Improving Fluorescent DNAzyme Biosensors by Combining Inter- and Intramolecular Quenchers

Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity

The catalytic beacon has emerged as a general platform for sensing metal ions and organic molecules. However, few reports have taken advantage of the true potential of catalytic beacons in signal amplification through multiple enzymatic turnovers, as existing designs require either equal concentrations of substrate and DNAzyme or an excess of DNAzyme in order to maintain efficient quenching, eliminating the excess of substrate necessary for multiple turnovers. On the basis of the large difference in the melting temperatures between the intramolecular molecular beacon stem and intermolecular products of identical sequences, we here report a general strategy of catalytic and molecular beacon (CAMB) that combines the advantages of the molecular beacon for highly efficient quenching with the catalytic beacon for amplified sensing through enzymatic turnovers. Such a CAMB design allows detection of metal ions such as Pb(2+) with a high sensitivity (LOD = 600 pM). Furthermore, the aptamer sequence has been introduced into DNAzyme to use the modified CAMB for amplified sensing of adenosine with similar high sensitivity. These results together demonstrate that CAMB provides a general platform for amplified detection of a wide range of targets.

A highly selective lead sensor based on a classic lead DNAzyme

A catalytic beacon sensor for Pb(2+) has been developed based on the first DNAzyme discovered in the field, and such a sensor has shown a much higher metal ion selectivity (40,000 times) than the previously reported Pb(2+) sensor based on 8-17 DNAzyme and thus is suitable for a wider range of practical applications.

Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb(2+) and adenosine with high sensitivity, selectivity, and tunable dynamic range

An abasic site called dSpacer has been introduced into duplex regions of the 8-17 DNAzyme and adenosine aptamer for label-free fluorescent detection of Pb(2+) and adenosine, respectively. The dSpacer can bind an extrinsic fluorescent compound, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), and quench its fluorescence. Addition of Pb(2+) enables the DNAzyme to cleave its substrate and release ATMND from DNA duplex, recovering the fluorescence of ATMND. Similarly, the presence of adenosine induces structural switching of the aptamer, resulting in the release of ATMND from the DNA duplex and a subsequent fluorescence enhancement. Under optimized conditions, this label-free method exhibits detection limits of 4 nM for Pb(2+) and 3.4 muM for adenosine, which are even lower than those of the corresponding labeled-DNAzyme and aptamer sensors. These low detection limits have been obtained without compromising any of the selectivity of the sensors. Finally, the dynamic range of the adenosine sensor has been tuned by varying the number of hybridized base-pairs in the aptamer duplex. The method demonstrated here can be applied for label-free detection and quantification of a broad range of analytes using other DNAzymes and aptamers.

Characterization of an RNA-cleaving deoxyribozyme with optimal activity at pH 5

An in vitro selection endeavor previously executed by our laboratory led to the isolation of a set of RNA-cleaving deoxyribozymes that thrive under acidic conditions [Liu, Z., Mei, S. H., Brennan, J. D., and Li, Y. (2003) J. Am. Chem. Soc. 125, 7539-7545]. One of these sequences, coined pH5DZ1, is a 100-nucleotide (nt) cis-acting enzyme that was found to exhibit high cleavage activity near pH 5. Herein, we seek to deduce the properties and sequence requirements of this enzyme. This deoxyribozyme was found to cleave a 23-nt chimeric DNA-RNA substrate, which contains a single ribonucleotide flanked by fluorophore- and quencher-modified nucleotides on each side of the cleavage junction. Extensive nucleotide deletion experiments indicated that only 42 bases within the original enzyme sequence are required for catalysis. Results from a reselection experiment further revealed that 26 of these nucleotides are absolutely conserved. In addition to sequence analysis and minimization studies, we successfully designed a trans-acting variant of this enzyme. Characterization of the cleavage products produced upon pH5DZ1-mediated RNA cleavage and analyses of possible structures of pH5DZ1 provided us with insights into the catalytic mechanism of pH5DZ1 and characteristics of deoxyribozymes that retain their activity under acidic conditions.

DNAzyme catalytic beacon sensors that resist temperature-dependent variations

The temperature-dependent variability of a Pb2+-specific 8-17E DNAzyme catalytic beacon sensor has been addressed through the introduction of mismatches in the DNAzyme, and the resulting sensors resist temperature-dependent variations from 4 to 30 degrees C.

Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: a paradigm for DNA sensors and aptasensors

The activation of a DNAzyme cascade by the cooperative self-assembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1. The resulting supramolecular nucleic acid structure includes the Mg(2+)-dependent DNAzyme that cleaves the ribonucleobase site of 4. The cleavage of the quasi-circular DNA 4 results in the fragmentation of the supramolecular structure and the release of two horseradish peroxidase (HRP) mimicking units that were incorporated in the blocked quasi-circular DNA 4. The HRP-mimicking DNAzyme catalyzed the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS(2-)) by H(2)O(2) to ABTS(*-), and the product provided the colorimetric readout signal for the analyzed DNA. The method enabled the analysis of DNA with a detection limit of 1 x 10(-12) M. Similarly, an analogous DNAzyme cascade was activated by the low-molecular-weight substrates, adenosine triphosphate (ATP) or cocaine. This was induced by the self-assembly of nucleic acids that included fragments of the respective aptamers and the Mg(2+)-dependent DNAzyme. Furthermore, nucleic acids consisting of fragments of the aptamers against ATP or cocaine and fragments of the HRP-mimicking DNAzyme self-assemble, in the presence of the respective substrates, to the active DNAzyme structure that catalyzes the oxidation of ABTS(2-) by H(2)O(2) to form the colored product ABTS(*-). The resulting product provided the readout signal for the recognition events. The cooperative interaction in the formation of the supramolecular nucleic acid assemblies and the activation of the DNAzymes are discussed.

Probing metal binding in the 8-17 DNAzyme by TbIII luminescence spectroscopy

Metal-dependent cleavage activities of the 8-17 DNAzyme were found to be inhibited by Tb(III) ions, and the apparent inhibition constant in the presence of 100 microM of Zn(II) was measured to be 3.3+/-0.3 microM. The apparent inhibition constants increased linearly with increasing Zn(II) concentration, and the inhibition effect could be fully rescued with addition of active metal ions, indicating that Tb(III) is a competitive inhibitor and that the effect is completely reversible. The sensitized Tb(III) luminescence at 543 nm was dramatically enhanced when Tb(III) was added to the DNAzyme-substrate complex. With an inactive DNAzyme in which the GT wobble pair was replaced with a GC Watson-Crick base pair, the luminescence enhancement was slightly decreased. In addition, when the DNAzyme strand was replaced with a complete complementary strand to the substrate, no significant luminescence enhancement was observed. These observations suggest that Tb(III) may bind to an unpaired region of the DNAzyme, with the GT wobble pair playing a role. Luminescence lifetime measurements in D(2)O and H(2)O suggested that Tb(III) bound to DNAzyme is coordinated by 6.7+/-0.2 water molecules and two or three functional groups from the DNAzyme. Divalent metal ions competed for the Tb(III) binding site(s) in the order Co(II)>Zn(II)>Mn(II)>Pb(II)>Ca(II) approximately Mg(II). This order closely follows the order of DNAzyme activity, with the exception of Pb(II). These results indicate that Pb(II), the most active metal ion, competes for Tb(III) binding differently from other metal ions such as Zn(II), suggesting that Pb(II) may bind to a different site from that for the other metal ions including Zn(II) and Tb(III).

Highly sensitive and selective colorimetric sensors for uranyl (UO2(2+)): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems

Colorimetric uranium sensors based on uranyl (UO2(2+)) specific DNAzyme and gold nanoparticles (AuNP) have been developed and demonstrated using both labeled and label-free methods. In the labeled method, a uranyl-specific DNAzyme was attached to AuNP, forming purple aggregates. The presence of uranyl induced disassembly of the DNAzyme functionalized AuNP aggregates, resulting in red individual AuNPs. Once assembled, such a "turn-on" sensor is highly stable, works in a single step at room temperature, and has a detection limit of 50 nM after 30 min of reaction time. The label-free method, on the other hand, utilizes the different adsorption properties of single-stranded and double-stranded DNA on AuNPs, which affects the stability of AuNPs in the presence of NaCl. The presence of uranyl resulted in cleavage of substrate by DNAzyme, releasing a single stranded DNA that can be adsorbed on AuNPs and protect them from aggregation. Taking advantage of this phenomenon, a "turn-off" sensor was developed, which is easy to control through reaction quenching and has 1 nM detection limit after 6 min of reaction at room temperature. Both sensors have excellent selectivity over other metal ions and have detection limits below the maximum contamination level of 130 nM for UO2(2+) in drinking water defined by the U.S. Environmental Protection Agency (EPA). This study represents the first direct systematic comparison of these two types of sensor methods using the same DNAzyme and AuNPs, making it possible to reveal advantages, disadvantages, versatility, limitations, and potential applications of each method. The results obtained not only allow practical sensing application for uranyl but also serve as a guide for choosing different methods for designing colorimetric sensors for other targets.

Highly sensitive "turn-on" fluorescent sensor for Hg2+ in aqueous solution based on structure-switching DNA

A simple design of "turn-on" fluorescent sensor for mercury was demonstrated based on structure-switching DNA with a low detection limit of 3.2 nM and high selectivity.

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.

DNAzyme-based colorimetric sensing of lead (Pb(2+)) using unmodified gold nanoparticle probes

Novel functional oligonucleotides, especially DNAzymes with RNA-cleavage activity, have been intensively studied due to their potential applications in therapeutics and sensors. Taking advantage of the high specificity of 17E DNAzyme for Pb(2+), highly sensitive and selective fluorescent, electrochemical and colorimetric sensors have been developed for Pb(2+). In this work, we report a simple, sensitive and label-free 17E DNAzyme-based sensor for Pb(2+) detection using unmodified gold nanoparticles (GNPs) based on the fact that unfolded single-stranded DNA could be adsorbed on the citrate protected GNPs while double-stranded DNA could not. By our method the substrate cleavage by the 17E DNAzyme in the presence of Pb(2+) could be monitored by color change of GNPs, thereby Pb(2+) detection was realized. The detection of Pb(2+) could be realized within 20 min, with a detection limit of 500 nM. The selectivity of our sensor has been investigated by challenging the sensing system with other divalent metal ions. Since common steps such as modification and separation could be successfully avoided, the sensor developed here could provide a simple, cost-effective yet rapid and sensitive measurement tool for Pb(2+) detection and may prove useful in the development of sensors for clinical toxicology and environmental monitoring in the future.

Recent advances in DNA catalysis

Studies of catalytically active DNA sequences have expanded considerably since the first artificial deoxyribozyme was identified in 1994. Nevertheless, the field is still quite young, and advances in both fundamental understanding and practical applications of deoxyribozymes are still developing. Deoxyribozymes that either cleave or ligate two RNA substrates have been most widely investigated, and this review describes recent advances in the fundamental studies and applications of these DNA enzymes. Deoxyribozymes with catalytic activities other than RNA ligation and cleavage are also increasingly pursued, and this review covers several key examples.

Simple fluorescent sensors engineered with catalytic DNA 'MgZ' based on a non-classic allosteric design

Most NAE (nucleic acid enzyme) sensors are composed of an RNA-cleaving catalytic motif and an aptameric receptor. They operate by activating or repressing the catalytic activity of a relevant NAE through the conformational change in the aptamer upon target binding. To transduce a molecular recognition event to a fluorescence signal, a fluorophore-quencher pair is attached to opposite ends of the RNA substrate such that when the NAE cleaves the substrate, an increased level of fluorescence can be generated. However, almost all NAE sensors to date harbor either NAEs that cannot accommodate a fluorophore-quencher pair near the cleavage site or those that can accept such a modification but require divalent transition metal ions for catalysis. Therefore, the signaling magnitude and the versatility of current NAE sensors might not suffice for analytical and biological applications. Here we report an RNA-cleaving DNA enzyme, termed ‘MgZ’, which depends on Mg²⁺ for its activity and can accommodate bulky dye moieties next to the cleavage site. MgZ was created by in vitro selection. The selection scheme entailed acidic buffering and ethanol-based reaction stoppage to remove selfish DNAs. Characterization of MgZ revealed a three-way junction structure, a cleavage rate of 1 min⁻¹, and 26-fold fluorescence enhancement. Two ligand-responsive NAE sensors were rationally designed by linking an aptamer sequence to the substrate of MgZ. In the absence of the target, the aptamer-linked substrate is locked into a conformation that prohibits MgZ from accessing the substrate. In the presence of the target, the aptamer releases the substrate, which induces MgZ-mediated RNA cleavage. The discovery of MgZ and the introduction of the above NAE sensor design strategy should facilitate future efforts in sensor engineering.

Dissecting metal ion-dependent folding and catalysis of a single DNAzyme

Protein metalloenzymes use various modes for functions for which metal-dependent global conformational change is required in some cases but not in others. In contrast, most ribozymes require a global folding that almost always precedes enzyme reactions. Herein we studied metal-dependent folding and cleavage activity of the 8-17 DNAzyme using single-molecule fluorescence resonance energy transfer. Addition of Zn2+ and Mg2+ induced folding of the DNAzyme into a more compact structure followed by a cleavage reaction, which suggests that the DNAzyme may require metal-dependent global folding for activation. In the presence of Pb2+, however, the cleavage reaction occurred without a precedent folding step, which suggests that the DNAzyme may be prearranged to accept Pb2+ for the activity. Neither ligation reaction of the cleaved substrates nor dynamic changes between folded and unfolded states was observed. These features may contribute to the unusually fast Pb2+-dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use.

Metal-Dependent Global Folding and Activity of the 8-17 DNAzyme Studied by Fluorescence Resonance Energy Transfer

The 8-17 DNAzyme is a DNA metalloenzyme catalyzing RNA transesterification in the presence of divalent metal ions, with activity following the order Pb2+ >> Zn2+ >>Mg2+. Since the DNAzyme has been used as a metal ion sensor, its metal-induced global folding was studied by fluorescence resonance energy transfer (FRET) by labeling the three stems of the DNAzyme with the Cy3/Cy5 FRET pair two stems at a time in order to gain deeper insight into the role of different metal ions in its structure and function. FRET results indicated that, in the presence of Zn2+ and Mg2+, the DNAzyme folds into a compact structure, stem III approaching a configuration defined by stems I and II without changing the angle between stems I and II. Correlations between metal-induced folding and activity were also studied. For Zn2+ and Mg2+, the metal ion with higher affinity for the DNAzyme in global folding (Kd(Zn) = 52.6 microM and Kd(Mg) = 1.36 mM) also displays higher affinity in activity (Kd(Zn) = 1.15 mM and Kd(Mg) = 53 mM) under the same conditions. Global folding was saturated at much lower concentrations of Zn2+ and Mg2+ than the cleavage activities, indicating the global folding of the DNAzyme occurs before the cleavage activity for those metal ions. Surprisingly, no Pb2+-dependent global folding was observed. These results suggest that for Pb2+ global folding of the DNAzyme may not be a necessary step in its function, which may contribute to the DNAzyme having the highest activity in the presence of Pb2+.

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

Here, we report a catalytic beacon sensor for uranyl (UO2(2+)) based on an in vitro-selected UO2(2+)-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 UO2(2+) 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 approximately 230 microM. 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.

Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates

RNA-cleaving deoxyribozyme 8-17 has been increasingly used in nanotechnology and biosensing applications. Conventional methods to equip 8-17 with fluorescent signaling property usually involve covalent attachment of two dyes at nucleotide positions that are far away from the catalytic core, such that the bulky dye structures would not affect the deoxyribozyme activity. However, the maximum fluorescent enhancement associated with these 8-17 constructs is typically ≤10-fold, due to a high fluorescent background. To find an optimal balance between signal enhancement and signaling speed, we have conducted a comprehensive study on the effects of the nature of dyes (Alexa Fluor 488, 546 and 647; QSY 9 and 21) as well as their attaching positions along the substrate strand on the catalytic and signaling performance of 8-17. Our results have indicated that 8-17 is able to cleave almost every modified substrate, including those that have chromophores only 1 nt away from the cleavage site. Most importantly, almost all of these substrates are able to generate 15- to 85-fold signal enhancement within 10 min. We have also provided guidelines for selecting substrates that could offer the best signal enhancement, the fastest signaling speed, or the best balance between signal enhancement and signaling speed.

Materials for Fluorescence Resonance Energy Transfer Analysis: Beyond Traditional Donor–Acceptor Combinations

The use of Förster or fluorescence resonance energy transfer (FRET) as a spectroscopic technique has been in practice for over 50 years. A search of ISI Web of Science with just the acronym "FRET" returns more than 2300 citations from various areas such as structural elucidation of biological molecules and their interactions, in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting and metallic nanomaterials. The advent of new classes of fluorophores including nanocrystals, nanoparticles, polymers, and genetically encoded proteins, in conjunction with ever more sophisticated equipment, has been vital in this development. This review gives a critical overview of the major classes of fluorophore materials that may act as donor, acceptor, or both in a FRET configuration. We focus in particular on the benefits and limitations of these materials and their combinations, as well as the available methods of bioconjugation.

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.

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).

In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

Over the last decade, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in vitro selection from random-sequence DNA pools. This article focuses on deoxyribozymes that cleave RNA substrates. The first DNA enzyme was reported in 1994 and cleaves an RNA linkage. Since that time, many other RNA-cleaving deoxyribozymes have been identified. Most but not all of these deoxyribozymes require a divalent metal ion cofactor such as Mg²⁺ to catalyze attack by a specific RNA 2′-hydroxyl group on the adjacent phosphodiester linkage, forming a 2′,3′-cyclic phosphate and a 5′-hydroxyl group. Several deoxyribozymes that cleave RNA have utility for in vitro RNA biochemistry. Some DNA enzymes have been applied in vivo to degrade mRNAs, and others have been engineered into sensors. The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional applications are developed.

In Vitro Selection of High Temperature Zn2+-Dependent DNAzymes

In vitro selection of Zn(2+)-dependent RNA-cleaving DNAzymes with activity at 90 degrees C has yielded a diverse spool of selected sequences. The RNA cleavage efficiency was found in all cases to be specific for Zn(2+) over Pb(2+), Ca(2+), Cd(2+), Co(2+), Hg(2+), and Mg(2+). The Zn(2+)-dependent activity assay of the most active sequence showed that the DNAzyme possesses an apparent Zn(2+)-binding dissociation constant of 234 muM and that its activity increases with increasing temperatures from 50-90 degrees C. A fit of the Arrhenius plot data gave E(a) = 15.3 kcal mol(-1). Surprisingly, the selected Zn(2+)-dependent DNAzymes showed only a modest (approximately 3-fold) activity enhancement over the background rate of cleavage of random sequences containing a single embedded ribonucleotide within an otherwise DNA oligonucleotide. The result is attributable to the ability of DNA to sustain cleavage activity at high temperature with minimal secondary structure when Zn(2+) is present. Since this effect is highly specific for Zn(2+), this metal ion may play a special role in molecular evolution of nucleic acids at high temperature.

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.

Fluorescent sensing and selective Pb(II) extraction by a dansylamide ion-exchanger

The (bis)dansylated sulfonamide 1,2-C6H4(NHSO2C10H6-5-N(CH3)2)2 (1) extracted Pb(II) selectively from water into 1,2-dichloroethane via an ion-exchange mechanism and showed fluorescence quenching upon Pb(II) extraction. The distribution ratios for metal extraction (determined by ICP-MS) for Pb(II) were 133-1410 times higher than those for other metal cations [Co(II), Ni(II), Cu(II), Zn(II), and Cd(II)] under identical conditions. Fluorescence quenching was observed upon Pb(II) extraction, which was dependent on Pb(II) concentration. The monodansylated control, C6H5NHSO2C10H6-5-N(CH3)2 (2), showed neither extraction nor quenching, indicating that the fluorescence effects are a direct result of Pb coordination to 1. The observed selectivity for Pb(II) is ascribed to the formation of a low-coordinate binary Pb(II)-Sulfonamido complex in the organic phase.