# Patent

## Title
Nucleic acid based fluorescent sensor for copper detection

## Abstract

A nucleic acid enzyme responsive to copper, comprising an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1, wherein the nucleic acid enzyme is not self-cleaving.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority to provisional application No. 60/950,062, entitled “NUCLEIC ACID BASED FLUORESCENT SENSOR FOR COPPER DETECTION” filed Jul. 16, 2007, the entire contents of which are hereby incorporated by reference, except where inconsistent with the present application.


FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This subject matter of this application may have been funded in part under the following research grants and contracts: National Science Foundation Contract Numbers CTS-0120978 and DMI-0328162, and U.S. Department of Energy Contract Number DE-FG02-01-ER63179. The U.S. Government may have rights in this invention.


BACKGROUND
Design of fluorescent metal sensors has recently become one of the most active research areas because the sensors can provide in situ and real-time information for a number of applications including environment monitoring, industrial process control, metalloneurochemistry, and biomedical diagnostics.1 A widely used strategy is to link the metal recognition portion closely with a signal generation moiety such as a fluorophore. While quite successful in designing sensors for diamagnetic metal ions such as Pb2+, Hg2+, Zn2+ and Cu+,2 this method has been applied to paramagnetic metal ions such as Cu2+ with only limited success, due to their intrinsic fluorescence quenching properties.3,4 Most Cu2+ sensors showed decreased emission upon Cu2+ binding,3 which was undesirable for analytical purposes. First, the room for signal change was at most one-fold. Second, such “turn-off” sensors may give false positive results by quenchers in real samples. Among the reported “turn-on” Cu2+ sensors,4 few have nanomolar sensitivity,4a,d,f,g with high selectivity,4a,d and are free of organic solvents.4a 
One way to circumvent this quenching problem is to spatially separate the metal recognition part from the fluorescent signaling moiety so that they are independent of each other. A significant challenge then is to transduce metal binding to signal enhancement when the two parts are well separated. Previously reported was a novel metal sensing platform with DNAzyme catalytic beacons that spatially separated the two parts by rigid double-stranded DNA,5,6 and sensors for diamagnetic metal ions such as Pb2+ and UO22+ have been demonstrated.7,8 
Copper is a widely used metal that can leak into the environment through various routes. Low concentration copper is an essential nutrient. However, exposure to high level of copper even for a short period of time can cause gastrointestinal disturbance; while long term exposure causes liver or kidney damage.9 The U.S. Environmental Protection Agency (EPA) set the limit of copper in drinking water to be 1.3 ppm ( ̃20 μM).
SUMMARY
In a first aspect, the present invention is a nucleic acid enzyme responsive to copper, comprising an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1. The nucleic acid enzyme is not self-cleaving.
In a second aspect, the present invention is a nucleic acid enzyme responsive to copper, comprising: an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1, and a quencher, attached at a 3′ end of the nucleic acid enzyme.
In a third aspect, the present invention is a sensor system for determining an amount of copper in a sample, comprising a nucleic acid enzyme responsive to copper, a substrate for the nucleic acid enzyme, a quencher attached to the substrate, and a fluorophore, attached to the substrate.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. (A) The secondary structure of the Cu2+ sensor DNAzyme. F and Q denote fluorophore and quencher, respectively. The cleavage site is indicated by an arrow. Top strand is shown in SEQ ID NO: 6, bottom strand in SEQ ID NO: 5. (B) Signal generation scheme of the Cu2+ catalytic beacon. (C) Fluorescence spectra of the sensor before and 10 min after addition of 20 μM Cu2+.
FIG. 2. (A) Kinetics of fluorescence increase over background at varying Cu2+ levels. The arrow indicates the point of Cu2+ addition. Inset: responses at low Cu2+ levels. (B) The rate of fluorescence enhancement plotted against Cu2+concentration. Inset: rates at the low Cu2+ region. (C) Sensor selectivity. The buffer contained 1.5 M NaCl, 50 mM HEPES, pH 7.0, and 50 μM ascorbate. Cu2+ concentrations were labeled on the left side of each well while others were on the right end (in μM).
FIG. 3. Responses of a DNAzyme sensor array to metal mixtures.
FIG. 4. Sequences and modifications of the DNAzyme-based UO22+ and Pb2+ sensors. In both sensors, the 5′-F denotes a FAM fluorophore. The 3′-Q on the substrate strands denotes a Black Hole Quencher. The 3′-Q on the enzyme strands denotes for a Black Hole Quencher and a Dabcyl for the UO22+ sensor and the Pb2+ sensor, respectively. Top strand of the UO22+sensor is shown in SEQ ID NO: 9, bottom strand in SEQ ID NO: 10 and the top strand of the Pb2+sensor is shown in SEQ ID NO: 11, bottom strand in SEQ ID NO: 12.
FIG. 5. Gel-based assay of the sensor DNAzyme. Lanes 2 to 5 are 0, 5, 10, and 25 min after addition of Cu2+, respectively.
FIG. 6. The effect of enzyme to substrate ratio on signal enhancement. The Cu2+ concentration was 4 μM and the experiments were performed in parallel to have a fair comparison. Other conditions are the same as previously described.
FIG. 7. Gel-based assay on Fe2+ and UO22+ cleavage of the Cu2+ sensor DNAzyme.
FIG. 8. Kinetics of the Cu2+ sensor fluorescence enhancement in the presence of 1 μM Cu2+ or varying concentrations of Fe2+.
FIG. 9. Gel-based assay on Fe3+ cleavage of the Cu2+ sensor DNAzyme.
FIG. 10. Kinetics of the Cu2+ sensor fluorescence enhancement in the presence of varying concentrations of Fe3+.
FIG. 11. Stern-Volmer plot of a FAM-labeled double stranded DNA quenched by Cu2+. The DNA concentration was 10 nM for the FAM-labeled DNA and 20 nM for its complementary DNA strand (annealed in the same buffer as Cu2+detection). The sequence of the 5′-FAM labeled 20-mer DNA was: FAM-5′-ACTCACTATAGGAAGAGATG-3′ (SEQ ID NO: 8).
FIG. 12. Comparing Cu2+ and Cu+ and the effect of ascorbate on the rate of cleavage of the DNAzyme.
FIG. 13. The effect of anions in the sensor system. Dash curves are the kinetics with varying concentration of NaCl (Cu2+ added at the time indicated by the arrow) and the solid curve is the background fluorescence with NaNO3 (no Cu2+ added). For all the samples with NaCl, the background levels were stable. For the sample with NaNO3, however, the background was not stabilized (no Cu2+ added for the curve). Therefore, NaCl was used in the sensor system.



DETAILED DESCRIPTION
The present invention makes use of the discovery of a new nucleic acid enzyme, which may be used in a sensor system for Cu, and in a method of determining the concentration of copper in a sample, especially in the presence of other ions. The sequence of the nucleic acid enzyme is indicated in the table below, along a specific example of the nucleic acid enzyme, the substrate for the enzyme, and an example of the substrate. For comparison, the DNAzyme of Breaker et al. and the substrate for this DNAzyme are also included in the table. R, Y and n represent purine, pyrimidine and any nucleotide, respectively. X, X′ and X′′ each indicate an optional spacer, F indicates a fluorophore, and Q indicates a quencher. In the table, m is at least 7, u is 0 or 1, w is 0 to 3, y is 0 or 1, and z is 0 or 1.














Nucleic acid
3′ CAR RRR RRR Rnn
SEQ ID 


enzyme for
nYY YYY YYY CCG GGT
NO: 1


copper (consensuS
Cnn nnn nn 5′



sequences)




 


Nucleic acid
3′ CAR RRR RRR Rnn
SEQ ID 


enzyme for copper
nYY YYY YYY CCG GGT
NO: 2



Cnm 5′



 


Nucleic acid
3′ CAR RRR RRR Rnn
SEQ ID 


enzyme for copper,
nYY YYY YYY CCG GGT
NO: 3


with quencher
CnmXz-Q 5′



 


Substrate for nucleic 
3′ F-X′ynmG CAT AAY
SEQ ID 


acid enzyme,
YYY YYY Ynw-X′′u-Q
NO: 4


with fluorophore




and quencher.




 


Example of
3′ CAA GAA AGA ATT
SEQ ID 


nucleic acid
TTT CTT TCT CCG GGT
NO: 5


enzyme
CCG AAT GG-Q 5′



 


Example of substrate 
3′ F-CCA TTC GGC ATA
SEQ ID 


for nucleic acid
ATC TTT CTT CGA-Q 5′
NO: 6


 enzyme




 


Self cleaving Breaker
3′ CAA GAA TTT TTC
SEQ ID 


et al. nucleic acid
TCC GGG TCT GAG TAA
NO: 7


enzyme and substrate
GAC TCA GCA TAA TCT




TAA G 5′









X, X′ and X′′ each indicate an optional spacer. The spacer is preferably an organic group, such as an alkanene, alkenene, alkynene, arylene, polyether, peptide, oligonucleotide, or combinations thereof. Examples include the following:




The subscript m is at least 7, and preferably is 7 to 100, more preferably 7 to 50, even preferably 7 to 20, and most preferably 7 to 15.
F indicates a fluorophore, and Q indicates a quencher. Essentially any fluorophore may be used, including BODIPY, fluoroscein, fluoroscein substitutes (Alexa Fluor dye, Oregon green dye), long wavelength dyes, and UV-excited fluorophores. These and additional fluorophores are listed in Fluorescent and Luminescent Probes for Biological Activity. A Practical Guide to Technology for Quantitative Real-Time Analysis, Second Ed. W. T. Mason, ed. Academic Press (1999)16. In preferred embodiments, the fluorophore is 6-carboxyfluorescein (FAM). FAM has an excitation range of 460-500 nm.
Other fluorophores included quantum dots and silica nanoparticles. Each type of quantum dot displays a unique emission wavelength. Preferred quantum dot particles include quantum dot semiconductors, such as CdS, CdSe, CdTe, ZnS, ZnSe, ZnTe, Pln, and PbSe. Additional preferred quantum dots may include ternary quantum dots, such as CdxZn1-xSe or CdSxSe1-x. Additional preferred quantum dots may include core-shell quantum dots, such as those having a CdSe core and ZnS shell. The quantum dots can also have different morphologies, including dots, rods, tetrapods, and the like. In a preferred aspect, the particles are quantum dot semiconductors having average diameter from 2 to 50 nanometers.
A quencher is a molecule that absorbs the energy of the excited fluorophore. Close proximity of a fluorophore and a quencher allow for the energy to be transferred from the fluorophore to the quencher. By absorbing this energy, the quencher prevents the fluorophore from releasing the energy in the form of a photon, thereby preventing fluorescence.
Quenchers may be categorized as non-fluorescent and fluorescent quenchers. Non-fluorescent quenchers are capable of quenching the fluorescence of a wide variety of fluorophores. Generally, non-fluorescent quenchers absorb energy from the fluorophore and release the energy as heat. Examples of non-fluorescent quenchers include 4-(4′-dimethylaminophenylazo)benzoic acid) (Dabcyl), QSY-7, and QSY-33.
Fluorescent quenchers tend to be specific to fluorophores that emit at a specific wavelength range. Fluorescent quenchers often involve fluorescence resonance energy transfer (FRET). In many instances the fluorescent quencher molecule is also a fluorophore. In such cases, close proximity of the fluorophore and fluorescent quencher is indicated by a decrease in fluorescence of the “fluorophore” and an increase in fluorescence of the fluorescent quencher. Commonly used fluorescent fluorophore pairs (fluorophore/fluorescent quencher) include fluorescein/tetramethylrhodamine, IAEDANS/fluorescein, fluorescein/fluorescein, and BODIPY FL/BODIPY FL.
When choosing a fluorophore, a quencher, or where to position these molecules, it is important to consider, and preferably to test, the effect of the fluorophore or quencher on the enzymatic activity of the nucleic acid enzyme. Also, it is preferable that the fluorophore display a high quantum yield and energy transfer efficiency. Long-wavelength (excitation and emission) fluorophores are preferred because of less interference from other absorbing species. The fluorophore should also be less sensitive to pH change or to non-specific quenching by metal ions or other species.
Methods and devices for detecting fluorescence are well developed. Essentially any instrument or method for detecting fluorescent emissions may be used. For example, WO 99/27351 describes a monolithic bioelectrical device comprising a bioreporter and an optical application specific integrated circuit (OASIC).17 The device allows remote sampling for the presence of substances in solution. Furthermore, the fluorescence may be measured by a number of different modes. Examples include fluorescence intensity, lifetime, and anisotropy in either steady state or kinetic rate change modes.18 
Sometimes other factors in a solution such as pH, salt concentration or ionic strength, or viscosity will have an effect on fluorescence, and may even affect the hybridization of the substrate and enzyme. Therefore, in preferred methods, controls are run to determine if the solution itself, regardless of enzymatic activity, is altering the fluorescence. Such controls include the use of non-cleavable substrates and or substrate without the presence of enzyme.
The sensor system may be used to determine an amount of copper in a sample, such as a water sample, a biological sample (such as blood or serum), or a solid sample, such as soil or paint. Preferably, a solid sample is first dissolved into solution. The samples may be diluted or concentrated prior to testing, and may also be buffered. The sensor system is able to determine an amount of copper in the presence of other ions, preferably other metal ions, such as Pb2, or in the presence of other transition metal ions.
The sensor system may also contained ascorbate, because it can significantly enhance the reaction rate. The sensor will operate without ascorbate, but preferably ascorbate is included. Another difference, as compared to prior sensor systems, such as those used to detect Pb2+, is that the substrate does not require a ribonucleotide as a condition for cleavage; the mechanism of the nucleic acid enzyme responsive to copper is oxidative, while previous sensors cleaved substrates by hydrolysis.
A Cu2+-dependent DNA-cleaving DNAzyme reported by Breaker et al. is know and has a reported consensus sequence; the sequence of the self-cleaving DNAzyme is included in the table.10-12 Based on the original DNAzyme sequences, we rationally designed a Cu2+ sensor as shown in FIG. 1A. The sensor contained two DNA strands that formed a complex. The substrate (Cu_sub) was labeled with a FAM fluorophore (6-carboxyfluorescein) on the 3′-end, and a quencher (Iowa Black FQ) on the 5′-end; while the enzyme (Cu_enzyme) contained a 5′-quencher. Such a dual-quencher approach was employed to suppress background signals.13 The substrate and enzyme associate through two base pairing regions. The 5′ portion of the enzyme binds the substrate via Watson-Crick base pairs; while the 3′ region through formation of a DNA triplex. Initially, the FAM emission was quenched by the nearby quenchers. In the presence of Cu2+, the substrate was irreversibly cleaved at the cleavage site (the guanine indicated by the arrow). Following cleavage, it has been hypothesized that the cleaved pieces were released due to decreased affinities to the enzyme, leading to increased fluorescence (FIG. 1B). This hypothesis was supported by the observation that the FAM emission increased by  ̃13-fold after addition of Cu2+ (FIG. 1C). Such a signal generation method was termed catalytic beacon because the involvement of catalytic reactions.7,8 
The sensor system also contained 50 μM ascorbate, because it can significantly enhance the reaction rate (FIG. 12).10-12 Ascorbate was also useful for suppressing quenching. For example, FAM quenching was <15% with 50 μM Cu2+ (FIG. 11).
To test sensitivity, the kinetics of fluorescence increase at 520 nm in the presence of varying concentrations of Cu2+ were monitored. As shown in FIG. 2A, fluorescence enhancement rates were higher with increasing levels of Cu2+. The rates in the time window of 2 to 4 min were plotted in FIG. 2B. A detection limit of 35 nM (2.3 ppb) was determined, which represents one of the most sensitive “turn-on” Cu2+ sensors.4a,d,f,g The sensor has a dynamic range up to 20 μM, which is useful for detecting Cu2+ in drinking water, because the U.S. EPA has defined a maximum contamination level of 20 μM. In addition to being highly sensitive and possessing “turn-on” signals, the sensor response was also fast, and quantitative results can be obtained within several minutes.
To test selectivity, 16 competing metal ions were assayed at three concentrations: 1 mM, 100 μM, and 10 μM. The assay was performed in a 96-well plate and emission intensities at 12-min after addition of metal ions were compared. As shown in FIG. 2C, besides Cu2+, only the spots with 1 mM Fe2+ and 1 mM UO22+ lit up and the intensities were lower than that with 0.5 μM of Cu2+. Therefore, the sensor selectivity for Cu2+ was at least 2,000-fold higher than these two metals, and >10,000-fold higher than any other tested metal ions. The relatively high selectivity of Cu2+ over paramagnetic Fe2+ may be due to either lack of DNAzyme recognition of Fe2+ as the DNAzyme was in vitro selected for Cu2+,11,12 or lack of H2O2 in the sensor solution that is needed for Fe2+ to go through the Fenton chemistry for DNA cleavage.14 In gel-based assays, UO22+ did not produce well-defined cleavage bands (FIG. 7). Therefore, the increased emission by UO22+ was attributed to DNA denaturation, although minor oxidative cleavage cannot be ruled out.15 Cu+ is unstable in water and Cu+ was tested using [Cu(MeCN)4](PF6) in acetonitrile as a metal source. With ascorbate, the rate of fluorescence increase was similar to that with Cu2+ (FIG. 12). In the absence of ascorbate, both Cu2+ and Cu+ can induce fluorescence increase, with the rate with Cu+ being much faster. Therefore, it is likely that Cu2+ was reduced by ascorbate to Cu+, which subsequently reacted with oxygen to oxidatively cleave DNA. Ag+ was not tested because the reaction buffer contained 1.5 M NaCl, which can form insoluble AgCl. Au+ was not tested because it is unstable in the open air aqueous solution. For testing environment samples, such as detection of Cu2+ in drinking water, Cu+ or Fe2+ is unlikely to interfere due to the oxidative aqueous environment. UO22+ is also unlikely to be present in millimolar concentration in drinking water. Fe3+ with ascorbate can also cleave the DNAzyme. However, little fluorescence increase was observed due to the slow reaction rate and the quenching effect of Fe3+ (FIGS. 9 and 10). It needs to be pointed out that the previously reported lead and uranium sensors were based on hydrolytic RNA cleavage.7,8 In the current copper DNAzyme, the substrate was made completely of DNA and the cleavage was oxidative.10 
Finally, a sensor array as shown in FIG. 3 was constructed. The array contained three rows and each row was loaded with a different DNAzyme-based sensor. Eight metal mixtures were prepared with all the possible combinations among Cu2+, Pb2+ and UO22+ (1 μM each). As can be observed from FIG. 3, the wells lit up only when the cognate metals were present and the metal compositions can be read directly from the array. We can imagine that larger metal sensor arrays can be built with the isolation of more metal-specific DNAzymes.5 
EXPERIMENTAL DETAILS
Sensor preparation: in a typical experiment, 1 μM of Cu_Sub and 2 μM of Cu_Enzyme (see FIG. 1A in the paper for DNA sequences and modifications) were prepared in a buffer of 200 μL volume containing 1.5 M NaCl, 50 mM HEPES, pH 7.0. The reason for using excess amount of the enzyme strand is given in FIG. 6. The mixture was warmed to 80° C. for 1 min and allowed to cool naturally to room temperature in 1 hour to anneal the DNAzyme. For each test, the annealed DNAzyme sensor (5 μL) was diluted into 490 μL of buffer (1.5 M NaCl, 50 mM HEPES, pH 7.0) in a quartz cuvette with 0.5 cm path length on each side, and 5 μL of 5 mM ascorbate was also added. The final Cu_Sub concentration was 10 nM, the final Cu_Enzyme concentration was 20 nM, and the final ascorbate concentration was 50 μM.
Detection: the above prepared cuvette was vortexed to mix all the reagents and placed into a fluorometer (SPEX Fluoromax-P, Horiba Jobin Yvon). The cuvette was allowed to incubate in the cuvette holder of the fluorometer for 1 min before taking any measurement. The temperature of the fluorometer was set at 23° C. (around room temperature). The fluorometer was set at the kinetics mode by exciting at 490 nm and monitoring emission at 520 nm with 15 sec intervals. After the first 4 readings, the cuvette was quickly taken out and a small volume (0.5 to 3 μL) of concentrated metal stock solutions was added. The cuvette was rapidly vortexed to mix the metal with the sensor, and was then placed back into the fluorometer to continue the kinetics monitoring. The obtained kinetics traces were normalized to the fluorescence intensity before metal addition. The slope of fluorescence increase over background from 1 min to 3 min after Cu2+ addition was calculated and plotted against metal concentration (FIG. 2B).
96-well plate based selectivity assays: 5.4 μL of 100 μM Cu_Sub and 10.8 μL of 100 μM Cu_Enzyme were annealed in 400 μL of buffer (1.5 M NaCl, 50 mM HEPES, pH 7.0). After annealing, the solution was diluted with 5 mL of the same buffer. Ascorbate was added to a final concentration of 50 μM. Therefore, the final Cu_Sub and Cu_Enzyme concentrations were 100 nM and 200 nM, respectively. The sensor solution was spotted into three rows (each row contained 8 wells) of a 96-well-plate with 200 μL in each well. Metal solutions at 2× of designated concentrations were prepared in the same buffer with 50 μL volume and were spotted in the plate. The sensor solution in the wells was taken out with an 8-channel pipet (each channel transferred 50 μL of sensor solution) and added to the metal solutions. At 12 min after mixing, the plate was imaged with a Fuji fluorescence scanner (FLA-3000G, Fuji) by exciting at 473 nm and the filter was set at 520 nm. The metal salts used include: MgCl2, CaCl2, SrCl2, BaCl2, Mn(OAc)2, Fe(NH4)2(SO4)2, FeCl3, CoCl2, NiCl2, Cu(NO3)2, ZnCl2, Cd(ClO4)2, Hg(ClO4)2, Pb(NO3)2, TbCl3, EuCl3, and UO2(OAc)2. Under the reaction condition (pH 7.0, 1.5 M NaCl), Fe(NH4)2(SO4)2 was quickly (within 5 min) oxidized into Fe3+ species and the color of the well turned from colorless to yellow. The well with Fe(NH4)2(SO4)2, FeCl3, Pb(NO3)2, and UO2(OAc)2 formed visible precipitation.
Gel-based assays: 1 μM of Cu_Sub and 2 μM of Cu_Enzyme were annealed in 750 mM NaCl, 25 mM HEPES, pH 7.0. After annealing, 50 μM of ascorbate was also added. Before addition of Cu2+, a 10 μL aliquot was taken out as the zero time point (lane 2 in the inset of FIG. 5). After adding Cu2+, 10 μL aliquots were taken out at designated time points and were quenched in a stop buffer containing 8 M urea, 50 mM EDTA, 0.05% xylene cyanol, and 50 mM Tris acetate, pH 8.2. A sample with only 1 μM Cu_Sub (no Cu_Enzyme), 20 μM Cu2+, and 50 μM ascorbate was also prepared (lane 1 in the inset of FIG. 1C, incubated at room temperature for 1 hour before adding the stop buffer). The samples were loaded into 20% polyacrylamide gel electrophoresis to separate cleaved and uncleaved substrate. The gel was imaged with a fluorescence scanner (FLA-3000G, Fuji) by exciting at 473 nm and setting the emission filter at 520 nm.
Test of Cu2+, Pb2+, and UO22+ DNAzymes: the design of the Pb2+ and UO22+ sensors have been described elsewhere and are also presented here in FIG. 4.7,8,13 The Cu2+ sensor was prepared with a final Cu_Sub concentration of 12 nM and Cu_Enzyme of 24 nM in 1.5 M NaCl, 50 mM HEPES, pH 7.0, 50 μM ascorbate. The Pb2+ sensor was prepared with a final substrate concentration of 6 nM and enzyme concentration of 6 nM in 100 mM NaCl, 25 mM Tris acetate, pH 8.2. The UO22+ sensor was prepared with a final substrate concentration of 200 nM and enzyme concentration of 400 nM in 300 mM NaCl, 50 mM MES, pH 5.5. The three sensors were spotted into three rows of a 96-well plate, respectively, with each row containing 8 wells. Eight metal mixtures were prepared with all the eight possible combinations among Cu2+, Pb2+ and UO22+. The metal concentrations in each mixture were either 0 or 20 μM. 5 μL of each metal mixture was spotted into three wells along the same column but in different rows. 95 μL of sensor was transferred into the wells containing the metal mixture and the reaction was allowed for 10 min at room temperature. The final metal concentration for each metal after mixing with the sensor was either 0 or 1 μM. The plate was imaged with the Fuji fluorescence scanner.
Results of gel-based assays: Gel-based assays were carried out to confirm the cleavage reaction (FIG. 5). Lane 1 contained the substrate alone and Cu2+. Lane 2 had the DNAzyme complex but no Cu2+. Cleavage was observed only after addition of Cu2+ to the DNAzyme complex (lanes 3-5).
The enzyme to substrate ratio in the Cu2+ sensor. The structure of the Cu2+-specific DNAzyme is different from the UO22+ and Pb2+ DNAzymes shown above. One of the substrate binding arms of the Cu2+ DNAzyme contained a DNA triplex. Therefore, the stability of the DNAzyme complex is not as high as that with normal Watson-Crick base pairs. To form stable DNAzyme complex at room temperature, high ionic strength conditions (1.5 M NaCl) were used. With the 1:1 enzyme to substrate ratio, the fluorescence enhancement was only-7-fold in 4 min (FIG. 6, red curve). With a 2:1 enzyme to substrate ratio, the enhancement was −10-fold in 4 min, which was attributed to more complete substrate hybridization. Therefore, we chose a ratio of 2:1 for the Cu2+ sensing experiment. Considering the consumption of materials, further increase of the enzyme was not tested.
Gel-based assay of the Cu2+ sensor in the presence of Fe2+ and UO22+: Since fluorescence enhancement was observed in the presence of 1 mM of Fe2+ or UO22+, gel-based assays were carried out to test whether the fluorescence increase was due to cleavage or due to DNA denature in the presence of high level of metal ions (FIG. 7). All the lanes contained the sensor DNAzyme complex shown in FIG. 1A with 1 μM Cu_Sub and 2 μM Cu_Enzyme. Lane 1 did not have any added metal ion. Lane 2 contained 1 μM Cu2+, lane 3 contained 10 μM Cu2+. Lane 4-6 contained 10, 100, and 1000 μM Fe2+, respectively. Lane 7-9 contained 10, 100, and 1000 μM UO22+, respectively. 1 mM Fe2+ produced clear cleavage products; while no well-defined cleavage bands were observed with 1 mM UO22+. Ascorbate (50 μM) was included in all the lanes.
Quantitative measurement of sensor response to Fe2+: The Cu2+ sensor was titrated with varying concentrations of Fe2+ and the results are presented in FIG. 8. The assay conditions were the same as that used for Cu2+ titration described previously. Only 1 mM Fe2+ showed enhanced fluorescence, which is consistent with the results in 96-well plate based measurements. The sensor response to 1 μM of Cu2+ is also measured for comparison. Based on this data, the selectivity for Cu2+ over Fe2+ is  ̃3000-fold.
Reaction of the Cu2+ sensor in the presence of Fe3+: Fe3+ with ascorbate is commonly used to generate reduced iron species. Therefore, it is surprising that there was no response from this combination in the selectivity experiment (FIG. 2C). To understand the reason behind it, a gel-based assay was carried out as shown in FIG. 9. Lane 1 and 2 contained 50 μM ascorbate. Lane 1 did not contain Cu2+ while lane 2 contained 10 μM Cu2+. These two lanes served as negative and positive controls, respectively. Lanes 3-5 contained 1 mM FeCl3 and 0, 50 μM, and 1 mM ascorbate, respectively. Lanes 6-8 contained 1 mM Fe(NO3)3 and 0, 50 μM, and 1 mM ascorbate, respectively. Cleavage products were observed in lanes 4, 5, 7, and 8. Therefore, Fe3+ with ascorbate can indeed induce cleavage. The reason for the failure to generate fluorescence increase in the selectivity experiment was attributed to the following two reasons. First, the cleavage even with 1 mM Fe3+ in the presence of 50 μM ascorbate (lanes 4 and 7) was very slow. Because only 50 μM ascorbate was used in the sensing experiment, such slow cleavage may give limited cleavage products. Second, Fe3+ is a strong quencher and even fluorescence did increase, the overall fluorescence intensity may still below background. To further confirm the effect of Fe3+, solution based fluorescence kinetics experiments were performed and the results are shown in FIG. 10. At all the three tested Fe3+ concentrations, quenched fluorescence was observed. There was slight recovery of fluorescence for the 100 μM Fe3+ sample. Even based on this enhancement, the selectivity for Cu2+ was still  ̃4200-fold higher for Cu2+ than for Fe3+.
Cu2+-induced FAM quenching: FAM was chosen as the signaling fluorophore to detect Cu2+ in this work. Although the Cu2+ recognition part of the sensor was spatially separated from FAM, Cu2+ could still induce quenching due to non-specific fluorophore/metal interactions. A FAM-labeled double stranded DNA was employed to quantitative measure the quenching effect of Cu2+ to FAM, and a Stem-Volmer plot was made as shown in FIG. 11 (red curve), the remaining fluorescence was less than 10% when Cu2+ concentration was higher than 100 μM (quenching efficiency >90%). In the current system, 50 μM of ascorbate was included, which significantly suppressed the quenching effect (blue curve). When Cu2+ concentration was lower than 50 μM, the quenching was less than 15%. This experiment was carried out under the identical conditions as the Cu2+ detection: 1.5 M NaCl, 50 mM HEPES, pH 7.0 at 23° C.
Test of Cu+ and the effect of ascorbate on the rate of cleavage: To test the effect of ascorbate on the rate of signal enhancement of the sensor, the sensor response in the absence of ascorbate was also carried out. As shown in FIG. 12 (pink curve), even though fluorescence did increase, the rate was much slower compared to that with 50 μM ascorbate (red curve). This result is consistent with literature reports that this DNAzyme can operate independent of ascorbate.10,11 The reaction of Cu+ with this DNAzyme has never been reported before and we also studied this effect. Cu+ was tested using [Cu(MeCN)4](PF6) in acetonitrile as the metal source (blue curve). With ascorbate, the rate of fluorescence increase was as fast as that with Cu2+. In the absence of ascorbate, Cu+ also can induce fast fluorescence increase (green curve), which was faster than that of Cu2+ in the absence of ascorbate (pink curve). Therefore, it is likely that Cu2+ was reduced by ascorbate to Cu+, which subsequently reacted with oxygen to oxidatively cleave DNA.
The effect of anions is shown in FIG. 13.
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## Claims

1. An isolated nucleic acid enzyme activated in the presence of copper, comprising an oligonucleotide comprising a nucleotide sequence shown in SEQ ID NO: 1, wherein the nucleic acid enzyme is not self-cleaving.

2. The nucleic acid enzyme of claim 1, wherein the oligonucleotide further comprises a first quencher at a 5′-end or a 3′-end of the nucleic acid enzyme, and optionally further comprises a spacer between the oligonucleotide and the first quencher.

3. The nucleic acid enzyme of claim 2, wherein the oligonucleotide comprises a nucleotide sequence shown in SEQ ID NO:5.

4. An isolated nucleic acid enzyme activated in the presence of copper, comprising:
an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1, and
a quencher, attached at a 3′ end of the nucleic acid enzyme.

5. The nucleic acid enzyme of claim 1, wherein the oligonucleotide further comprises a first quencher at a 3′-end of the nucleic acid enzyme, and a spacer between the oligonucleotide and the first quencher.

6. The nucleic acid enzyme of claim 2, wherein the oligonucleotide comprises a first quencher at a 5′-end of the nucleic acid enzyme.

7. A sensor system for determining an amount of copper in a sample, comprising:
the nucleic acid enzyme of claim 2,
a substrate for the nucleic acid enzyme,
a second quencher, attached to the substrate, and
a fluorophore, attached to the substrate.

8. A sensor system for determining an amount of copper in a sample, comprising:
the nucleic acid enzyme of claim 5,
a substrate for the nucleic acid enzyme,
a second quencher, attached to the substrate, and
a fluorophore, attached to the substrate.

9. A sensor system for determining an amount of copper in a sample, comprising:
the nucleic acid enzyme of claim 6,
a substrate for the nucleic acid enzyme,
a second quencher, attached to the substrate, and
a fluorophore, attached to the substrate.

10. The sensor system of claim 7, wherein the substrate comprises an oligonucleotide comprising a nucleotide sequence shown in SEQ ID NO:4, wherein the second quencher is at a 5′-end of the substrate, the fluorophore is at a 3′-end of the substrate, wherein the substrate optionally further comprises a spacer between the oligonucleotide and the second quencher, and wherein the substrate optionally further comprises a spacer between the oligonucleotide and the fluorophore.

11. The sensor system of claim 8, wherein the substrate comprises an oligonucleotide comprising a nucleotide sequence shown in SEQ ID NO:4, wherein the second quencher is at a 5′-end of the substrate, the fluorophore is at a 3′-end of the substrate, wherein the substrate optionally further comprises a spacer between the oligonucleotide and the second quencher, and wherein the substrate optionally further comprises a spacer between the oligonucleotide and the fluorophore.

12. The sensor system of claim 7, wherein the substrate comprises an oligonucleotide comprising a nucleotide sequence shown in SEQ ID NO:6, wherein the second quencher is at a 5′-end of the substrate, the fluorophore is at a 3′-end of the substrate, wherein the substrate optionally further comprises a spacer between the oligonucleotide and the second quencher, and wherein the substrate optionally further comprises a spacer between the oligonucleotide and the fluorophore.

13. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 7; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

14. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 8; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

15. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 9; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

16. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 10; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

17. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 11; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

18. A method of measuring an amount of copper in a sample, comprising:
mixing the sample with the sensor system of claim 12; and
detecting fluorescence, wherein detecting an increase in fluorescence indicates the presence of copper.

19. The sensor system of claim 7, wherein the fluorophore is 6-carboxyfluorescein and the first and second quencher are Iowa Black FQ.

20. The method of claim 13, wherein the sample is further mixed with ascorbate.