was three orders of magnitude lower than that of doxorubicin. Given its ability to perform real-time cell monitoring in a simple and inexpensive manner, the proposed system may be useful for a range of cell-based biosensing applications.

Convection-driven generation of long-range material gradients.

Natural materials exhibit anisotropy with variations in soluble factors, cell distribution, and matrix properties. The ability to recreate the heterogeneity of the natural materials is a major challenge for investigating cell-material interactions and for developing biomimetic materials. Here we present a generic fluidic approach using convection and alternating flow to rapidly generate multi-centimeter gradients of biomolecules, polymers, beads and cells and cross-gradients of two species in a microchannel. Accompanying theoretical estimates and simulations of gradient growth provide design criteria over a range of material properties. A poly(ethylene-glycol) hydrogel gradient, a porous collagen gradient and a composite material with a hyaluronic acid/gelatin cross-gradient were generated with continuous variations in material properties and in their ability to regulate cellular response. This simple yet generic fluidic platform should prove useful for creating anisotropic biomimetic materials and high-throughput platforms for investigating cell-microenvironment interactions.

Hydrogel-coated microfluidic channels for cardiomyocyte culture

The research areas of tissue engineering and drug development have displayed increased interest in organ-on-a-chip studies, in which physiologically or pathologically relevant tissues can be engineered to test pharmaceutical candidates. Microfluidic technologies enable the control of the cellular microenvironment for these applications through the topography, size, and elastic properties of the microscale cell culture environment, while delivering nutrients and chemical cues to the cells through continuous media perfusion. Traditional materials used in the fabrication of microfluidic devices, such as poly(dimethylsiloxane) (PDMS), offer high fidelity and high feature resolution, but do not facilitate cell attachment. To overcome this challenge, we have developed a method for coating microfluidic channels inside a closed PDMS device with a cell-compatible hydrogel layer. We have synthesized photocrosslinkable gelatin and tropoelastin-based hydrogel solutions that were used to coat the surfaces under continuous flow inside 50 μm wide, straight microfluidic channels to generate a hydrogel layer on the channel walls. Our observation of primary cardiomyocytes seeded on these hydrogel layers showed preferred attachment as well as higher spontaneous beating rates on tropoelastin coatings compared to gelatin. In addition, cellular attachment, alignment and beating were stronger on 5% (w/v) than on 10% (w/v) hydrogel-coated channels. Our results demonstrate that cardiomyocytes respond favorably to the elastic, soft tropoelastin culture substrates, indicating that tropoelastin-based hydrogels may be a suitable coating choice for some organ-on-a-chip applications. We anticipate that the proposed hydrogel coating method and tropoelastin as a cell culture substrate may be useful for the generation of elastic tissues, e.g. blood vessels, using microfluidic approaches.

A 3D Interconnected Microchannel Network Formed in Gelatin by Sacrificial Shellac Microfibers

3D microfluidic networks are fabricated in a gelatin hydrogel using sacrificial melt-spun microfibers made from a material with pH-dependent solubility. The fibers, after being embedded within the gel, can be removed by changing the gel pH to induce dissolution. This process is performed in an entirely aqueous environment, avoiding extreme temperatures, low pressures, and toxic organic solvents.

Incorporation of a DNAzyme into Au-coated nanocapillary array membranes with an internal standard for Pb(II) sensing

A Pb(ii)-specific DNAzyme has been successfully incorporated into Au-coated polycarbonate track-etched (PCTE) nanocapillary array membranes (NCAMs) by thiol-gold immobilization. Incorporation of the DNAzyme into the membrane provides a substrate-bound sensor using a novel internal control methodology for fluorescence-based detection of Pb(ii). A non-cleavable substrate strand, identical to the cleavable DNAzyme substrate strand except the RNA-base is replaced by the corresponding DNA-base, is used for ratiometric comparison of intensities. The cleavable substrate strand is labeled with fluorescein, and the non-cleavable strand is labeled with a red fluorophore (Cy5 or Alexa 546) for detection after release from the membrane surface. This internal standard based ratiometric method allows for real-time monitoring of Pb(ii)-induced cleavage, as well as standardizing variations in substrate size, solution detection volume, and monolayer density. The result is a Pb(ii)-sensing structure that can be stored in a prepared state for 30 days, regenerated after reaction, and detect Pb(ii) concentrations as low as 17 nM (3.5 ppb).

Detection of the Superoxide Radical Anion Using Various Alkanethiol Monolayers and Immobilized Cytochrome c

The superoxide radical anion (SO) is a critical biomarker for monitoring cellular stress responses. Electrochemical SO biosensors are frequently constructed through the covalent immobilization of cytochrome c (Cyt c) onto self-assembled monolayers (SAMs); however, a detailed comparison of these systems as well as configuration influence on SO detection is needed to enable robust applications. Two reaction pathways, oxidation of SO by the SAM-modified gold electrode or electron transfer through a protein and monolayer relay, may be involved during the electrochemical detection of SO with Cyt c, depending on the SAM that is used. Although electrodes with SAMs alone can exhibit a high sensitivity and low limit of detection (LOD) for the SO, they can suffer from a strong response to the presence of interferents such as hydrogen peroxide and ascorbic acid. Electrodes with immobilized Cyt c show decreased sensitivity, but exhibit better selectivity and resistance to fouling in complex media. Considering the trade-offs between sensitivity, selectivity, and LOD for SO detection, a bioelectrode made with Cyt c immobilized on dithiobis(succinimidyl)propionate (DTSP) appears to be the most suitable configuration. In phosphate buffer, the DTSP/Cyt c electrode has a sensitivity of 410 nA microM(-1) cm(-2) and an LOD for SO of 73 nM. Results are also presented for the detection of SO in a complex tissue culture media (MEM) with and without serum, and the sensitivity of the DTSP/Cyt c in MEM in the absence of serum increased to 640 nA microM(-1) cm(-2). By measuring SO with a DTSP/Cyt c electrode before and after the addition of a bolus of the superoxide dismutase (SOD) enzyme, the specificity of the SOD enzyme can be combined with the sensitivity of Cyt c system.

Development of a troponin I biosensor using a peptide obtained through phage display.

A small synthetic peptide with nanomolar affinity for cardiac troponin I (TnI), previously identified from a polyvalent phage displayed library, has been immobilized on a gold surface for TnI detection. The binding affinity of gold-immobilized peptides for TnI was studied and compared with that of phage-immobilized peptides. Quartz crystal microbalance (QCM), cyclic voltammetry, and electrochemical impedance spectroscopy (EIS) were used to monitor both the immobilization and target binding processes. All three techniques show that the binding is specific for TnI as compared to a streptavidin (SA) control. The response curves obtained at TnI concentrations ranging from 0 to 10 μg/mL, using both QCM and EIS, were also compared. For the EIS measurements, the sensitivity was 0.30 ± 0.030 normalized impedance/(μg/mL) and the limit of detection (LOD) was 0.34 μg/mL. Using the QCM, a sensitivity of 18 ± 1 Hz/(μg/mL) was obtained, corresponding to an LOD of 0.11 μg/mL. Although the QCM demonstrated a lower LOD as compared to EIS, the latter technique exhibited a larger linear dynamic range than QCM. In a relevant tissue culture milieu, Minimum Essential Media (MEM), the sensitivity of the EIS measurement was greater than that obtained in a phosphate buffer system (PBS). The kinetics of target binding using QCM were analyzed by two independent methods, and the dissociation constants (K(D) = 66 ± 4 nM and 17 ± 8 nM) were an order of magnitude higher than that calculated for the polyvalent phage particles (K(D) = 2.5 ± 0.1 nM). Even though the affinity of the immobilized peptides for TnI was somewhat reduced, overall, these results demonstrate that peptides obtained from the biopanning of phage display libraries can be readily used as sensing probes in biosensor development.

Immobilization of DNAzyme catalytic beacons on PMMA for Pb2+ detection

Due to the numerous toxicological effects of lead, its presence in the environment needs to be effectively monitored. Incorporating a biosensing element within a microfluidic platform enables rapid and reliable determinations of lead at trace levels. A microchip-based lead sensor is described here that employs a lead-specific DNAzyme (also called catalytic DNA or deoxyribozyme) as a recognition element that cleaves its complementary substrate DNA strand only in the presence of cationic lead (Pb(2+)). Fluorescent tags on the DNAzyme translate the cleavage events to measurable, optical signals proportional to Pb(2+) concentration. The DNAzyme responds sensitively and selectively to Pb(2+), and immobilizing DNAzyme in the sensor permits both sensor regeneration and localization of the detection zone. Here, the DNAzyme has been immobilized on a PMMA surface using the highly specific biotin-streptavidin interaction. The strategy includes using streptavidin physisorbed on a PMMA surface to immobilize DNAzyme both on planar PMMA and on the walls of a PMMA microfluidic device. The immobilized DNAzyme retains its Pb(2+) detection activity in the microfluidic device and can be regenerated and reused. The DNAzyme shows no response to other common metal cations and the presence of these contaminants does not interfere with the lead-induced fluorescence signal. While prior work has shown lead-specific catalytic DNA can be used in its solubilized form and while attached to gold substrates to quantitate Pb(2+) in solution, this is the first use of the DNAzyme immobilized within a microfluidic platform for real time Pb(2+) detection.

High affinity peptides for the recognition of the heart disease biomarker troponin I identified using phage display

Troponin I is a specific and sensitive clinical biomarker for myocardial injury. In this study we have used polyvalent phage display to isolate unique linear peptide motifs which recognize both the human and rat homologs of troponin I. The peptide specific for human troponin I has a sequence of FYSHSFHENWPS and the peptide specific for the rat troponin I has a sequence of FHSSWPVNGSTI. Enzyme‐linked immunosorbent assays (ELISAs) were used to evaluate the binding interactions, and the two phage‐displayed peptides exhibited some cross‐reactivity, but they were both more specific for the troponin I homolog they were selected against. The binding affinities of the phage‐displayed peptides were decreased by the presence of complex tissue culture media (MEM), and the addition of 10% calf serum further interfered with the binding of the target proteins. Kinetic indirect phage ELISAs revealed that both troponin I binding peptides were found to have nanomolar affinities for the troponin proteins while attached to the phage particles. To our knowledge, this is the first example of isolation and characterization of troponin I binders using phage display technology. These new peptides may have potential utility in the development of new clinical assays for cardiac injury as well as in monitoring of cardiac cells grown in culture. Biotechnol. Bioeng. 2010. 105: 678–686.