A simple and sensitive "dipstick" test in serum based on lateral flow separation of aptamer-linked nanostructures.
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Aptamers, Nucleotide↗
Biomedical subjects
Juewen Liu
Publications and source records attributed to Juewen Liu.
Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers.
In the past 25 years, DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as versatile programmable templates for assembly of nanomaterials. In parallel, the functions of DNA molecules have been expanded from pure genetic information storage to catalytic functions like those of protein enzymes (DNAzymes) and specific binding functions like antibodies (aptamers). In the past few years, a new interdisciplinary field has emerged that aims to combine functional DNA biology with nanotechnology to generate more dynamic and controllable DNA-based nanostructures or DNA-templated nanomaterials that are responsive to chemical stimuli.
Aptamers, Nucleotide↗
Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli.
Dynamic control of nanomaterial assembly states in response to chemical stimuli is critical in making multi-component materials with interesting properties. Previous work has shown that a Pb2+-specific DNAzyme allowed dynamic control of gold nanoparticle aggregation states in response to Pb2+, and the resulting color change from blue aggregates to red dispersed particles can be used as a convenient way of sensing Pb2+. However, a small piece of DNA (called invasive DNA) and low ionic strength (approximately 30 mM) were required for the process, limiting the scope of application in assembly and sensing. To overcome this limitation, a series of asymmetric DNAzymes, in which one of the two substrate binding regions is longer than the other, has been developed. With such a system, we demonstrated Pb2+-induced disassembly of gold nanoparticle aggregates and corresponding color change at room temperature without the need for invasive DNA, while also making the system more tolerant to ionic strength (33-100 mM). The optimal lengths of the long and short arms were determined to be 14 and 5 base pairs, respectively. In nanoparticle aggregates, the activity of the DNAzyme increased with decreasing ionic strength of the reaction buffer. This simpler and more versatile system allows even better dynamic control of nanoparticle aggregation states in response to chemical stimuli such as Pb2+, and can be used in a wider range of applications for colorimetric sensing of metal ions.
Base Sequence↗
Multi-fluorophore fluorescence resonance energy transfer for probing nucleic acids structure and folding.
Fluorescence resonance energy transfer (FRET) is a widely used technique to study the structure and dynamics of nucleic acids in solution. Such a technique often uses only one donor fluorophore and one acceptor fluorophore to probe the distance and its changes between the two labeled sites. To fully understand molecules with complicated structures, such as three- or four-way DNA junctions, several dual-fluorophore experiments have to be performed. Here, we describe an emerging alternative technique using multi-fluorophore FRET, in which simultaneous labeling of one molecule with several different fluorophores is performed to acquire all the distance information in a single experiment. This method decreases the number of experiments necessary to perform and increases the consistency of the results. In this chapter, FRET study of a tri-fluorophore-labeled DNAzyme serves as an example to illustrate the design of multi-fluorophore FRET experiments and the related data processing and analysis. The (ratio)A method used to calculate FRET efficiency in dual-fluorophore systems is extended to multi-fluorophore systems. An important difference between dual- and multi-fluorophore systems is that, when a multi-fluorophore system is used, FRET efficiency is no longer a reliable parameter to assess folding. Instead, fluorophore-to-fluorophore distance should be used.
DNA↗
Fluorescent DNAzyme biosensors for metal ions based on catalytic molecular beacons.
In this chapter, methods for designing metal ion sensors using fluorophore- and quencher-labeled DNAzymes are discussed. In contrast to the classical molecular beacon method based on binding, the methods described here utilize catalytic cleavage to release the fluorophore for detection and quantification, making it possible to take advantage of catalytic turnovers for signal amplification. Unlike classical molecular beacons that detect only nucleic acids, catalytic molecular beacons can be applied to different DNAzymes to detect a broad range of analytes. The methods described are based on the finding that almost all known trans-cleaving DNAzymes share a similar structure comprised of a catalytic DNAzyme core flanked by two substrate recognition arms. Using a typical DNAzyme called the "8-17" DNAzyme as an example, the design of highly sensitive and selective Pb2+ sensors is described in detail. The initial design employs a single fluorophore-quencher pair in close proximity, with the fluorophore on the 5'-end of the substrate and the quencher on the 3'-end of the enzyme. Although this sensor is highly sensitive and selective at 4 degrees C, high background fluorescence is observed at higher temperatures. Therefore a new design with an additional quencher attached to the 3'-end of the substrate is employed to suppress background fluorescence. The dual quencher method allows the sensor to perform at ambient temperatures with a high signal-to-noise ratio.
Biosensing Techniques↗
Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles.
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Adenosine↗
Proofreading and error removal in a nanomaterial assembly.
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Base Pair Mismatch↗
Stimuli-responsive disassembly of nanoparticle aggregates for light-up colorimetric sensing.
Controlled assembly of nanomaterials has been the focus of much research. In contrast, controlled disassembly has not received much attention, even though both processes have been shown to be important in biology. By using a Pb2+-dependent RNA-cleaving DNAzyme, we demonstrate here control of the disassembly of gold nanoparticle aggregates in response to Pb2+. In the process, we show that nanoparticle alignment plays an important role in the disassembly process, with the tail-to-tail configuration being the most optimal, probably because of the large steric hindrance of other configurations. The rate of disassembly is significantly accelerated by using small pieces of DNA to invade the cleaved substrate of the DNAzyme. Investigation of such a controlled disassembly process allows the transformation of previously designed "light-down" colorimetric Pb2+ sensors into "light-up" sensors.
Colorimetry↗
Highly active and stable DNAzyme-carbon nanotube hybrids.
We report herein the generation and characterization of DNAzyme-carbon nanotube conjugates. Biotinylated DNAzyme was attached to streptavidin-functionalized MWNTs. The resultant DNAzyme-MWNT conjugates exhibited Michaelis-Menten kinetics and multiple catalytic turnovers. The specific activity of the nanoscale conjugates was approximately 1/3 of that for freely soluble DNAzyme. Such high activity may allow myriad applications ranging from the directed assembly of nanomaterials to nanoscale cellular therapeutics that rely on the RNA cleaving ability of DNAzymes.
Catalysis↗
A modular microfluidic architecture for integrated biochemical analysis.
Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.
Biochemistry↗
Miniaturized lead sensor based on lead-specific DNAzyme in a nanocapillary interconnected microfluidic device.
A miniaturized lead sensor has been developed by combining a lead-specific DNAzyme with a microfabricated device containing a network of microfluidic channels that are fluidically coupled via a nanocapillary array interconnect. A DNAzyme construct, selective for cleavage in the presence of Pb2+ and derivatized with fluorophore (quencher) at the 5' (3') end of the substrate and enzyme strands, respectively, forms a molecular beacon that is used as the recognition element. The nanocapillary array membrane interconnect is used to manipulate fluid flows and deliver the small-volume sample to the beacon in a spatially confined detection window where the DNAzyme is interrogated using laser-induced fluorescence detection. A transformed log plot of the fluorescent signal exhibits a linear response (r2 = 0.982) over a Pb2+ concentration range of 0.1 - 100 microM, and a detection limit of 11 nM. The sensor has been applied to the determination of Pb2+ in an electroplating sludge reference material, the result agreeing with the certified value within 4.9%. Quantitative measurement of Pb2+ in this complex sample demonstrates the selectivity of this sensor scheme and points favorably to the application of such technologies to analysis of environmental samples. The unique combination of a DNAzyme with a microfluidic-nanofluidic hybrid device makes it possible to change the DNAzyme to select for other compounds of interest, and to incorporate multiple sensing systems within a single device for greater flexibility. This work represents the initial steps toward creation of a robust field sensor for lead in groundwater or drinking water.
Biosensing Techniques↗
Accelerated color change of gold nanoparticles assembled by DNAzymes for simple and fast colorimetric Pb2+ detection.
The combination of high metal selectivity of DNAzymes with the strong distance-dependent optical properties of metallic nanoparticles has presented considerable opportunities for designing colorimetric sensors for metal ions. We previously communicated a design for a colorimetric lead sensor based on the assembly of gold nanoparticles by a Pb(2+)-dependent DNAzyme. However, heating to 50 degrees C followed by a cooling process of approximately 2 h was required to observe the color change. Herein we report a new improved design that allows fast (<10 min) detection of Pb(2+) at ambient temperature. This improvement of sensor performance is a result of detailed studies of the DNAzyme and nanoparticles, which identified "tail-to-tail" nanoparticle alignment, and large (42 nm diameter) nanoparticle size as the major determining factors in allowing fast color changes. The optimal conditions for other factors such as temperature (35 degrees C) and concentrations of the DNAzyme (2 microM), its substrate (3 nM), and NaCl (300 mM) have also been determined. These results demonstrate that fundamental understanding of the DNAzyme biochemistry and nanoparticle science can lead to dramatically improved colorimetric sensors.
Biosensing Techniques↗
Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor.
Previous work has shown that DNAzyme-directed assembly of gold nanoparticles can be utilized to make effective colorimetric biosensors. However, the method is restricted to analytes that are directly involved in phosphodiester cleavage. To expand the methodology to a broader range of analytes, a colorimetric adenosine biosensor based on the aptazyme-directed assembly of gold nanoparticles is reported here. The aptazyme is based on the 8-17 DNAzyme with an adenosine aptamer motif that can modulate the DNAzyme activity through allosteric interactions depending on the presence of adenosine. In the absence of adenosine, the aptazyme is inactive and the substrate strands can serve as linkers to assemble DNA-functionalized 13-nm-diameter gold nanoparticles, resulting in a blue color. However, the presence of adenosine activates the aptazyme, which cleaves the substrate strand, disrupting the formation of nanoparticle aggregates. A red color of separated gold nanoparticles is observed. Concentrations of adenosine of up to 1 mM can be measured semiquantitatively by the degree of blue to red color changes or quantitatively by the extinction ratio at 520 and 700 nm. Under the same conditions, 5 mM guanosine, cytidine, or uridine resulted in a blue color only, indicating good selectivity of the sensor. The color difference can be clearly observed by the naked eye by spotting the resulting sensor solution onto an alumina TLC plate. Since aptamers that can target many classes of important analytes have already been selected, they can be adapted into aptazyme systems through rational design or further selection. Thus, colorimetric biosensors for many analytes of interest can be designed using the method presented here, regardless of whether the analytes are directly involved in the cleavage reaction or not.
Adenosine↗
Colorimetric biosensors based on DNAzyme-assembled gold nanoparticles.
Taking advantage of recent developments in the field of metallic nanoparticle-based colorimetric DNA detection and in the field of in vitro selection of functional DNA/RNA that can recognize a wide range of analytes, we have designed highly sensitive and selective colorimetric biosensors for many analytes of choice. As an example of the sensor design strategy, a highly sensitive and selective colorimetric lead biosensor based on DNAzyme-directed assembly of gold nanoparticles is reviewed. The DNAzyme consists of an enzyme and a substrate strand, which can be used to assemble DNA-functionalized gold nanoparticles. The aggregation brings gold nanoparticles together, resulting in a blue-colored nanoparticle assembly. In the presence of lead, the DNAzyme catalyzes specific hydrolytic cleavage of the substrate strand, which disrupts the formation of the nanoparticle assembly, resulting in red-colored individual nanoparticles. The application of the sensor in lead detection in leaded paint is also demonstrated. In perspective, the use of allosteric DNA/RNAzymes to expand the range of the nanoparticle-based sensor design method is described.
Biosensing Techniques↗
Improving fluorescent DNAzyme biosensors by combining inter- and intramolecular quenchers.
A previously reported DNAzyme-based biosensor for Pb(2+) has shown high sensitivity and selectivity at 4 degrees C. In the system, the substrate and the enzyme strand of the DNAzyme are labeled with a fluorophore and a quencher, respectively. In the presence of Pb(2+), the substrate strand is cleaved by the enzyme strand, and the release of the cleaved fragment results in significant fluorescence increase. However, the performance of the sensor decreases considerably if the temperature is raised to room temperature because of high background fluorescence. A careful analysis of the sensor system, including measurement of the melting curve and fluorescence resonance energy-transfer (FRET) study of the free substrate, suggests that a fraction of the fluorophore-labeled substrate strand is dissociated from the enzyme strand, resulting in elevated background fluorescence signals at room temperature. To overcome this problem, we designed a new sensor system by introducing both inter- and intramolecular quenchers. The design was aided by the FRET study that showed the dissociated substrate maintained a random coil conformation with an end-to-end distance of approximately 39 A, which is much shorter than that of the fully extended DNA. With this new design, the background fluorescence was significantly suppressed, with 660% increase of fluorescence intensity as compared to 60% increase for the previous design. This suppression of background fluorescence signals was achieved without losing selectivity of the sensor. The new design makes it possible to use the sensor for practical applications in a wide temperature range. The design principle presented here should be applicable to other nucleic acid-based biosensors to decrease background fluorescence.
Biosensing Techniques↗
A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles.
A highly sensitive and selective colorimetric lead biosensor based on DNAzyme-directed assembly of gold nanoparticles is reported. It consists of a DNAzyme and its substrate that can hybridize to a 5'-thio-modified DNA attached to gold nanoparticles. The hybridization brings gold nanoparticles together, resulting in a blue-colored nanoparticle assembly. In the presence of lead, the DNAzyme catalyzes specific hydrolytic cleavage, which prevents the formation of the nanoparticle assembly, resulting in red-colored individual nanoparticles. The detection level can be tuned to several orders of magnitude, from 100 nM to over 200 muM, through addition of an inactive variant of the DNAzyme. The concept developed here can be applied to the design of nucleic acid enzyme/nanoparticle sensors for analytes that are subject to in vitro selection, and thus can significantly expand the scope of nanomaterial applications and provide a novel approach to designing simple colorimetric biosensors.
Biosensing Techniques↗
New highly sensitive and selective catalytic DNA biosensors for metal ions.
While remarkable progress has been made in developing sensors for metal ions such as Ca(II) and Zn(II), designing and synthesizing sensitive and selective metal ion sensors remains a significant challenge. Perhaps the biggest challenge is the design and synthesis of a sensor capable of specific and strong metal binding. Since our knowledge about the construction of metal-binding sites in general is limited, searching for sensors in a combinatorial way is of significant value. Therefore, we have been able to use a combinatorial method called in vitro selection to obtain catalytic DNA that can bind a metal ion of choice strongly and specifically. The metal ion selectivity of the catalytic DNA was further improved using a 'negative selection' strategy where catalytic DNA that are selective for competing metal ions are discarded in the in vitro selection processes. By labeling the resulting catalytic DNA with a fluorophore/quencher pair, we have made a new class of metal ion fluorescent sensors that are the first examples of catalytic DNA biosensors for metal ions. The sensors combine the high selectivity of catalytic DNA with the high sensitivity of fluorescent detection, and can be applied to the quantitative detection of metal ions over a wide concentration range and with high selectivity. The use of DNA sensors in detection and quantification of lead ions in environmental samples such as water from Lake Michigan has been demonstrated. DNA is stable, cost-effective, environmentally benign, and easily adaptable to optical fiber and microarray technology for device manufacture. Thus, the DNA sensors explained here hold great promise for on-site and real-time monitoring of metal ions in the fields of environmental monitoring, developmental biology, clinical toxicology, wastewater treatment, and industrial process monitoring.
Biosensing Techniques↗
FRET study of a trifluorophore-labeled DNAzyme.
A fluorescence resonance energy transfer (FRET) study of biomolecules typically employs two fluorophores. The increasing number of branches and complexity of biomolecules call for simultaneously monitoring structures and dynamics of several branches in a single system. Furthermore, despite recent studies that show DNAzymes can be a stable and cost-effective alternative to protein and ribozymes for pharmaceutical and biotechnological applications, no FRET study of DNAzymes has been reported. Here, we describe the FRET study of a trifluorophore-labeled "8-17" DNAzyme, in which each of the three branches is labeled with a different fluorophore. From the study, we found that the (ratio)(A) method that has been commonly used in dual-fluorophore-labeled systems is also applicable to trifluorophore-labeled systems. However, while both FRET efficiency and fluorophore-to-fluorophore distance can be used to measure FRET in dual-fluorophore-labeled systems, only the average distance should be used in trifluorophore-labeled systems. The ability to monitor all three branches in a single system allowed us to reveal new metal-ion-dependent conformational changes in the DNAzyme. The trifluorophore-labeled "8-17" DNAzyme has been found to adopt a two-step folding process in the presence of Zn(2+). Each step is induced by one Zn(2+) binding, with apparent dissociation constants of 19 microM and 260 microM for binding the first and second Zn(2+), respectively. The trifluorophore FRET results are verified by a dual-labeled control experiment. The results demonstrated that the trifluorophore-labeled system is simple and yet powerful in studying complicated biomolecular structure and dynamics and is capable of revealing new sophisticated structural changes that may have functional implications.
DNA, Catalytic↗