# Patent

## Title
Enzymatic biosensors with enhanced activity retention for detection of organic compounds

## Abstract

Enzymatic biosensors and methods of producing distal tips for biosensor transducers for use in detecting one or more analytes selected from organic compounds susceptible to dehalogenation, organic compounds susceptible to oxygenation and organophosphate compounds susceptible to hydrolysis are disclosed herein, as well as biosensor arrays, methods of detecting and quantifying analytes within a mixture, and devices and methods for delivering reagents to enzymes disposed within the distal tip of a biosensor.

## Background
RELATED APPLICATIONS
This application is a continuation-in-part of U.S. patent application Ser. No. 10/478,822, filed Aug. 9, 2004 which issued as U.S. Pat. No. 7,381,538 on Jun. 3, 2008, and was a national phase entry under 35 U.S.C. §371 of PCT/US02/17407, filed Jun. 1, 2002, which claimed the benefit of priority to U.S. Provisional Patent Application Ser. No. 60/295,211, filed Jun. 1, 2001. This application also claims the benefit of priority to U.S. Provisional Patent Application Ser. No. 60/922,496, filed Apr. 9, 2007, and 61/024,453, filed Jan. 29, 2008. Each of these applications is incorporated by reference herein.


GOVERNMENT RIGHTS
This invention was made with Government support under contract number BES-0529048 awarded by the National Science Foundation and contract number DACA71-01-C-0009 awarded by the U.S. Army Research Office. The U.S. Government has certain rights in this invention.


BACKGROUND
A biosensor contains a biological component (e.g., enzyme, antibody, DNA/RNA, aptamer) coupled to a transducer, which is typically a physical sensor, such as an electrode, or a chemical sensor that produces a signal proportional to analyte concentration. The analyte is normally detected by the biocomponent through a chemical reaction or physical binding. For example, in the case of an enzyme biosensor, a product of the enzyme-catalyzed reaction, such as oxygen, ammonia, hydrochloric acid or carbon dioxide, may be detected by an optical or electrochemical transducer.
Enzymes are preferred biocomponents because they are catalytic, specific to a particular substrate (analyte) and fast acting. Generally, enzymes for use in a biosensor may be disposed within whole cells or extracted from cells and purified. Whole cells are less expensive than purified enzymes and may provide an environment for longer enzyme stability, but cell-based biosensors typically have longer response times and less specificity to a single analyte than purified enzymes due to the presence of multiple enzymes within the cells. Whole-cell biosensors may utilize dead cells or living cells; the later may require proper control of environment and maintenance to retain their efficacy.
The use of purified enzymes in biosensors has also been explored. In D. W. Campbell, entitled “The Development of Biosensors for the Detection of Halogenated Groundwater Contaminants.” Spring 1998, Colorado State University, Fort Collins, Colo., reference is made to a pH optode featuring the reaction illustrated schematically in FIG. 2.4 of Campbell: the cleavage of halide ion X− and proton H+ from a halogenated hydrocarbon by the appropriate hydrolytic dehalogenase. An earlier reference entitled “Multicomponent fiberoptical biosensor for use in hemodialysis monitoring” (C. Müller, F. Schubert and T. Scheper, Multicomponent fiberoptical biosensor for use in hemodialysis monitoring, SPIE Proc., Vol. 2131, Biomedical Fiber Optic Instrumentation, Los Angeles, Calif., USA (1994) ISBN 0-8194-1424-7, pp. 555-562) employed a pH optode-type biosensor limited to the use of urease as a catalyst (urea is split into ammonia & CO2): the bifunctional reagent glutaraldehyde was used to bind urease directly to the head of a pH optode. These examples demonstrate the feasibility of utilizing purified enzymes in biosensors with the advantage that the enzymes are not exposed to proteases, found in whole cells, that degrade intracellular proteins. However, extraction, isolation and purification of a particular enzyme can be expensive, tedious and complicated, as well as cause the enzyme to lose a high percentage of its activity.
In addition to the particular circumstances affecting whole cells and purified enzymes discussed above, there are two important challenges to the overall development of enzyme-based biosensors. First, the resolution of similar analytes within a mixture has proven difficult. Although enzymes are generally considered specific, most have activity toward similar molecules within the same chemical family. Second, biosensors containing enzymes that require a cofactor, such as nicotinamide adenine dinucleotide (NADH), have limited lifetimes because cofactors, which are consumed during enzyme-catalyzed detection of an analyte, must be regenerated. The supply of cofactors, either through an ancillary reaction that occurs outside the cell or a metabolic process within a living cell, is non-trivial and has hindered the development of biosensors that require cofactors.
SUMMARY
The present instrumentalities advance the art and overcome the problems discussed above by providing biosensors and methods of producing distal tips for biosensor transducers for use in detecting one or more analytes selected from organic compounds susceptible to dehalogenation, organic compounds susceptible to oxygenation and organophosphate compounds susceptible to hydrolysis.
In an embodiment, a distal tip of a biosensor ion-sensing transducer for use in detecting an analyte comprising a halogenated organic compound includes a biocomponent comprising a dehalogenase for carrying out dehalogenation of the compound.
In an embodiment, a distal tip of a biosensor oxygen-sensing transducer for use in detecting an analyte comprising an organic compound includes a biocomponent comprising at least one enzyme selected from the group consisting of oxygenases from EC family 1.13 and oxygenases from EC family 1.14 for carrying out an oxidation of the compound.
In an embodiment, a distal tip of a biosensor transducer for use in detecting organic compounds includes a biocomponent comprising at least two enzymes selected from the group consisting of oxygenases from EC family 1.13 and oxygenases from EC family 1.14 for carrying out an oxidation of one organic compound, a dehalogenase for carrying out dehalogenation of an organic compound, and a hydrolase from subclass EC 3.1 for carrying out a hydrolysis of an ester.
In an embodiment, an array of biosensors for use in detecting organic compounds within a mixture of organic compounds includes a plurality of biosensors, each biosensor having a distal tip including a biocomponent for use in detecting the organic compounds. The biocomponent of each biosensor includes a variant enzyme having a distinct selectivity toward the organic compounds.
In an embodiment, a distal tip of a biosensor ion-sensing transducer for use in detecting an analyte comprising a hydrolase selected from subclass EC 3.1 for carrying out hydrolysis of the compound.
In each of the embodiments above, the biocomponent is immobilized to a surface of the tip by one or more of (a) entrapment within a hydrogel; (b) entrapment within a polymeric network; (c) encapsulation; (d) covalent bonding; and (e) adsorption. The biocomponent is further stabilized to the tip by one or more of crosslinking a surface of the immobilized biocomponent, crosslinking a polymer layer to the biocomponent, adding a gel-hardening agent to the biocomponent, adding a stabilizing agent to the biocomponent, and modifying a component used to immobilize the biocomponent to the surface of the tip.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a depiction of several pathways derived from general knowledge of the degradation of atrazine.
FIG. 2 depicts a hydrolytic dehalogenation of atrazine using atrazine chlorohydrolase.
FIG. 3 schematically depicts features of a known system suitable for use in connection with a pH optode as the transducer (Campbell, 1998).
FIG. 4 schematically depicts features of a distal tip utilizing a pH optode to which a dehalogenase has been immobilized by entrapment within a hydrogel or polymer matrix, according to an embodiment.
FIG. 5 schematically depicts features of a distal tip where two different matrices of a hydrogel or polymer are superimposed, and the layer adjacent the distal tip surface preferably has a higher concentration of dehalogenase than the outermost layer, according to an embodiment.
FIG. 6 schematically depicts features of a distal tip employing a pH microelectrode transducer, according to an embodiment.
FIG. 7 schematically depicts further details of the pH electrode depicted in FIG. 6.
FIG. 8 schematically depicts several immobilization techniques, according to multiple embodiments.
FIG. 9 schematically depicts features of a micro-sized biosensor where the transducer employed is a Field Effect Transistor (FET)-type to which a biocomponent is immobilized, according to an embodiment.
FIG. 10 schematically depicts further details of the pH-sensitive FET transducer depicted in FIG. 9.
FIG. 11 schematically depicts a fiber optic biosensor array having a capillary tube charged with a reagent, such as oxygen or hydrogen peroxide, according to an embodiment.
FIG. 12 depicts contours representing a fraction of maximum dissolved O2 concentration, 1.3×10−3 M, in an aqueous solution above an oxygen-filled capillary.
FIG. 13 schematically depicts the monooxygenase peroxide shunt pathway.
FIG. 14 depicts a time course of biosensor response to 4.7 ppb of 1,2-dichloroethane using X. autotrophicus GJ10 Dh1A dehalogenase as the biocomponent, according to an embodiment.
FIG. 15 depicts a calibration curve for an ethylene dibromide (EDB) biosensor, according to an embodiment.
FIG. 16 depicts results of atrazine monitoring in a soil column, according to an embodiment.
FIG. 17 depicts a biosensor response to 5 μg/L 1,2-dibromoethane using E. coli pAQN (linB) as the biocomponent, measured repeatedly over 50 days, according to an embodiment.
FIG. 18 depicts results from phenol monitoring using Burkholderia cepacia JS150, immobilized in calcium alginate on the end of an oxygen optode, as the biocomponent, according to an embodiment.
FIG. 19 depicts a calibration curve for a toluene biosensor utilizing toluene o-monooxygenase (TOM) as the biocomponent, according to an embodiment.
FIG. 20 depicts a calibration curve for a trichloroethene biosensor utilizing a variant of toluene o-monooxygenase (TOM-Green) as the biocomponent, according to an embodiment.



DETAILED DESCRIPTION
The present technology relates to real-time, in situ, reagentless techniques for monitoring organic chemicals (pollutants, pesticides, etc.) in soil, groundwater, drinking water, waste water and other aqueous environments, as well as a wide variety of other applications. For example, medical uses include disposable one-way sensors (assays) for routine blood, saliva and urine testing, and in vivo sensors for monitoring crucial parameters during surgery and other procedures. In one example, the biosensor may be made small enough to be placed within a catheter for measurements within blood vessels. Food and drink industry applications include contaminant detection, verification of product content (glucose and sucrose concentrations), monitoring of raw material conversion and evaluation of product freshness. Process control applications include monitoring pH, temperature and substrate and dissolved gas concentrations in various processes such as fermentation and microbial cell growth. Environmental monitoring applications include monitoring concentration and toxicity of contaminants (e.g., analytes such as heavy metals, pesticides, etc.) in surface and groundwater, waste streams and soil. Defense and security industry applications include measuring the presence of chemical warfare agents such as nerve gases and mustard gas, detection of trace vapors, explosives and drugs.
Water Contamination
Measurements of water contaminant concentrations are critical to site characterization and remediation process monitoring. However, current techniques for groundwater contaminant monitoring suffer from several problems. Measurements are expensive, slow and require removal of the sample from the site, thereby adding to the cost and altering the analyte concentration through nonlinear volume averaging and volatile losses. Currently, the primary method for monitoring groundwater involves removing a groundwater sample from a well (an average of a large volume), packaging it into several sample vials, shipping it to a laboratory and receiving the analysis weeks later.
Although analysis is traditionally performed by gas or liquid chromatography, immunoassays for contaminant measurements have recently become available. However, immunoassays still require sample removal and provide a single, time-delayed measurement. Moreover, immunoassays are not sufficiently specific for small molecules, such as toluene, benzene and chlorinated ethenes, because it is difficult to obtain antibodies for small molecules.
Biosensor Distal Tips
Biosensor distal tips disclosed herein have transducers to which one or more biocomponents comprising a dehalogenase, a hydrolase and/or an oxygenase are immobilized, treated and/or stabilized. The biosensors may continuously monitor soil or an aqueous environment in situ to detect the presence and/or concentration of one or more analytes, such as s-triazines, chlorinated ethenes or organophosphates. S-triazines include, for example, the chlorinated herbicide atrazine (used to control broadleaf and grassy weeds), simazine, terbuthylazine, propazine, cyanazine, deethylatrazine and deisopropylatrazine, plus other s-triazines, lindane and DDT. Chlorinated ethenes include, for example, tetrachloroethene (a.k.a., perchloroethene (PCE)), trichloroethene (TCE), dichloroethene isomers and vinyl chloride (VC).
Techniques for detecting and measuring one or more analytes and associated biosensors capable of measuring pH (hydrogen ion concentration) and/or oxygen concentration are disclosed. In one aspect, a biosensor includes a fiber optic element (an optical fiber or bundle), the tip of which has a layer of bacteria atop a layer of a pH-sensitive fluorophore (dye). In another aspect, a biosensor includes a fiber optic element (an optical fiber or bundle), the top of which has a layer of bacteria atop a layer of an oxygen-sensitive fluorophore. In yet another aspect, the pH-sensitive biosensor and the oxygen-sensitive biosensor may be combined into a single biosensor. The bacteria may be selected such that they carry one or more enzymes to catalyze a reaction involving one or more analytes. For example, a single type of natural or recombinant bacteria may express more than one enzyme useful for detecting analytes. Alternatively, multiple types of bacteria, each expressing one enzyme useful for detecting a single analyte, may be combined on a biosensor distal tip. The enzymatic reaction(s) may, for example, release protons (and cause a detectable pH change), produce a measurable halide ion concentration or consume oxygen. Further, prior to being ‘glued’ (immobilized or otherwise affixed) to the tip of the fiber optic transducer, the bacteria may be specially treated and/or stabilized.
The disclosed biosensors have distal tips which include an ion-sensing and/or an oxygen-sensing transducer for use in detecting one or more analytes and at least one biocomponent comprising a dehalogenase, a hydrolase and/or an oxygenase. A dehalogenase may, for example, be selected from the hydrolases, subclass EC 3.8, or lyases, subclass EC 4.5 (TABLE 1A), for carrying out a dehalogenation of an analyte. An oxygenase may, for example, be selected from monooxygenases and dioxygenases selected from EC family 1.13 and EC family 1.14 (TABLE 2A), for carrying out an oxidation of an analyte. A hydrolase may, for example, be selected from subclass EC 3.1 (TABLE 3A), for carrying out a hydrolysis of an analyte. Advantages of the disclosed distal tips and biosensors include, without limitation:
Disposable use with real-time results. The distal tips and/or biosensors may be used for single or multiple use applications, or for continuous real-time monitoring over an extended period.
Simplicity and versatility. The distal tips and/or biosensors may be used to collect information about physical properties of a wide range of analytes without requiring sophisticated equipment and complicated procedures. Simplicity of design may reduce fabrication costs and allow for off-site use, thereby making information readily available.
Structural design. A combination of immobilization and stabilization provides a robust distal tip design.
Several biosensor tips having similar or dissimilar transducer types (e.g., optical, electrochemical) may be incorporated into a bundle providing a package of different types of information where the biosensors acquire information simultaneously or sequentially.







TABLE 1A







Exemplary dehalogenating enzymes for use in a biosensor. See


“Enzyme Nomenclature” of the Nomenclature Committee of the


International Union of Biochemistry and Molecular Biology


(www.chem.qmul.ac.uk/iubmb/enzyme) and from the University of MN


Biocatalysis/Biodegradation Database (umbbd.ahc.umn.edu).











EC
Known substrates
Refer-


Enzyme name(s)
code
(analytes)
ence(s)










Enzyme subclass 3.8: hydrolases acting on halide bonds:










alkyl-halide
3.8.1.1
Bromochloromethane
 [1]


halidohydrolase(alkyl-





halidase, halogenase;





haloalkane halido-





hydrolase; haloalkane





dehalogenase)





2-haloacid halidohydro-
3.8.1.2
Acts on 2-haloacids of
 [2]


lase (2-haloacid

short chain lengths, C2 to
 [3]


dehalogenase, 2-

C4



haloalkanoid acid





halidohydrolase; 2-





haloalkanoic acid





dehalogenase; L-2-halo-





acid dehalogenase; DL-2-





haloacid dehalogenase)





haloacetate halidohydro-
3.8.1.3
Fluoroacetate and other
 [4]


lase (haloacetate dehalo-

haloacetates
 [5]


genase, monohaloacetate





dehalogenase)





L-thyroxine iodohydrolase
3.8.1.4
A group of enzymes,
 [6]


(reducing) (thyroxine

removing iodine atoms
 [7]


deiodinase, thyroxine 5-

sequentially from
 [8]


deiodinase; diiodo-

thyroxine.



thyronine 5′-deiodinase;





iodothyronine outer ring





monodeiodinase; iodo-





thyronine 5′-deiodinase)





1-haloalkane halidohydro-
3.8.1.5
Acts on a wide range of 1-
 [9]


lase (haloalkane 

haloalkanes, haloalcohols,
[10]


dehalogenase, 1-chloro-

haloalkenes and some
[11]


hexane halidohydrolase;

haloaromatic compounds.



1-haloalkane





dehalogenase)





4-chlorobenzoate
3.8.1.6
4-chlorobenzoate and other
[12]


chlorohydrolase (4-

halogenated benzoates
[13]


chlorobenzoate dehalo-





genase, halobenzoate





dehalogenase)





4-chlorobenzoyl CoA
3.8.1.7
Specific for dehalogenation
[14]


chlorohydrolase (4-

at the 4-position.
[15]


chlorobenzoyl-CoA

Can dehalogenate





substrates bearing fluorine,





chlorine, bromine and





iodine in the dehalogenase)





4-position. This enzyme is





part of the bacterial 2,4-





dichlorobenzoate





degradation pathway.



atrazine chlorohydrolase
3.8.1.8
Atrazine, simazine, and
[16]




other halogenated s-
[17]


s-triazine hydrolase
3.8.1.—
triazines



dichloroacetate
3.8.1.—




halidohydrolase





DL-2-haloacid
3.8.1.—




dehalogenase





1,3,4,6-tetrachloro-1,4-
3.8.1.—




cyclohexadiene





halidohydrolase





cis-chloroacrylic acid
3.8.1.—




dehalogenase





trans-chloroacrylic acid
3.8.1.—




dehalogenase










Enzyme subclass 4.5: lyases acting on carbon-halide bonds:










DDT-dehydrochlorinase
4.5.1.1
DDT (1,1,1-trichloro-2,2-
[18]


(DDT-ase)

bis(4-chlorophenyl)ethane)
[19] [20]


3-chloro-D-alanine 
4.5.1.2
3-chloro-D-alanine
[21]


chloride-lyase


[22]


(deaminating) (3-chloro-D-





alanine dehydrochlorinase,





B-chloro-D- alanine





dehydrochlorinase)





dichloromethane chloride-
4.5.1.3
Dichloromethane,
[23]


lyase (chloride-hydro-

dibromoethane, bromo-



lysing) (dichloromethane

chloromethane,



dehalogenase)

diiodomethane



L-2-amino-4-chloropent-4-
4.5.1.4
L-2-amino-4-chloropent-4-
[24]


enoate chloride-lyase

enoate



(deaminating) (L-2-amino-





4-chloropent-4-enoate





dehydrochlorinase, L-2-





amino-4-chloro-4-





pentenoate dehalogenase)





3-chloro-L-alanine 
4.5.1.5
3-chloro-L-alanine
[25]


chloride-lyase (adding





thioglycolate) (S-





carboxymethylcysteine





synthase, S-carboxy-





methyl-L-cysteine 





synthase)





halohydrin hydrogen-
4.5.1.—




halide-lyase





halohydrin hydrogen-
4.5.1.—




halide-lyase B





DDD dehydrochlorinase
4.5.1.—




DDMS dehydrochlorinase
4.5.1.—




gamma-
4.5.1.—




hexachlorocyclohexane





dehydrochlorinase 5-
4.5.1.—




chloro-1,2,4-trihydroxy-





benzene dechlorinase





tribromobisphenol lyase
4.5.1.—
















TABLE 2A







Exemplary oxidizing enzymes for use in a biosensor.












Known substrates
Refer-


Enzyme name(s)
EC code
(analytes)
ence(s)










Enzyme subclass 1.13: monooxygenases acting on the CH—OH group of


single donors with incorporation of molecular oxygen:










catechol 1,2-dioxygenase
1.13.11.1
catechol, requires Fe3+
[26]


catechol 2,3-dioxygenase
1.13.11.2
catechol, requires Fe2+
[27]


protocatechuate 3,4-
1.13.11.3
3,4-dihydroxybenzoate,
[28]


dioxygenase

requires Fe3+



gentisate 1,2-
1.13.11.4
2,5-dihydroxybenzoate,
[29]


dioxygenase

requires Fe2+



homogentisate 1,2-
1.13.11.5
homogentisate, requires
[30]


dioxygenase

Fe2+



lactate 2-monooxygenase
1.13.12.4
(S)-lactate
[31]







Enzyme subclass 1.14: dioxygenases acting on the CH—OH group of


paired donors with incorporation or reduction of molecular oxygen:










toluene dioxygenase
1.14.12.11
toluene
[32]


naphthalene 1,2-
1.14.12.12
naphthalene
[33]


dioxygenase





2-chlorobenzoate 1,2-
1.14.12.13
2-chlorobenzoate,
[34]


dioxygenase

requires Fe2+



salicylate 1-
1.14.13.1
salicylate
[35]


monooxygenase





4-hydroxybenzoate 3-
1.14.13.2
4-hydroxybenzoate
[36]


monooxygenase





phenol 2-monooxygenase
1.14.13.7
phenol, resorcinol and o-
[37]


flavin-containing
1.14.13.8
cresol N,N-dimethyl-
[38]


monooxygenase

aniline, as well as





hydrazines, phosphines,





boron-containing





compounds, sulfides,





selenides, iodide, as well





as primary, secondary





and tertiary amines



methane monooxygenase
1.14.13.25
methane, alkanes can be
[39]




hydroxylated, alkenes are





converted into epoxides;





CO is oxidized to CO2,





ammonia is oxidized to





hydroxylamine, and





some aromatic





compounds and cyclic





alkanes can also be





hydroxylated.



pentachlorophenol
1.14.13.50
pentachlorophenol, 
[40]


monooxygenase

2,3,5,6-tetrachlorophenol



alkane 1-monooxygenase
1.14.15.3
octane
[41]
















TABLE 3A







Exemplary hydrolyzing enzymes for use in a biosensor.











EC

Refer-


Enzyme name(s)
code
Known substrates (analytes)
ence(s)










Enzyme subclass 3.1: hydrolases acting on ester bonds:










carboxylesterase
3.1.1.1
carboxylic esters
[42]


arylsulfatase
3.1.6.1
phenol sulfates
[43]


aryldialkylphosphatase
3.1.8.1
aryl dialkyl phosphates,
[44]


(organophosphate

organophosphorus compounds



hydrolase)

including esters of phosphonic





and phosphinic acids



diisopropyl-
3.1.8.2
diisopropyl fluorophosphate, acts
[45]


fluorophosphatase

on phosphorus anhydride bonds



(organophosphorus acid

(such as phosphorus-halide and



anhydrolase; organo-

phosphorus-cyanide) in



phosphate acid 

organophosphorus compounds



anhydrase)









Features of the distal tip include: a biocomponent comprising at least one enzyme for carrying out a dehalogenation, oxidation or hydrolysis of an analyte; the biocomponent is immobilized to a surface of the tip; treatment of the biocomponent for maintaining a period of enzymatic efficacy; and the biocomponent stabilized by one or more of crosslinking a surface of the immobilized biocomponent, crosslinking a polymer layer to the biocomponent, adding a gel-hardening agent to the biocomponent, adding a stabilizing agent to the biocomponent, and modifying a component used to immobilize the biocomponent to the surface of the tip.
Detection of Halogenated Organic Compounds Using Dehalogenases
In an embodiment, a distal tip of a biosensor ion sensing transducer for use in detecting an analyte comprising a halogenated organic compound is selected from the following: a pH optode, a pH electrode, a field-effect transistor (FET) and a halide ion-selective electrode (ISE). Analytes of interest include without limitation: s-triazine compounds, which include both pesticides and non-pesticides, such as atrazine, simazine, terbuthylazine, propazine, cyanarine, deethylatrazine and deisopropylatrazine, and others including those shown in FIG. 1 and listed in TABLE 4; beta-, or the more common, gamma-hexachlorocyclohexane (“lindane”) and DDT (1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane). Microorganisms that can initiate pathways identified in TABLE 5 are for the widely used herbicide atrazine (degradation example shown in FIG. 2). Without limitation, these microorganisms include: Pseudomonas sp. ADP; Ralstonia sp. M91-3; Clavibacter michiganese sp. ATZ1; Agrobacterium sp. J14a; Alcaligenes sp. SG1; Rhodococcus spp. N186/21, TE1; Pseudomonas spp. 192, 194; and Streptomyces sp. PS1/5.
S-triazines are characterized by a symmetrical hexameric ring consisting of alternating carbon and nitrogen atoms. Atrazine is one of the most commonly applied s-triazine herbicides (structure below):







TABLE 4





Non-pesticide s-triazine groups with comments about use and


biodegradability.



















 Cyanuric acid
Cyanuric (isocyanuric) acids: N-Chlorination of cyanuric acid at the R1, R2 and R3 sites yields chloroisocyanurates that are used as disinfectants (in swimming pools and hot- tubs), sanitizers (in household cleansers and automatic dishwashing compounds) and bleaches (in both the industrial and household bleaching of fabrics). The most common chloroisocyanurates are trichloro and dichloro isocyanuric acid (TCCA, DCCA) and sodium dichloroisocyanuric acid (SDCC).


 





 SDCC
Triallyl isocyanurate (R1, R2 and R3 = propenyl) is used as a crosslinking agent for poly(vinyl chloride) and other systems. Methylamine (also on the metapathway map) and N-substituted methylamines are sometimes used as finishing agents for textiles.


 





 RDX
Nitramine explosives: Cyclotrimethylenetrinitramine (RDX) is an explosive and a propellant used in military rockets. The partial biodegradation of RDX by mixed microbial culture is reported in (Binks et al. 1995).


 





 Triazone
Triazone: A cyclic urea used as a crosslinking agent in textile finishing. 1,3- di-methylol-5-alkyltriazone is still widely used for this purpose. Crosslinking agents are used in the preparation of textiles to induce “memory” and to add luster.
















TABLE 5




















FIG. 2 illustrates (see, also, left-hand column in above map) a hydrolytic dehalogenation of atrazine, the first step of which can be carried out by several microorganism species, such as Pseudomonas sp. ADP, Ralstonia sp. M91-3, Clavibacter sp. ATZ1, Agrobacterium sp. J14a and Alcaligenes sp. SG1. The reaction depicted in the middle column in the above map represents an oxygenase attack on the isopropyl amino group. This reaction can be carried out by several microorganism species, such as Rhodococcus spp. NI86/21 and TE1, Pseudomonas spp. 192 and 194, and Streptomyces sp. PS1/5. The reaction depicted in the right-hand column in the above map represents an oxygenase attack on the ethyl amino group. This reaction can be carried out by several species, such as Rhodococcus spp. NI86/21 and TE1, Pseudomonas spp. 192 and 194, and Streptomyces sp. PS1/5.
Two microorganisms suitable for use in degrading atrazine are Pseudomonas sp. strain ADP and Clavibacter michiganese ATZ1. Studies have shown that strain ADP has three genes (atz-A, atz-B and atz-C) that encode enzymes responsible for the degradation of atrazine to cyanuric acid. Strain ATZ1 has 100% homology only with atz-A; and thus only carries out reactions similar to the first two steps of strain ADP. For further reference, see Tables 6.1-6.3 below:







TABLE 6.1





Physical methods used to design the ADP and ATZ1 biosensors
















PHYSICAL
Optical transduction: fluorescent dye


TRANSDUCER



IMMOBILIZATION
Entrapment: Ca-alginate gel matrix, time of


METHOD
gelation = 20 minutes


BIOCOMPONENT
Whole cell of atrazine degrading strain: treated



under various conditions


STABILIZATION
Storage in refrigerator at 4° C.


METHOD



SIZE
Less than 2 mm diameter of immobilized gel:



cell density ~1 g of wet wt. of cells/wt. of



alginate
















TABLE 6.2







Summary of sensitivity parameters


for the ADP and ATZ1 biosensors














Response Time






(90% of response
Reproducibility


Micro-


for change of 25
(standard


organism
Linear
Detec-
ppb of atrazine
deviation


used as a
Range
tion
conc., ~2 mm
based on 3


biocomponent
(ppb)
Limit
bead dia.)
measurements)





ADP
0-125
<1 ppb
19.7 ± 2.5
<6%


ATZ1
0-100
<1 ppb
10.7 ± 2.3
<5%
















TABLE 6.3







Summary of results of activity retention of the biosensors


using different types of biocomponents.









Type of microorganism
Activity
Activity


Used as biocomponent
retention > 90% (days)
retention > 30% (days)





ADP
5
 7


Heat-treated ADP
7 (dry heating time = 
11



30 sec)




9 (dry heating time = 
12



60 sec)



Chloramphenicol-
8 (Conc. of
9-10


treated ADP
chloramphenicol =




50 μg/mL)




10 (Conc. of
60% activity



chloramphenicol =
retention on the



200 μg/mL)
12th day.


Protease inhibitor-
6
10


treated ADP
5
11


ATZ1









Once again, turning to the figures: FIG. 1 is a depiction of several pathways derived from general knowledge of the degradation of the s-triazine, atrazine. FIG. 2 depicts a hydrolytic dehalogenation of atrazine using atrazine chlorohydrolase. FIG. 3 schematically depicts features of a known system 30 suitable for use in connection with a pH optode as the transducer (Campbell, 1998). This fiber optic pH sensor system 30 includes the pH optode with biocomponent, a lens focusing system, a photomultiplier (PMT), an A/D converter and suitable microprocessor.
FIG. 4 schematically depicts features of a distal tip 42, an embodiment utilizing a pH optode 49 to which biocomponent 44 comprising the dehalogenase 45 (either in pure form or carried in a microorganism at 45) has been immobilized by entrapment within a hydrogel or polymer matrix 46, shown enlarged for clarity. The pH optode 49 has suitable cladding 41 for purposes of protecting the fiber(s) of the optical element (single or bundle) therewithin. Information about the environment 40 (soil or aqueous, for example) can be collected as disclosed herein.
FIG. 5 schematically depicts features of a distal tip 52 where two different matrices of a hydrogel or polymer are superimposed, and the layer adjacent the distal tip 54 surface preferably has a higher concentration of dehalogenase (whether carried by whole cells or in purified form) than the outermost layer 57. The pH optode 59 has suitable cladding 51 for purposes of protecting the fiber(s) of the optical element (single or bundle) therewithin. Information about the environment 50 (soil or aqueous, for example) can be collected as disclosed herein.
FIG. 6 schematically depicts features of a distal tip embodiment employing a pH microelectrode transducer, an enzyme-containing biocomponent immobilized to the distal tip. FIG. 7 schematically represents further details of the pH electrode depicted in FIG. 6, featuring the reaction of the analyte (here, S, for ‘substrate’) within the enzymatic layer. In general terms, the diffusion of S results in products P and H+. FIG. 8 schematically represents several immobilization techniques as identified according to multiple embodiments. FIG. 9 schematically depicts features of a micro-sized embodiment where the transducer employed is a Field Effect Transistor (FET)-type to which a biocomponent is immobilized. FIG. 10 schematically represents further details of the pH-sensitive FET transducer depicted in FIG. 9, featuring the reaction of the analyte (here, S, for ‘substrate’) within the enzymatic layer.
One might choose to target a dehalogenase which produces a measurable pH change and needs no reactant other than the halogenated analyte (e.g., atrazine) and perhaps water. This methodology excludes the reductive dehalogenases, which require an ancillary reagent to be oxidized while the halogenated analyte is reduced, as well as other classes of enzymes that require oxygen or energy from the cell. On the other hand, methods of introducing oxygen and other reagents are described below, so enzymes requiring cofactors are not necessarily precluded from use as biocomponents in the present biosensors.
Detection of Organophosphate Compounds Using Hydrolases
In an embodiment, a distal tip of a biosensor ion-sensing transducer for use in detecting an analyte comprising an organophosphate organic compound is selected from the following: a pH optode, a pH electrode, a field-effect transistor (FET) and an ion-selective electrode (ISE). Analytes of interest include without limitation: esters of phosphoric acid including pesticides, such as methyl parathion (O,O-dimethyl O-p-nitrophenyl phosphorothioate), parathion (O-p-nitrophenyl phosphorothioate), EPN (o-ethyl O-p-nitrophenyl phenylphosphonothioate), diazinone (O,O-diethyl O-2-isopropyl-4-methyl-6-pyrimidinylthiophosphate), malathion (S-1,2-bis(ethoxycarbonyl)ethyl O,O-dimethyl phosphorodithioate), paraoxon (diethyl 4-nitrophenyl phosphate), fenitrothion (O,O-dimethyl-O-(4-nitro-meta-tolyl)), coumaphos (O,O-diethyl O-(3-chloro-4-methyl-7-coumarinyl)phosphorothioate), diazinon (O,O-diethyl-O-(2-isopropyl-6-methyl-pyrimidine-4-yl)phosphorothioate) and chlorpyrifos (O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphorothioate), and nerve agents, such as Tabun, Sarin, Soman and VX.
An ion-sensing biosensor may be based on the activity of orthophosphorous hydrolase (OPH) enzymes selected from subclass EC 3.1.8.2 and/or sulfatase enzymes selected from subclass 3.1.6.1 and/or organophosphorus acid anhydrolase (OPAA) enzymes selected from subclass EC 3.1.8.1 and/or carboxylesterase enzymes selected from subclass EC 3.1.1.1. Hydrolysis of an orthophosphate compound by OPH, sulfatease, OPAA or carboxylesterase produces protons that may, for example, be monitored using a pH-dependent biosensor having a fluorescent dye, such as carboxynaphthofluorescein. Alternatively, a chromophoric/fluorescent product, such as p-nitrophenol or coumarin, may be directly monitored by an optical detector. Similarly, enzyme catalyzed reaction products of parathion, methyl parathion, fenitrothion and EPN, such as p-nitrophenol (PNP), may be monitored amperometrically either directly or, for example, by conversion to hydroquinone, nitrocatechol or benezenetriol by oxygenases from PNP-degrading Arthrobacter species and Moraxella species.
Detection of Organic Compounds Using Oxygenases
In an embodiment, a distal tip of a biosensor oxygen-sensing transducer for use in detecting an analyte comprising an organic compound is an oxygen optode. More specifically, an optical enzymatic biosensor may be based on the activity of mono- and/or dioxygenase enzymes selected from EC family 1.13 and EC family 1.14. These enzymes catalyze the reaction of oxygen with a wide range of organic chemicals, resulting in the consumption of molecular oxygen, as well as NADH or NADPH.
An oxygen-based biosensor typically contains a layer of oxygenase-expressing bacteria immobilized on the tip of an optical sensor. Since the reaction of oxygenase with analyte consumes molecular oxygen, the oxygen concentration at the tip of the optical fiber decreases, and the magnitude of the decrease is proportional to the concentration of analyte in the surrounding environment. An oxygen-sensitive fluorophore, such as tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) chloride, may be immobilized on an optical fiber, e.g., a polymethylmethacrylate fiber. Alternatively, a commercially available FOXY fiber optic oxygen sensor (Ocean Optics Inc.) may be used. The optical fiber interfaces with an optical-electronic unit that provides excitation light of the correct wavelength for the oxygen-sensitive fluorophore (e.g., using a halogen lamp or light-emitting diode), and detects the emitted fluorescent light (e.g., using a photomultiplier tube).
Analytes of interest include without limitation: chlorinated ethenes such as tetrachloroethene (a.k.a., perchloroethene (PCE)), trichloroethene, dichloroethene isomers and vinyl chloride (VC), which are the most frequently detected groundwater contaminants in the world. Experimental and modeling conditions described herein detect chlorinated ethenes at 0-100 μg/L (application-relevant levels).
Immobilization Techniques
Methods of producing a biosensor distal tip having an ion-sensing and/or oxygen-sensing transducer and at least one biocomponent for use in detecting one or more analytes are disclosed herein. An exemplary method includes: immobilizing the biocomponent(s) including at least one enzyme for carrying out a dehalogenation, a hydrolysis and/or oxygenation of an analyte to a surface of the tip by one or more of (a) entrapping the enzyme within a hydrogel secured to the tip surface; (b) entrapping the enzyme within a polymeric network secured to the tip surface; (c) encapsulating the enzyme; (d) covalently bonding a second component of the biocomponent to the tip surface; (e) crosslinking the enzyme to a support material secured to the tip surface; and (f) adsorbing the enzyme into the tip surface; treating the biocomponent for maintaining a period of enzymatic efficacy; and stabilizing the biocomponent by one or more of crosslinking a polymer layer to the biocomponent, adding a gel-hardening agent to the biocomponent, adding a stabilizing agent to the biocomponent, and modifying a component used to immobilize the biocomponent to the surface of the tip.
The hydrogel or polymeric matrix used for entrapment of the biocomponent in the form of pure enzymes or whole cells (whether naturally occurring or recombinant) may be selected as follows: suitable hydrogels include algal polysaccharides (such as agar, agarose, alginate, and K-carrageenan), gelatin, collagen, pectin, poly(carbamoyl) sulfonate, locust bean gum and gellan; and suitable polymers include polyacrylamide, polystyrene, polymethacrylate, polyvinylalcohol and polyurethane. The biocomponent treatment may be selected from the following: applying an inhibitor of protein synthesis, adding a protease inhibitor, freeze drying and dry heating. Further focusing on particular features, the protein synthesis inhibitor may include any suitable antibiotic, such as one selected from chloramphenicol, aminoglycosides (e.g., kanamycin), tetracyclines and macrolides (e.g., erythromycin); the polymer layer crosslinked for stabilization may be selected from suitable polymers including poly-L-lysine (PLL), polyethylenimine, polyacrylic acid, polyvinyl alcohol, polyacrylamide and polyurethane; a crosslinking agent, such as glutaraldehyde, may be used to crosslink the biocomponent surface; and a suitable polyalcohol or sugar may be selected for addition to the biocomponent as a stabilizing agent.
It is critical that the biocomponent be properly bound to the transducer. Biocomponent immobilization techniques include:
Adsorption—Enzymes may be adsorbed onto, at least part of, one or more surfaces of a biocomponent material. Examples of materials to which enzymes may be adsorbed include: ion-exchange resins, ceramics, glass, polyvinyl chloride, chitin, chitosan, alumina, charcoal, glassy carbon, clay, cellulose, kaolin, silica gel and collagen. Adsorption has been classified as physical adsorption (physisorption) and chemical adsorption (chemisorption). Physisorption is usually weak and occurs via the formation of van der Waals bonds or hydrogen bonds between the substrate and the enzyme molecules. Chemisorption is stronger and involves the formation of covalent bonds.
Encapsulation—A thin microporous semipermeable membrane is used to surround the biocomponent. Because of the proximity between the biocomponent and transducer, and the minimal membrane thickness, biosensor response can be maximized. Suitable materials for encapsulation include, for example, nylon and cellulose nitrate. Further bonding of the biocomponent to the transducer surface may be accomplished using a conductive polymer, such as polypyrrole. The membrane may be selected for its ability to serve additional functions, such as selective ion permeability, enhanced electrochemical conductivity or mediation of electron transfer. Membrane types used for encapsulation include without limitation: cellulose acetate, polycarbonate, collagen, acrylate copolymers, poly(ethylene glycol), polytetrafluoroethylene (PTFE), agarose, as well as alginate-polylysine-alginate microcapsules formed of alginate and polylysine.
Entrapment—Cells or purified enzymes are physically constrained (entrapped) inside a three-dimensional matrix. Suitable materials (both natural and synthetic) for entrapment include those that permit substantially uniform cell distribution and have biocompatibility and good transport mechanisms. Such materials include without limitation alginate, agarose and collagen. One might also choose to utilize mild polymerization techniques for more rugged immobilization. Hydrogels are preferably used as agents for biosensor entrapment. They provide a hydrophilic environment for the biocomponent and require only mild conditions to polymerize. Hydrogels can absorb large quantities of water, which can facilitate desirable reactions such as hydrolysis. Both natural and synthetic hydrogels are suitable for use. The naturally occurring algal polysaccharides, such as agar, agarose, alginate and carrageenan, and synthetic polymers, such as polyacrylamide, polystyrene and polyurethane, are examples of suitable hydrogels. Synthetic polymers generally have a smaller pore size which can lead to less leakage of biocomponent, and hence longer stability; however, synthetics are generally toxic and the immobilization process is accompanied by generation of heat and production of free radicals. Natural polymers are typically non-toxic and biodegradable, and the immobilization process is less stressful to the biocomponent. Natural polymers may, however, provide less mechanical strength and stability, and their larger pore size may allow for predation by protozoans and other soil or water dwelling predators, as well as degradation by hydrolase enzymes within the environment being tested.
Alginate, a hydrogel formed via a gentle encapsulation process, provides a good, biocompatible microenvironment for a biocomponent. Alginate is a naturally occurring linear polymer composed of β-(1,4) linked D-mannuronic acid and α-(1,4)-L-guluronic acid monomers. Commercially, alginate is obtained from kelp, but bacteria such as Azotobacter vinelandii, several Pseudomonas species and various algae also produce alginate. When alginate is exposed to Ca+2 ions, a crosslinking network is formed by the bonding of Ca+2 ions and polyguluronic portions of the polymer strand by a process known as ionic gelation. The gelation process is temperature-independent. Complete gelling time without cells may be as little as 30 minutes. Sol gel technology has enabled extension of the entrapment principle to silicate networks that have some advantageous characteristics, such as requiring milder polymerization processes and matrices that exhibit good mass transport and molecular access properties, particularly for electrochemical and optical transduction modes.
Crosslinking—The biocomponent is chemically bonded to a solid support or supporting material, such as a gel. Bifunctional agents such as glutaraldehyde, hexamethylene diisocyanate and 1,5-dinitro-2,4-difluorobenzene may be used to bind the biocomponent to the support. By way of example, a tyrosinase biosensor for polyphenols was made by pretreating the electrode via polymerization of pyrrole in 0.1 M tetraethylammonium sulfonate on the surface of the biosensor. The tyrosinase solution and glutaraldehyde were then repetitively and alternately coated on the surface to crosslink the enzyme to the polypyrrole surface. While there is little leaching of the biocomponent and the layer tends to exhibit long-term stability under strenuous experimental conditions, such as exposure to flowing samples, stirring, washing, etc., crosslinking causes damage to enzymes and may limit diffusion of analyte during operation.
Covalent Bonding—A particular chemical group present in the biocomponent, which is not involved in catalytic action, may be attached to a support matrix (transducer or membrane) by covalent bonding. Radicals that take part in such a reaction are generally nucleophilic in nature (e.g., —NH2, —COOH, —OH, —SH and imidazole groups). In order to retain enzyme activity, the reaction is typically performed under mild conditions. Materials suitable for covalent bonding include without limitation: cellulose and cellulose derivatives, silica, glass, dextran, starch, agarose, porous silica, chitin and chitosan.
Transduction Techniques
The nature of the interaction of the biocomponent with the analyte impacts the choice of transduction technology. Transduction techniques can be categorized as follows:
Amperometric electrode (an electrochemical transducer)—A constant potential is maintained on a working electrode with respect to a reference electrode, and the current generated by oxidation or reduction of an electroactive species at the surface of the working electrode is measured; the response is linear. The reference electrode need not be drift-free to have a stable response. Since the signal generated is highly dependent on mass transfer of the electroactive species to the electrode surface, there can be a loss in sensitivity due to fouling by species that adsorb to the electrode surface. Enzymes, particularly oxidoreductases, are well suited to amperometric transduction as their catalytic activity is concerned with electron transfer. Electroactive species that can be monitored at the electrode surface include substrates of a biological reaction (e.g., O2, NADH), final products (e.g., hydrogen peroxide for oxidase reactions, benzoquinone for phenol oxidation) and also electrochemical mediators that can directly transfer electrons from an enzyme to a working electrode surface (e.g., hexacyanoferrate, ferrocene, methylene blue).
Potentiometric electrode (an electrochemical transducer)—The potential difference between an active electrode and a reference electrode is measured under zero current flow. The three most commonly used potentiometric devices are ion-selective electrodes (ISEs), gas-sensing electrodes and field-effect transistors (FETs). All of these devices obey a logarithmic relationship between the potential difference and the activity of the ion of interest. Thus, potentiometric electrode sensors have a wide dynamic range. One disadvantage of potentiometric electrodes is the requirement of an extremely stable reference electrode. ISEs are commonly used to monitor aqueous environments (groundwater, waste water, etc.). FETs are commercially attractive because they can be used to build micro-biosensors according to currently available, widely used micro-electronic device production techniques.
Conductimetric electrode (an electrochemical transducer)-Conductimetric electrodes are used to measure salinity of marine environments. Conductance is measured by the application of an alternating current between two noble-metal electrodes immersed in a solution. Due to specific enzyme reactions, the electrodes convert neutral substrates into charged products, causing a change in conductance.
Optical Transducers—Several types of photometric behavior are utilized by optical biosensors: ultraviolet-visible absorption, fluorescence (and phosphorescence) emission, bioluminescence, chemiluminescence, internal reflection spectroscopy (evanescent wave technology) and laser light scattering methods. When fluorescent reagents are utilized, a fluorescent substance is excited by incident light and, as a result, the substance emits light of a longer wavelength. The intensity of emitted light changes as analyte binds with the fluorescent substance. The change in intensity can be measured as a response to a particular analyte. Suitable fluorescent reagents include trisodium 8-hydroxy-1,3,6-trisulphonate for pH sensors, fluoro(8-anilino-1-naphthalene sulphonate) for Na+ ion sensors, and acridinium- and quinidinium-based reagents for halides. Chemiluminescence occurs by the oxidation of certain substances, usually with oxygen or hydrogen peroxide, to produce visible light. Bioluminescence is produced by certain biological substances, such as luciferins produced by firefly. Internal reflectance is a method based on the principle of total internal reflection of a light beam into an optically dense medium when the incident angle is greater than the critical angle. When such a process occurs, not all of the energy is confined in the optically dense medium. The internally reflected light generates an electromagnetic evanescent wave, which penetrates the lower density medium at the point of reflection, for a distance comparable to the wavelength of light. Techniques falling within the category of “light scattering” include: quasi-elastic light-scattering spectroscopy, photon correlation spectroscopy and laser Doppler velocimetry.
Stabilization of an Immobilized Biocomponent
The active lifetime of a biosensor, i.e., its period of enzymatic efficacy, depends upon the type of biocomponent used. Sensor lifetime can vary from a few days to a few months. Generally, pure enzymes have the lowest stability, while cell and tissue preparations provide longer lifetimes. There are three aspects of lifetime of a biosensor: the active lifetime of the biosensor in use, the lifetime of biosensor in storage, and the lifetime of the biocomponent in storage prior to being immobilized.
Stabilization of an immobilized biocomponent is important in order to maximize performance of the biosensor, especially where a biosensor is to be stored for a prolonged period of time before use. Stabilization techniques depend on the biocomponent and type of transducer employed. Techniques for stabilizing a biocomponent include:
Molecular Modification—The stability of enzymes can be improved by changing certain amino acids in the protein sequence, such as by site-directed mutagenesis, grafting of polysaccharides (or short chains of sugar molecules) onto the protein molecules, and other methods involving chemical and carbohydrate modifications.
Crosslinking, Covalent Bonding, Entrapment, Encapsulation—These techniques, considered useful as immobilization methods, can be used as supplements to the immobilization technique. The techniques improve enzyme stability by, for example: reducing the protein's mobility and thereby reducing degradation of its three-dimensional structure or preventing loss of biocomponent from the immobilization matrix. For example, a selected gel-hardening agent, such as glutaraldehyde, polyethyleneimine, hexamethylenediamine or formaldehyde, may be used as a stabilizing agent in connection with entrapment as the mode of immobilization.
Freeze Drying (Lyophilization)-Freeze drying can provide for long-term preservation of microorganisms and enzymes. It involves removal of water from frozen bacterial suspensions by sublimation under reduced pressure. This process is performed in the presence of cryoprotective agents, such as glycerol and DMSO, which reduce damage caused during freezing. Dried cells can be kept for a long period at 4° C. if oxygen, moisture and light are excluded. The cells can later be rehydrated and restored to their previous state. Two types of useful freeze drying include centrifugal freeze drying and pre-freezing. Microorganisms that are sensitive to freeze drying can be dried using the liquid-drying method.
Heat Shock—A heat shock process involves heating vacuum-dried cells at a high temperature ( ̃300° C.) for a very short time ( ̃2-3 minutes). With the proper temperature and heating time selected for cell type, cells can be killed but retain a viable enzyme system. These dead cells can be kept for a long time away from moisture without any requirement of nutrients.
Addition of Carbohydrates and Polymers—Freeze-dried enzymes are often stabilized by the addition of stabilizers, such as polyalcohols and sugars like trehalose, maltose, lactose, sucrose, glucose and galactose. This stabilization is due to the interaction of the polyhydroxyl compound with water in the system, which effectively reduces interaction between protein and water, thereby strengthening hydrophobic interactions of the protein molecule to its surroundings.
Freezing—The metabolic activities of a microorganism may be reduced by storing the microorganism at very low temperatures (−150° C. to −190° C.) using liquid nitrogen.
Oxygenases as Biosensor Detection Elements
A biosensor utilizing monooxygenase enzymes and/or dioxygenase enzymes as the biocomponent may be used to detect oxygen-consumption in a biosensor environment. Oxygenase enzymes use molecular oxygen and insert either one atom (monooxygenases) or two atoms (dioxygenases) into an organic substrate. For example, cells containing oxygenase enzymes, which catalyze an oxygen-consuming reaction, may be layered on the tip of a fiber optic sensor (an oxygen optode), to form an optical biosensor.
Using whole cells, the final products of monooxygenase attack on chlorinated ethenes are chloride and carbon dioxide:

C2Cl3H+NADH+H++2O2→2CO2+NAD++3HCl.  (1)

Hence, for whole cells, TCE is converted to CO2 and chloride ions through formation of TCE epoxide. Other chlorinated ethenes (e.g., cis-DCE, trans-DCE and VC) have also been shown to degrade in a similar manner through epoxides under the action of monooxygenases. Although chlorinated epoxides are toxic to the bacteria that produce them, this toxicity has been substantially reduced by cloning genes for glutathione-S-transferase and glutathione synthesis (Rui, L., Y.-M. Kwon, K. F. Reardon, and T. K. Wood, “Metabolic Pathway Engineering to Enhance Aerobic Degradation of Chlorinated Ethenes and to Reduce Their Toxicity by Cloning a Novel Glutathione S-Transferase, an Evolved Toluene o-Monooxygenase, and γ-Glutamylcysteine Synthetase,” Environmental Microbiology, 2004, 6: pp. 491-500). In addition, toxicity has been reduced by using DNA shuffling and site-directed mutagenesis to create epoxide hydrolase enzymes from Agrobacterium radiobacter ADI which detoxify the chloroepoxides (Rui, L. Y., L. Cao, W. Chen, K. F. Reardon, and T. K. Wood, “Active site engineering of the epoxide hydrolase from Agrobacterium radiobacter ADI to enhance aerobic mineralization of cis-1,2-dichloroethylene in cells expressing an evolved toluene ortho-monooxygenase,” Journal of biological Chemistry, 2004. 279(45): pp. 46810-46817).

It was previously thought that PCE was completely resistant to oxygenase attack; however, it has been shown that the fully chlorinated PCE may be degraded by aerobic systems using toluene/xylene-o-monooxygenase (TOMO) from P. stutzeri (Ryoo, D., H. Shim, K. Canada, P. Barbieri, and T. K. Wood, “Aerobic Degradation of Tetrachloroethylene by Toluene-o-Xylene Monooxygenase of Pseudomonas stutzeri OX1,” Nature Biotechnology, 2000. 18(7): pp. 775-778). It has also been discovered that the chlorinated aliphatics PCE, TCE, 1,1-DCE, cis-DCE, trans-DCE, VC and chloroform may all be degraded individually and as mixtures by ToMO (Shim, H., D. Ryoo, P. Barbieri, and T. K. Wood, “Aerobic Degradation of Mixtures of Tetrachloroethylene, Trichloroethylene, Dichloroethylenes, and Vinyl Chloride by Toluene-o-Xylene Monooxygenase of Pseudomonas stutzeri OX1,” Applied Microbiology and Biotechnology, 2001. 56: pp. 265-269; Chauhan, S., P. Barbieri, and T. K. Wood, “Oxidation of Trichloroethylene, 1,1-Dichloroethylene, and Chloroform by Toluene/o-Xylene Monooxygenase from Pseudomonas stutzeri OX1,” Applied and Environmental Microbiology, 1998. 64(8): pp. 3023-3024). In the case of TCE and PCE, nonspecific oxygenases have been found that allow co-metabolic degradation of chlorinated species (Arciero, D.; T. Vannelli, M. Logan, and A. B. Hooper, “Degradation of Trichloroethylene by the Ammonia-Oxidizing Bacterium, Nitrosomonas europaea,” Biochemistry and Biophysics Research Communications, 1989. 159: pp. 640-643; Little, C. D., A. V. Palumbo, S. E. Herbes, M. E. Lidstrom, R. L. Tyndall, and P. J. Gilmer, “Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium,” Applied and Environmental Microbiology, 1988. 54(4): pp. 951-956; Shim, 2001).
As shown in equation (1), conversion of TCE requires input of NADH and O2. This requirement for cofactors is common to all of the chlorinated ethenes, and has limited development of biosensors utilizing oxygenases. The present inventors have developed methods, described below, to address delivery of cofactors.
Oxygen Delivery
Oxygen may be delivered through microcapillary tubing, to overcome sensor dependence on the local dissolved O2 concentration. FIG. 11 schematically depicts a fiber optic biosensor array having a capillary tube charged with one to two bars of oxygen. The capillary tube may, for example, have a diameter of about 1 to 2 mm (600 to 1600 μm ID). One end of the capillary may be fused shut, while the other end—the end proximal to the biosensor distal tips—may be capped with an oxygen permeable membrane. Such membranes are ubiquitous in the gas separation industry (Noble, R. D. and S. A. Stern, eds. Membrane Separations Technology: Principles and Applications. 1995, Elsevier. 499-552). Selecting a membrane with low permeation flux (<10−7 mol cm−2 s−1) should ensure that O2 remains in a saturated state in the liquid phase near the membrane surface without reaching a supersaturated state such that bubbles form. For the low mass transfer rates required to supply oxygenases with sufficient oxygen, it may be possible to use dense inorganic membranes (van der Haar, L. M. and H. Verweij, “Homogeneous porous perovskite supports for thin dense oxygen separation membranes,” Journal of Membrane Science, 2000. 180: pp. 147-155) having intrinsic permeation fluxes up to three orders of magnitude lower than typical polymeric membranes. It is known that oxygen diffusing through a membrane will quickly saturate the liquid near the surface—less than 0.005 seconds is needed to saturate the liquid within 10 μm of the membrane surface (Seinfeld, J. H. and S. N. Pandis, Atmospheric Chemistry and Physics: From Air Pollution to Climate Change. 1998, New York: John Wiley & Sons), and Henry's law can be used to calculate the liquid phase O2 concentration at the interface. The saturated dissolved O2 concentration at the membrane surface will drive diffusive mass transfer of oxygen away from the surface. In some embodiments, a ratio of oxygen capillaries to biosensors may be between 6:1 to 1:50, or between 1:1 to 1:25, or between 1:6 to 1:10. To optimize use of O2 by the oxygenases, the oxygen capillary may be ringed by four to ten fiber optical biosensors, depending on capillary diameter, as shown in FIG. 11. In an embodiment, this bundle of fiber optic cables surrounding an oxygen capillary may be viewed as a base unit, so that if more biosensors are required the unit can be repeated as necessary. It will be appreciated that the base unit may include cladding.
Calculations have been made to demonstrate the feasibility of the base unit configuration. In the model, a 1 mm diameter membrane is ringed by six 1 mm diameter optodes. Water surrounding the membrane and optodes is initially free of dissolved O2, and oxygen diffuses away from the membrane into pure water. The monooxygenase reactions are not included in this model, so the predicted diffusion rates will be lower than in the actual system. For the temperature used in the model, 298 K, the saturated O2 concentration at the membrane surface will be 1.3×10−3 M, with 1 bar O2 in the capillary.
The contours in FIG. 12 indicate fractions of this saturated concentration at three different times. After only five minutes of operation, the minimum dissolved O2 concentration above the 1 mm optodes is 10−4 M, a value three times greater than the level at which oxygen limits the rate of oxygenase reactions (Leahy, J. G. and R. H. Olsen, “Kinetics of toluene degradation by toluene-oxidizing bacteria as a function of oxygen concentration, and the effect of nitrate,” FEMS Microbiology Ecology, 1997. 23(1): pp. 23-30). Further, for the conditions considered, the calculated O2 dissolution rates indicate that a 600 μm ID, 10 cm long capillary will contain enough oxygen for more than two weeks of biosensor operation. This two week figure is lower bound because the dissolution rate will be slower if the aqueous sample contains any dissolved O2 when the experiment begins.
Alternatively, an oxygen capillary may have a distal end that is attached to a continuous and replaceable oxygen source, rather than a fused end that encloses a fixed concentration of oxygen.
Hardware for Fiber Optic Monitoring of Single Contaminants
Fiber optic biosensors suffer from less signal loss than electronic sensors, so they can be used at longer distances, and they have a small size, typically 1 mm or less in diameter, that allows them to be easily transported and utilized in a wide range of applications. The small size of fiber optic sensors allows for bundling of sensors for different contaminants into an optical cable that provides simultaneous measurements with one device. Fiber optic sensors also allow for low cost, simultaneous measurements at different locations or depths (i.e., spatial resolution), as well as continuous monitoring (i.e., temporal resolution).
Fiber optic oxygen sensors (oxygen “optodes”) as transducers for enzyme biosensors have been described (Wolfbeis, O. S., Fiber Optic Chemical Sensors and Biosensors, Vols. I and II. 1991, Boca Raton: CRC Press; Scheper, T., C. Müller, K. D. Anders, E. F., F. Plotz, O. Thordsen, and K. Schügerl, “Optical Sensors for Biotechnological Applications,” Biosens. Bioelectron., 1994. 9(1): pp. 73-83). These sensors are based on attenuation by oxygen of the fluorescence of a tip-immobilized dye, which is often a ruthenium complex (Amao, Y., “Probes and polymers for optical sensing of oxygen,” Microchimica Acta, 2003. 143(1): pp. 1-12; Tang, Y, T. E. C., Tao Z Y, Bright F V, “Sol-gel-derived sensor materials that yield linear calibration plots, high sensitivity, and long-term stability,” Analytical Chemistry, 2003. 75(10): pp. 2407-2413; Zhang P, Guo J, Wang Y, Pang W, “Incorporation of luminescent tris(bipyridine)ruthenium(II) complex in mesoporous silica spheres and their spectroscopic and oxygen-sensing properties,” Materials Letters, 2002. 53(6): pp. 400-405; Klimant, I. and O. S. Wolfbeis, “Oxygen-Sensitive Luminescent Materials Based on Silicone-Soluble Ruthenium Diimine Complexes,” Analytical Chemistry, 1995. 67(18): pp. 3160-3166).
Higher pO2 levels at the optode will quench the florescence of the dye on the oxygen optode tip; thus, the dynamic response of these biosensors to an analyte will be opposite that of the pH-based biosensors. Namely, oxygen-based biosensors fluoresce more as oxygen is consumed whereas pH-based biosensors fluoresce more as protons are produced. Measurement of the pO2-dependent florescence requires an optoelectronic instrumentation system to provide optical excitation to the optode, collect florescence, and convert this optical signal into an amplified electronic signal with minimal noise. In addition to maximum sensitivity, application to in situ groundwater contamination monitoring requires the optoelectronic instrumentation to be portable with corresponding constraints on size, weight, ruggedness and power consumption. Similar hardware has previously been developed for pH-based fiber optic biosensors (see FIG. 3).
An exemplary system comprises an optical excitation source, a fiber optic system for delivering the excitation and returning the florescence signal, a photodetector for optical to electronic conversion, and electronic amplification and signal processing circuitry. Although halogen lamps have previously been used for florescence excitation in fiber optic florescent sensors, advances in blue and ultraviolet GaN LED technology over the past decade have made LEDs a superior choice due to their better fiber coupled power efficiency, adequate spectral characteristics without filtering, easy modulation at MHz rates and long operating life. GaN laser diodes or near-infrared laser diodes doubled into the blue with non-linear optic crystals may also be used. The fiber optic system must separate the return florescence out of the same fiber used to carry the excitation to the optode. Options for splitting include bifurcated fibers, double-clad fibers, multimode fiber couplers, fiber or free-space dichroic beam splitters and circulators. The optical geometry of the fiber optic probe is also important, and improvements have been reported with the use of tapered fibers (Fielding, A. J. and C. C. Davis, “Tapered Single-Mode Optical Fiber Evanescent Coupling,” IEEE Photonics Technology Letters, 2002. 14(1): pp. 53-55). Photomultiplier tubes (PMTs) and avalanche photodiodes (APDS) offer internal electrical gain and are often used for high sensitivity florescent detection. However, cost, weight, size and power supply requirements favor simpler hybrid p-i-n photodiodes with integrated amplifiers and may offer sufficiently low noise for many applications.
Researchers have developed oxygen-based sensors for ethanol (Mitsubayashi, K., T. Kon, and Y. Hashimoto, “Optical bio-sniffer for ethanol vapor using an oxygen-sensitive optical fiber,” Biosensors & Bioelectronics, 2003. 19(3): pp. 193-198), glucose (Wolfbeis, O. S., I. Oehme, N. Papkovskaya, and I. Klimant, “Sol-gel based glucose biosensors employing optical oxygen transducers, and a method for compensating for variable oxygen background,” Biosensors and Bioelectronics, 2000. 15(1-2): pp. 69-76), L-glutamate (Dremel, B. A. A., R. D. Schmid, and Wolfbeis O, S., “Comparison of 2 fiber-optic L-glutamate biosensors based on the detection of oxygen or carbon-dioxide, and their application in combination with flow-injection analysis to the determination of glutamate,” Analytica Chimica Acta, 1991. 248(2): pp. 351-359), lactate, cholesterol and other analytes. However, development of enzymatic biosensors has been limited where NADH is required as a cofactor.
The Peroxide Shunt
Although NADH-requiring biosensors have been made (Taylor, M., D. C. Lamb, R. J. P. Cannell, M. J. Dawson, and S. L. Kelly, “Cofactor recycling with immobilized heterologous cytochrome P450 105D1 (CYP105D1),” Biochemical and Biophysical Research Communications, 2000, 292(2): pp. 708-711; Lisdat, F. and U. Wollenberger, “Trienzyme amplification system for the detection of catechol and catecholamines using internal co-substrate regeneration,” Analytical Letters, 1998. 31(8): pp. 1275-1285), their long-term use and performance are limited because of problems encountered in supplying NADH. Thus, any oxygenase sensor must either provide an alternative electron donor or recycle NADH (Park, D. H., C. Vieille, and J. G. Zeikus, “Bioelectrocatalysts—Engineered oxidoreductase system for utilization of fumarate reductase in chemical synthesis, detection, and fuel cells,” Applied Biochemistry and Biotechnology, 2003. 111(1): pp. 41-53). In electronic biosensors, efforts have been made to directly supply electrons. However, this approach has limitations, requiring very stable enzymes that nonetheless do not survive long on the biosensor surface.
An alternative approach to addressing the “NADH problem” is to utilize the so-called peroxide shunt (see FIG. 13). This approach has not been implemented in biosensors, but it is known that hydrogen peroxide can be used, instead of NADH, to donate both two electrons and atomic oxygen in the monooxygenase reaction (Jiang, Y., P. C. Wilkens, and H. Dalton, “Activation of the Hydroxylase of sMMO from Methylococcus capsulatus (Bath) by Hydrogen Peroxide,” Biochimica et Biophysica Acta, 1993. 1163: pp. 105-112). With the peroxide shunt, O2 and NADH are no longer needed for monooxygenase-catalyzed oxidations. This mechanism has been shown for methane monooxygenases and toluene o-monooxygenase (Newman, L. M. and L. P. Wackett, “Purification and Characterization of Toluene 2-Monooxygenase from Burkholderia cepacia G4,” Biochemistry, 1995. 34: pp. 14066-14076), which along with the entire family of TCE-degrading monooxygenases contains a common oxygen-bridged iron cluster, Fe—O—Fe, in the common 250 KDa hydroxylase.
The peroxide shunt may remove the need for NADH regeneration, which may increase biosensor lifetime since living cells are not required, where electrons and oxygen are supplied in the form of peroxide, and energy metabolism is no longer necessary. This is important for some oxygenases, such as those that act on chlorinated aliphatics, since these enzymes are not stable outside the cell (Fox, B. G., W. A. Froland, J. E. Dege, and J. D. Lipscomb, “Methane Monooxygenase from Methylosinus trichosporium OB3b,” Journal of Biological Chemistry, 1989. 264(17): pp. 10023-10033; Oppenheim, S. F., J. M. Studts, B. G. Fox, and J. S. Dordick, “Aromatic hydroxylation catalyzed by toluene-4-monooxygenase in organic solvent/aqueous buffer mixtures,” Applied Biochemistry & Biotechnology, 2001. 90: pp. 187-197).
The peroxide shunt changes the overall reaction of TCE, from that shown in equation (1), to:

C2Cl3H+H2O2→2CO2+3HCl.  (2)

Based on equation (2), at least three detection schemes are feasible: detection of pH changes using fluoresceinamine fluorescence (higher TCE concentrations result in lower pH values); co-immobilization of catalase and iron or MnO2 to catalyze the breakdown of H2O2 to O2 and H2O, and detection of O2 (higher TCE concentrations result in lower O2 concentrations); detection of H2O2 removal using luminol chemiluminescence.
The first approach is similar to that described above to produce biosensors based on dehalogenases. H2O2 sensors based on the second and third options have been reported (Freeman, T. M. and W. R. Seitz, “Chemiluminescence fiber optic probe for hydrogen peroxide based on the luminol reaction,” Anal. Chem., 1978. 50: pp. 1242-1246; Genovesi, L., H. Pedersen, and G. H. Sigel. The development of a generic peroxide sensor with application to the detection of glucose. in SPIE—International Society of Optical Engineering. 1988.), as have glucose biosensors based on the third approach (Swindlehurst, C. A. and T. A. Nieman, “Flow-injection determination of sugars with immobilized enzyme reactors and chemiluminescence detection,” Anal. Chim. Acta, 1988. 205: pp. 195-205).
A key requirement of being able to use the peroxide shunt is delivery of H2O2 to the cells on the optical fibers. The peroxide concentration must be high enough to drive the reaction, but low enough so as not to damage the cells or impact the environment of the sensor tip. Delivery of H2O2 may occur via diffusion from a membrane-capped capillary tube that may be bundled with the optical fibers, in a manner analogous to the delivery of oxygen described above (FIG. 11).
Biosensor Arrays for Evaluating Mixtures of Analytes
In biosensor arrays, where a number of different biocomponents are present, each providing a signal, the set of signals may be interpreted to provide multianalyte identification and measurement. With effective chemometric analysis to interpret the signal set, sensor arrays have been shown to be highly effective at resolving analyte mixtures, even if each individual sensor is only moderately specific and the analyte range of one sensor overlaps with that of another (Epstein, J. R. and D. R. Walt, “Fluorescence-based fibre optic arrays: a universal platform for sensing,” Chemical Society Reviews, 2003. 32(4): pp. 203-214; Schauer, C. L. F. J. Steemers, and D. R. Walt, “A cross-reactive, class-selective enzymatic array assay,” Journal of the American Chemical Society, 2001. 123(38): pp. 9443-9444; Albert, K. J., N. S. Lewis, C. L. Schauer, G. A. Sotzing, S. E. Stitzel, T. P. Vaid, and D. R. Walt, “Cross-reactive chemical sensor arrays,” Chemical Reviews, 2000. 100(7): pp. 2595-2626; Lee, M. and D. R. Walt, “A fiber-optic microarray biosensor using aptamers as receptors,” Analytical Biochemistry, 2000. 282(1): pp. 142-146).
To evaluate mixtures of analytes, an array of biosensors can be employed, where each biosensor utilizes a different biocomponent or a mixture of biocomponents (and each biocomponent interacts with one type of fluorophore on the biosensor that fluoresces at a particular wavelength). In an embodiment, individual biocomponents may detect analytes that are not chemically similar. For example, one biocomponent on a biosensor in an array may detect a halogenated organic compound, while another biocomponent on the same or a different biosensor in the array detects a heavy metal, and a third biocomponent on the same or a different biosensor in the array detects starch.
In another embodiment, biosensors/biocomponents in an array may detect closely-related, chemically similar compounds. In this case, a single type of biocomponent, e.g., toluene o-monooxygenase (TOM), may detect multiple analytes, e.g., TCE and DCE. In order to detect and resolve closely-related compounds, each biosensor in an array may utilize a different variant of one type of biocomponent. The biocomponent variants have different specificities for each analyte, which allows for measurement and resolution of complex mixtures.
To illustrate how the use of variant biocomponents addresses the detection and quantification of similar analytes in a mixture, the following example is provided. Consider three biosensors, each of which responds linearly to increasing concentrations of each of three similar analytes. If the response factors of the biosensor/analyte pairs are those shown in Table 7 (response factor=sensor signal/analyte concentration), the response of each of the sensors to a mixture of the three analytes can be described by the algebraic equations:

S1=10CA+5CB+1.5CC 

S2=3CA+8CB+1.5CC 

S3=1.5CA+3CB+7CC 

in which Si is the signal of each sensor (1, 2 or 3) and Cj is the concentration of the analyte (A, B or C). When a single sensor is placed in a sample of unknown concentrations CA, CB and CC, the resulting signal (e.g., S1) cannot be used to determine the individual values of CA, CB and CC. However, if all three Si values are available, then the equations above can be solved to yield the values CA, CB and CC.








TABLE 7







Hypothetical linear response factors of three sensors to three analytes


when each analyte is measured separately from the others.












Response factor for:
Analyte A
Analyte B
Analyte C















Sensor 1
10
5
1.5



Sensor 2
3
8
1.5



Sensor 3
1.5
3
7









In more complex situations, the response of a biosensor to an analyte may not be linear. Methods from the field of chemometrics, the application of statistics to chemical problems, can be applied to the information obtained by biosensor arrays. For example, principle component analysis is well suited for linear problems, while neural networks can be used for nonlinear problems. Although the minimum number of biosensors/biocomponents in an array must be equal to the number of analytes to be detected, it will generally be desirable to have more biosensors/biocomponents present in an array to provide redundant information and thus more certainty in the resulting measurements.
Transducers for biosensor arrays include any of those described above which utilize any optical, electrochemical or physical method that allows the signal from each biosensor in the array to be measured independently.
Biocomponents with different ranges of specificity can be developed or obtained through a variety of methods, including bioprospecting, DNA shuffling and/or selection by display (e.g., yeast or phage), as described in more detail below.
DNA Shuffling/Saturation Mutagenesis
Frequently, known enzymes do not have certain desired properties (e.g., selectivity toward TCE). Although traditional mutagenesis methods can be used to improve enzymes, they are slow and not likely to truly optimize the enzyme. Directed evolution or DNA shuffling (Stemmer, W. P. C., “DNA Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution,” Proceedings of the National Academy of Sciences, 1994. 91: pp. 10747-10751; Stemmer, W. P. C., “Rapid Evolution of a Protein in vitro by DNA Shuffling,” Nature, 1994. 370: pp. 389-391; Crameri, A. and W. P. C. Stemmer, “Combinatorial Multiple Cassette Mutagenesis Creates All the Permutations of Mutant and Wild-Type Sequences,” BioTechniques, 1995. 18(2): pp. 194-196; Crameri, A., E. A. Whitehorn, E. Tate, and W. P. C. Stemmer, “Improved Green Fluorescent Protein by Molecular Evolution Using DNA Shuffling,” Nature Biotechnology, 1996. 14: p. 315-319) is a powerful mutagenesis technique that mimics the natural molecular evolution of genes in order to efficiently redesign them. The power of DNA shuffling lies in its ability to introduce multiple mutations into a gene in order to create new enzymatic activity.
DNA shuffling uses PCR without oligo primers to reassemble a gene from random 10-300 bp DNA fragments generated by first cleaving the gene with DNase. After reassembling the original gene from these fragments using a series of homologous recombinations and extensions with dNTPs and polymerase, normal PCR is performed to yield the full-length gene with random mutations. The mutations arise from infidelity in the assembly process, PCR infidelity and errors introduced in the assembly process by insertion of mutated gene fragments (controlled by the researcher by adding specific oligos or DNA fragments from related but not identical genes). DNA shuffling advantageously introduces mutations much more efficiently than other methods, and it may be used to create a chimeric gene by reassembling closely related genes. It has been used to increase β-lactamase antibiotic activity by 32,000-fold (Stemmer, Nature, 1994), to increase the fluorescence of green fluorescent protein by 45-fold (Crameri, 1996), and to evolve a fucosidase from β-galactosidase (Zhang, J.-H., G. Dawes, and W. P. C. Stemmer, “Directed Evolution of a Fucosidase from a Galactosidase by DNA Shuffling and Screening,” Proceedings of the National Academy of Sciences, 1997. 94: pp. 4504-4509). In the presently disclosed biosensors, DNA shuffling may be used, for example, to increase the specificity of monooxygenases for chlorinated ethenes.
Molecular breeding, the combination of similar genes from different bacteria to introduce even greater genetic diversity (Minshull, J. and W. P. C. Stemmer, “Protein Evolution by Molecular Breeding,” Current Opinion in Chemical Biology, 1999. 3: pp. 284-290), may also be used with a set of monooxygenase genes to make advances in enzymatic activity for chlorinated ethenes. Molecular breeding has been used successfully to produce better subtilisin proteases by combining twenty-six unrelated protease genes (Ness, J. E., M. Welch, L. Giver, M. Bueno, J. R. Chemy, T. V. Borchert, W. P. C. Stemmer, and J. Minshull, “DNA Shuffling of Subgenomic Sequences of Subtilisin,” Nature Biotechnology, 1999. 17: pp. 893-896).
Saturation mutagenesis may also be used to enhance enzyme selectivity since it can be used to introduce all possible mutations at key sites, for activity identified by DNA shuffling, or adjacent sites to explore a larger fraction of the protein sequence space. Saturation mutagenesis can provide more comprehensive information than can be achieved by single-amino acid substitutions and can overcome drawbacks of random mutagenesis.
Hardware for Monitoring Multiple Optodes
Oxygen optode hardware based on fiber optic sensors is readily adaptable to the collection of measurements from multiple sensors. Each of the multiple optical biosensors may be connected to an optoelectronic instrumentation system, described above, via its own dedicated fiber. In an embodiment, optical source and detection hardware can be used to interrogate a number of fiber sensors by switching connections. A biosensor array system may use commercially available fiber optic switches to allow a single optical source and detector to be switched between the different fiber probes on a time scale of milliseconds with minimal insertion loss. However, low cost LED and amplified p-i-n technology may be used to obtain adequate sensitivity, and separate sources and detectors may instead be provided for each channel, thereby creating a system that can provide tradeoffs between redundancy for greater reliability and the number of different channels.
Example 1
A biosensor employing a pH optode with dehalogenase carried by whole cells immobilized by gel entrapment as a biocomponent was produced by the following method (see FIGS. 5 and 7). A distal tip was coupled to a 1 m long polymethylmethacrylate (PMMA) fiber optic cable. Cells stored at 4° C. in phosphate-buffered saline were centrifuged at 15,000×g for 2 minutes. The pellet was washed twice with saline (9 g/L NaCl, pH 7.1) containing 50 μg/mL of chloramphenicol. Next, sodium-alginate (4% w/v in water) containing about 100 μg/mL of chloramphenicol was added and mixed well with the cell pellet. This cell-alginate mixture was kept for 5 minutes at room temperature before it was used to make the biosensor. The cell-alginate mixture was stirred well with a pipette tip and a small drop of the gel was carefully deposited on the tip of the pH optode. The tip was dipped into an ice-cold solution of 7% (w/v) of CaCl2.2H2O for 15 minutes to form a crosslinked network. After immobilization, the tip was about 2 mm in diameter. A protease inhibitor cocktail in 1 mL of saline solution was prepared by adding 215 mg of lyophilized protease inhibitor in a solution containing 1 mL DMSO (dimethyl sulfoxide) and 4 mL deionized water. The cocktail had a broad specificity for the inhibition of serine, cysteine, aspartic and metalloproteases, and aminopeptidases.
Example 2
A biosensor was prepared with microorganism strain ADP encapsulated in alginate, according to the method of Example 1, and then coated with poly-L-lysine (PLL). The Ca-alginate bead on the biosensor tip (nearly 1 mm) was washed twice with saline solution (9 g/L NaCl in water). The biosensor tip was immersed in 10 mL of 0.4% (w/v) of poly-L-lysine followed by HCl in saline for 30 minutes at 30° C. In order to remove unreacted PLL from the bead surface, the tip was washed with saline solution.
Example 3
The release of a proton from the dehalogenation reaction is detected as a pH change at the end of the optical fiber, and thus as a change in fluorescence intensity (FIG. 14). Fiber optic biosensors for 1,2-dichloroethane (DCA), ethylene dibromide (EDB), atrazine, 1-chlorohexane and Lindane (γ-hexachlorocyclohexane) have been developed (Campbell, 1998; Das, N., Development and Characterization of a Biosensor for Atrazine in Groundwater, Chemical Engineering. 2000, Colorado State University: Fort Collins). These biosensors have linear response ranges over several orders of magnitude in concentration, and detection in the ppt (ng/L) range has been achieved (FIG. 15). Because dehalogenases do not require energy or cofactors, the cells in which they are immobilized need not be living. This fact, and the stability of the enzymes, allows the biosensors to retain activity for many weeks. In one test (FIG. 16), the biosensor response to 5 ppb of 1,2-dibromoethane declined by only 20% in more than 50 days. Sensitive measurement is still possible even at the end of the test; only a recalibration is required.
Example 4
The ability of the biosensors to provide a continuous signal and to function in a soil environment has been demonstrated in laboratory soil column tests. Atrazine at three increasing concentrations was pumped through a 0.5 m glass column filled with silty sand and the signal from an atrazine biosensor was monitored (FIG. 17). Responses are scaled to Day 0.
Example 5
FIG. 18 shows the response of a biosensor to a pulse of phenol. The biocomponent was Burkholderia cepacia JS150, immobilized in calcium alginate on the end of an oxygen optode. Initially, the solution contained no phenol. At the time indicated, a pulse of phenol was added to increase the concentration to 30 ppm (0.3 mM). The response of the phenol biosensor was large (45 units), indicating good sensitivity. A bare oxygen optode located in the same solution recorded a steady signal during this time. The signal from the phenol biosensor decreased because oxygen was consumed in the oxygenase-catalyzed degradation of phenol at the tip of the biosensor. Approximately 85 minutes after the pulse of phenol, the signal stabilized at a new steady state.
Example 6
The enzyme toluene o-monooxygenase (TOM), expressed by a strain of Escherichia coli bacteria carrying the TOM genes on a plasmid has been used in a biosensor. The analyte was toluene, and the sensor was tested on aqueous solutions containing 1-10 mg/L toluene. As shown in FIG. 19, a linear relationship between the aqueous toluene concentration and the change in the intensity of the emitted fluorescent light was obtained.
Example 7
DNA shuffling is used to generate monooxygenases with differing specificities (reaction rates) toward each of six chlorinated ethenes (PCE, TCE, three DCEs and VC). A set of bacteria, each containing one of these modified monooxygenases, is used to create a set of biosensors, the signals of which can be used to resolve individual concentrations of analytes within a mixture.
In the family of seven monooxygenases (Table 8), each enzyme is encoded by six open-reading frames that give rise to an active monooxygenase. These six genes code for a hydroxylase (dimer of 3 proteins that contains two active sites that each hold the binuclear, oxygen-bridged iron cluster, Fe—O—Fe), reductase ( ̃40 KDa, which transfers two electrons from NADH), small coupling protein ( ̃16 KDa), and either a 12.5 KDa Rieske-type ferredoxin (tbuB of T3MO, touC of ToMO, and tmoC of T4MO) or a 11 KDa protein whose function is not known, but which has recently been suggested to insert iron into the hydroxylase apoenzyme (Powlowski, J., J. Sealy, V. Shingler, and E. Cadieux, “On the Role of DmpK, and Auxiliary Protein Associated with Multicomponent Phenol Hydroxylase from Pseudomonas sp. strain CF600,” Journal of Biological Chemistry, 1997. 272: pp. 945-951).
Random mutagenesis for enhanced PCE, DCE and VC degradation is initiated using vector pBSKan-ToMO (8983 bp) with the complete, wild-type tou locus expressed constitutively in the stable pBSKan vector (4139 bp), since this monooxygenase is the only one with known activity for PCE. The pBSKan-ToMO vector is purified with Qiagen MIDI prep kits, and the touABCDEF genes, which encode the complete ToMO, are amplified using PCR. Shuffling then proceeds by DNase treatment of the isolated touABCDEF locus and recovery of smaller than 50 bp fragments using Centr-Sep columns. The original DNA fragments are re-built using high-fidelity Pfu polymerase (so that most of the introduced errors are from mismatches during annealing rather than from polymerase error), deoxyribonucleotides and thermal cycling without oligos for about 40 cycles. After checking for a smear of size approximately the same as ToMO via gel electrophoresis, re-assembly PCR is conducted using oligo primers containing the built-in restriction sites KpnI and NotI and designed to produce the touABCDEF locus. The resulting reassembly DNA is viewed using horizontal gel electrophoresis, purified with an ethanol/phenol/chloroform extraction, digested with KpnI and NotI, and ligated into the purified pBSKan-ToMO vector with the wild-type touABCDEF path removed. The ligated plasmids with shuffled variants are cleaned with butanol and electroporated into E. coli TG1 using a Bio-Rad Gene Pulser. Electroporation of E. coli TG1 with plasmids containing the shuffled touABCDEF locus yields about 100 colonies per plate after incubation for 16 hr at 37° C. Colonies expressing active ToMO are distinguished based on their blue color on LB plates.
The variant monooxygenases are screened using live cells by detecting the final product of chlorinated ethene degradation, chloride, measured spectrophotometrically by the procedure of Bergmann and Sanik modified for use in a 96-well plate format (Canada, K. A., S. Iwashita, H. Shim, and T. K. Wood, “Directed Evolution of Toluene ortho-Monooxygenase for Enhanced 1-Naphthol Synthesis and Chlorinated Ethene Degradation,” Journal Bacteriology, 2002. 184: pp. 344-349). Bacteria from wells with the highest signals are saved, re-checked on additional 96-well plates, and the plasmids isolated from the highest-expressing strains used for subsequent rounds of shuffling as well as DNA sequencing. In this way, enzymes are generated that are specific for individual chlorinated ethenes (e.g., PCE, DCE, VC).
Molecular breeding (combining similar genes from different bacteria) (Minshull, 1999) may be conducted in the manner described above using the seven monooxygenase operons available in Table 8 in order to find variants with enhanced rates for specific chlorinated ethenes. Shuffling proceeds as described above except seven monooxygenase loci are shuffled at once rather than just ToMO; screening proceeds as for shuffling of the individual ToMO. This method introduces greater genetic diversity and can lead to even larger increases in enzymatic activity (Minshull, 1999).







TABLE 8







Family of similar monooxygenases for DNA shuffling.













Fe—O—Fe


Monooxygenase
Bacterium
Locus
cofactor





soluble methane
M. trichosporium
mmoXYBZY′C [46]
Present [47]


monooxygenase
OB3b




(sMMO)





soluble methane
M. capsulatus
mmoXYBZY′C [48]
Present [49]


monooxygenase
Bath




(sMMO)





toluene-o-
B. cepacia G4
tomA0A1A2A3A4A5
Present [51]


monooxygenase

[50]



(TOM)





toluene/xylene-o-
P. stutzeri OX1
TouABCDEF [52]
Present [53]


monooxygenase





(ToMO)





toluene-p-
P. mendocina KR1
TmoABCDEF [54]
Present


monooxygenase


[51, 55]


(T4MO)





toluene-m-
R. pickettii PK01
tbuA1UBVA2C [56]
Present [56]


monooxygenase





(T3MO)





phenol 
P. CF600
DmpKLMNOP [57]
Present [51]


hydroxylase (PH)









Example 8
DNA shuffling and saturation mutagenesis of toluene o-monooxygenase (TOM) of Burkholderia cepacia G4, toluene o-xylene-monooxygenase (TOMO) of Pseudomonas stutzeri OX1, toluene 4-monooxygenase (T4MO) of P. mendocina KR1, and toluene 3-monooxygenase (T3MO) of R. pickettii PK01 have been performed. DNA shuffling has also been used to create the more efficient TOM-Green for the oxidation of naphthalene and the mineralization of TCE (Canada, 2002). FIG. 20 depicts a trichloroethene biosensor utilizing TOM-Green as the biocomponent.
Saturation mutagenesis was used to refine the TOM-Green enzyme to create an enzyme with three times greater activity for chloroform and a variant with two times greater naphthalene oxidation (Rui, L., Y.-M. Kwon, A. Fishman, K. F. Reardon, and T. K. Wood, “Saturation Mutagensis of Toluene ortho-Monooxygenase of Burkholderia cepacia G4 for Enhanced 1-Naphthol Synthesis and Chloroform Degradation,” Applied and Environmental Microbiology, 2004. 70: pp. 3246-3252). These efforts have produced a set of enzymes that have the differential reaction rates needed for multianalyte monitoring. For example, as compared with TOM, TOM-Green is 180% faster at degrading TCE and 240% faster at degrading 1,1-DCE, but only 70% as fast at degrading toluene. And, as compared to TOM, ToMO is 1600% faster for VC and 370% faster for cis-1,2-DCE, but only 76% as fast for chloroform degradation. Enzymes of varying specificity, as illustrated by the examples for toluene and TCE in Table 9, have been produced.







TABLE 9







Reaction rates of selected monooxygenase


variants produced via protein engineering











Toluene

Initial TCE



oxidation ratea, 

degradation rateb, 



nmol/min/mg

nmol/min/mg


Enzyme
protein
Enzyme
protein





Wild-type ToMO
6.1 ± 0.1
wild-type ToMO
0.41 ± 0.02


TmoA I100S
22.7 ± 1.6 
I100Q
0.85 ± 0.01


TmoA
1.5 ± 0.3
K160N
0.53 ± 0.01


G103S/A107G





aToluene oxidation rate determined via GC with 109 μM toluene calculated based on Henry's law.


bInitial TCE degradation rates at 67 μM (actual liquid phase concentration) TCE






Example 9
The haloalkane dehalogenase LinB was used to develop biosensors for several halogenated hydrocarbons. Comparison of the sensitivity of these biosensors for two analytes with the reported activity of LinB toward those compounds (Table 10) reveals that even relatively small differences in activity—well within the range of the protein engineering—can produce significantly different biosensor sensitivities.







TABLE 10







Comparison of reported activity and biosensor


sensitivity for LinB haloalkane dehalogenase.










LinB activity (% of 1-
Biosensor sensitivity


Analyte
chlorobenzene rate)*
(ΔV/ppb analyte)





1,2-dibromoethane
355
0.29


1-chlorohexane
145
0.21





*Damborsky, J., E. Rorije, A. Jesenska, Y. Nagata, G. Klopman, and W. J. G. M. Peijnenburg, “Structure-Specificity Relationships for Haloalkane Dehalogenases,” Environ. Toxicol. Chem., 2001. 20(12): pp. 2681-2689.






All patents, patent applications and literature publications cited in the present disclosure and/or shown in the attached list of “REFERENCES” are incorporated herein by reference in their entirety.
Changes may be made in the above systems and methods without departing from the scope hereof. It should thus be noted that the matter contained in the above description or shown in the accompanying drawings should be interpreted as illustrative and not in a limiting sense. The following claims are intended to cover all generic and specific features described herein, as well as all statements of the scope of the present systems and methods, which, as a matter of language, might be said to fall there between.
REFERENCES


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## Claims

1. A biosensor for use in measuring a concentration of an organic compound analyte, said biosensor comprising:
a distal portion;
an optical transducer disposed in the distal portion of said biosensor capable of measuring oxygen concentration in situ;
a biocomponent disposed in the distal portion of said biosensor, said biocomponent immobilized within a hydrogel or polymer matrix, and said biocomponent comprising one or more oxygenases from EC family 1.13 and EC family 1.14 for carrying out an oxidation of the organic compound analyte.

2. The biosensor of claim 1, wherein the one or more oxygenases are selected from the group consisting of toluene o-monooxygenase (TOM), soluble methane monooxygenase (sMMO), toluene xylene-o-monooxygenase (ToMO), toluene p-monooxygenase (T4MO), toluene-m-monooxygenase (T3MO), phenol hydroxylase (PH) and TOM-Green.

3. The biosensor of claim 1, wherein the organic compound analyte is one or more halogenated ethene.

4. The biosensor of claim 3, wherein the one or more halogenated ethene is a chlorinated ethene selected from the group consisting of tetrachloroethene (PCE), trichloroethene (TCE), dichloroethene isomers and vinyl chloride (VC).

5. The biosensor of claim 1, further comprising a device for delivering one or more reagents.

6. The distal biosensor of claim 5, wherein the reagent is selected from oxygen and hydrogen peroxide.

7. The biosensor of claim 1 wherein the biocomponent is a microorganism containing the one or more oxygenases selected from the group consisting of Burkholderia cepacia G4, Pseudomonas stutzeri OX1, P. mendocina KR1, M. trichosporium OB3b, M capsulatus Bath, P. stutzeri OX1, and R. pickettii PK01.

8. The biosensor of claim 7 wherein the one or more oxygenases include a monooxygenase.

9. The biosensor of claim 8 wherein the monooxygenase is encoded by a polynucleotide comprising one or more molecular modifications obtainable using one or more methods selected from the group consisting of site-directed mutagenesis, DNA shuffling and saturation mutagenesis.

10. The biosensor of claim 7 wherein the one or more oxygenases include a dioxygenase.

11. The biosensor of claim 7, wherein the microorganism comprises at least one plasmid comprising one or more polynucleotides encoding for the one or more oxygenases.

12. The biosensor of claim 11 wherein one or more nucleic acids in the at least one plasmid is mutated using one or more methods selected from the group consisting of site-directed mutagenesis, DNA shuffling and saturation mutagenesis.

13. The biosensor of claim 7 wherein said microorganism is selected from the group consisting of live cells and dead cells.

14. The biosensor of claim 1 wherein the biocomponent is layered atop a transducer layer of an oxygen-sensitive fluorophore.

15. The biosensor of claim 1 wherein the biocomponent is lyophilized.

16. The biosensor of claim 1, wherein said biocomponent further comprises one or more of a gel-hardening agent and a stabilizing agent.

17. The biosensor of claim 16, wherein the one or more of a gel-hardening agent and a stabilizing agent comprises one or more of glutaraldehyde, polyethyleneimine, hexamethylenediamine and formaldehyde.

18. The biosensor of claim 1, wherein the hydrogel comprises one or more of algal polysaccharides, agar, agarose, alginate, K-carrageenan, gelatin, collagen, pectin, poly(carbamoyl) sulfonate, locust bean gum and gellan.

19. The biosensor of claim 1, wherein the polymer matrix comprises one or more of polyacrylamide, polystyrene, polymethacrylate, polyvinylalcohol and polyurethane.

20. The biosensor of claim 1, wherein said biocomponent is encapsulated in a microporous semipermeable membrane.

21. The biosensor of claim 20, wherein the membrane comprises one or more of cellulose acetate, polycarbonate, collagen, acrylate copolymers, poly(ethylene glycol), polytetrafluoroethylene (PTFE), agarose, and alginate-polylysine-alginate microcapsules formed of alginate and polylysine.