U.S. patent application number 14/254817 was filed with the patent office on 2015-07-16 for novel chemistry used in biosensors.
This patent application is currently assigned to OHMX Corporation. The applicant listed for this patent is OHMX Corporation. Invention is credited to Michael J. Ahrens, Paul A. Bertin, Amanda Eckermann, Dimitra Georganopoulou, Harry B. Gray, Markus Franz Wunder.
Application Number | 20150198552 14/254817 |
Document ID | / |
Family ID | 40567805 |
Filed Date | 2015-07-16 |
United States Patent
Application |
20150198552 |
Kind Code |
A9 |
Ahrens; Michael J. ; et
al. |
July 16, 2015 |
NOVEL CHEMISTRY USED IN BIOSENSORS
Abstract
The invention relates to novel compositions and methods for the
detection of analytes using the nuclear reorganization energy,
.lamda., of an electron transfer process.
Inventors: |
Ahrens; Michael J.; (West
Lafayette, IN) ; Bertin; Paul A.; (Western Springs,
IL) ; Eckermann; Amanda; (Evanston, IL) ;
Georganopoulou; Dimitra; (Lincolnwood, IL) ; Gray;
Harry B.; (Pasadena, CA) ; Wunder; Markus Franz;
(Evanston, IL) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
OHMX Corporation |
Evanston |
IL |
US |
|
|
Assignee: |
OHMX Corporation
Evanston
IL
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20140311922 A1 |
October 23, 2014 |
|
|
Family ID: |
40567805 |
Appl. No.: |
14/254817 |
Filed: |
April 16, 2014 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
12253875 |
Oct 17, 2008 |
8734631 |
|
|
14254817 |
|
|
|
|
61087102 |
Aug 7, 2008 |
|
|
|
61087094 |
Aug 7, 2008 |
|
|
|
60980733 |
Oct 17, 2007 |
|
|
|
Current U.S.
Class: |
205/777.5 ;
204/292; 29/825; 546/2 |
Current CPC
Class: |
C12Q 1/485 20130101;
C12Q 1/37 20130101; G01N 27/30 20130101; Y10T 29/49117 20150115;
C12Q 1/003 20130101 |
International
Class: |
G01N 27/30 20060101
G01N027/30 |
Claims
1. A composition comprising 1) an electrode comprising a covalently
attached electroactive complex (EAM), said EAM comprising a
transition metal and at least one cyano ligand; or 2) an electrode
comprising a) a first species comprising a functional group, and b)
an EAM, said EAM comprising a transition metal and at least one
cyano ligand; or 3) a) a first anchor, b) a charge-neutralizing
ligand linked to said first anchor, c) an EAM covalently attached
to said charge-neutralizing ligand, and d) a capture ligand; or 4)
an electrode comprising a self-assembled monolayer (SAM), wherein
said SAM comprises a compound having the formula: Anchor-Spacer
1-EAM-Spacer 2-CL (II), wherein said anchor is linked to said
electrode group through a disulfide group, EAM is an electroactive
moiety comprising a solvent accessible redox compound, CL is a
capture ligand, Spacer 1 is either insulating or conducting, and
Spacer 2 is optional; or 5) an array of electrode, each electrode
comprising a compound having the formula: Anchor-Spacer
1-EAM-(Spacer 2).sub.n-CL (I), wherein said anchor comprises a
cyclic-disulfide group, EAM is an electroactive moiety comprising a
solvent accessible redox compound, CL is a capture ligand, Spacer 1
is either insulating or conduction, and n=0 or 1.
2. The composition according to claim 1, wherein said EAM of 1)
comprises at least two cyano ligands.
3. The composition according to claim 1, wherein said EAM of 1)
comprises at least three cyano ligands.
4. The composition according to claim 1, wherein said EAM of 1)
comprises at least four cyano ligands.
5. The composition according to claim 1, wherein said EAM of 1)
comprises at least five cyano ligands.
6. The composition according to claim 1, wherein said transition
metal of 1) is osmium.
7. The composition according to claim 1, wherein said electrode of
1) is gold and said EAM of 1) is covalently attached to said
electrode via a sulfur atom.
8. The composition according to claim 1, wherein said electrode of
1) is gold and said EAM of 1) is covalently attached to said
electrode via two sulfur atoms.
9. The composition according to claim 7, wherein said EAM is
attached to said electrode using an attachment linker with a first
terminus comprising said sulfur atom(s).
10. The composition according to claim 7, wherein said attachment
linker comprises a second terminus that provides a coordination
atom for said transition metal.
11. The composition according to claim 9, wherein said attachment
linker is an alkyl chain.
12. The composition according to claim 11, wherein said alkyl chain
is substituted.
13. The composition according to claim 1, wherein said electrode of
1) comprises a redox active capture complex (REAMC) comprising said
EAM and a capture ligand.
14. The composition according to claim 13, wherein said capture
ligand provides a coordination atom for said transition metal.
15. The composition according to claim 13, wherein electrode is
gold and said REAMC is covalently attached to said electrode via a
sulfur atom.
16-24. (canceled)
25. A method of detecting a target enzyme comprising: a) contacting
a sample with a composition comprising an electrode comprising: i)
an electroactive moiety (EAM) comprising a transition metal and at
least one cyano ligand with a first E.sup.0; ii) a capture ligand;
under conditions whereby said target enzyme, if present, alters
said capture ligand such that said EAM has a second E.sup.0; and b)
measuring said second E.sup.0; or a) contacting a sample with a
composition comprising a REAMC comprising: i) an electroactive
moiety (EAM) comprising a transition metal and at least one cyano
ligand with a first E.sup.0; and ii) a capture ligand; under
conditions whereby said target enzyme, if present, alters said
capture ligand such that said EAM has a second E.sup.0; and b)
measuring said second E.sup.0.
26-29. (canceled)
30. A method of making a biosensor comprising: a) providing an
electrode comprising: i) a first species comprising a first
functional group; and ii) an electroactive complex (EAM), said EAM
comprising a transition metal and at least one cyano ligand; and c)
contacting said electrode with a biomolecule comprising a second
functional group to form a covalent bond between said first species
and said biomolecule.
31-33. (canceled)
34. A compound having the formula: Anchor-Spacer 1-EAM-(Spacer
2).sub.n--CL (I) wherein said anchor comprises a cyclic-disulfide
group, EAM is an electroactive moiety comprises a solvent
accessible redox compound, CL is a capture ligand, Spacer 1 is a
SAM forming species, and n=0 or 1; or Anchor-Spacer 1-EAM-(Spacer
2).sub.n--CL (I) wherein said anchor comprises a pyridyl group, EAM
is an electroactive moiety comprises: i) a solvent accessible redox
compound, and ii) a charge-neutralizing ligand, CL is a capture
ligand, Spacer 1 is a SAM forming species, and n=0 or 1.
35-46. (canceled)
47. A method, comprising: a) providing a compound having the
formula: Anchor-Spacer 1-EAM-(Spacer 2).sub.n--CL (I), wherein said
anchor comprises a cyclic-disulfide group, EAM is an electroactive
moiety comprises a solvent accessible redox compound, CL is a
capture ligand, Spacer 1 is either insulating or conduction, and
n=0 or 1; and b) contacting said compound to an electrode by
opening said cyclic disulfide to form an attachment of said anchor
to said electrode.
48-49. (canceled)
50. A method of detecting a target analyte in a test sample,
comprising: a) providing an electrode comprises a compound having
the formula: Anchor-Spacer 1-EAM-(Spacer 2).sub.n--CL (I) wherein
said anchor comprises a cyclic-disulfide group, EAM is an
electroactive moiety comprises a solvent accessible redox compound,
CL is a capture ligand, Spacer 1 is either insulating or
conduction, and n=0 or 1; and b) contacting said electrode with
said test sample; and c) determining the presence of said target
analyte by measuring the reorganization energy of said EAM.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 12/253,875, filed on Oct. 17, 2008, allowed, which claims the
benefit of, and priority to, U.S. Provisional Patent Application
Ser. Nos. 60/980,733, filed on Oct. 17, 2007, and 61/087,094 and
61/087,102, filed on Aug. 7, 2008, the entire disclosures of which
are herein incorporated by reference in their entireties.
FIELD OF THE INVENTION
[0002] The invention relates to novel compositions and methods for
the detection of analytes using change in E.sup.0 of target
analytes.
BACKGROUND OF THE INVENTION
[0003] Electron transfer reactions are crucial steps in a wide
variety of biological transformations ranging from photosynthesis
or aerobic respiration. Studies of electron transfer reactions in
both chemical and biological systems have led to the development of
a large body of knowledge and a strong theoretical base, which
describes the rate of electron transfer in terms of a small number
of parameters.
[0004] Electronic tunneling in proteins and other biological
molecules occurs in reactions where the electronic interaction of
the redox centers is relatively weak. Semiclassical theory reaction
predicts that the reaction rate for electron transfer depends on
the driving force (-.DELTA.G.degree.), a nuclear reorganization
parameter (.lamda.), and the electronic-coupling strength between
the reactants and products at the transition state (H.sub.AB),
according to the following equation:
k.sub.ET=(4.pi..sup.3/h.sup.2.lamda.k.sub.BT).sup.1/2(H.sub.AB).sup.2exp-
[(-.DELTA.G.degree.+.lamda.)2/.lamda.k.sub.BT]
[0005] The nuclear reorganization energy, A, in the equation above
is defined as the energy of the reactants at the equilibrium
nuclear configuration of the products. For electron transfer
reactions in polar solvents, the dominant contribution to A arises
from the reorientation of solvent molecules in response to the
change in charge distribution of the reactants. The second
component of A comes from the changes in bond lengths and angles
due to changes in the oxidation state of the donors and
acceptors.
[0006] Previous work describes using change in reorganization
energy, X, as the basis of novel sensors. See for example, U.S.
Pat. Nos. 6,013,459, 6,013,170, 6,248,229, and 7,267,939, all
herein incorporated by reference in their entirety. The methods
generally comprise binding an analyte to or near a redox active
complex. The redox active complex comprises at least one
electroactive molecule and a capture ligand which will bind the
target analyte, and the complex is bound to an electrode. Upon
analyte binding, the reorganization energy of the redox active
molecule is altered, thus changing the E.sup.0, and allowing
detection.
[0007] It is an object of the present invention to provide
composition and methods for the detection of target analytes using
alterations in the solvent reorganization energy, such as utilizing
cyano ligands with the transition metals of the biosensor,
corresponding to changes in the E.sup.0 of redox active
molecules.
SUMMARY OF THE INVENTION
[0008] The present invention provides methods and compositions
relating to biosensors for use in the detection of target
analytes.
[0009] In one aspect, the invention provides compositions
comprising a solid support (sometimes referred to herein as a
"substrate") comprising an electrode comprising a covalently
attached electroactive complex (EAM) with a particular E.sup.0. The
substrates can optionally comprise an array of electrodes. The
electrode(s) each comprise an EAM, that optionally can be part of a
ReAMC. Suitable transition metals include iron, ruthenium and
osmium, as well as others outlined herein. In some embodiments, the
EAMs comprise at least one cyano ligand, with 2, 3, 4 and 5 also
finding use in the invention. The EAMs (as well as the ReAMCs and
diluent SAM forming species) can be linked to the electrodes using
attachment linkers, including alkyl groups (including substituted
alkyl groups).
[0010] In a further aspect, the electrodes optionally comprise self
assembled monolayer (SAM) species.
[0011] In an additional aspect, the EAM/ReAMCs of the invention are
attached to the electrode using an anchor ligand, which can be
"unipodal" or "multipodal", for example including the use of
bipedal attachments such as two sulfur atoms or cyclic disulfide
anchor groups.
[0012] In a further aspect, the EAM is part of a redox active
capture complex (REAMC) comprising said EAM and a capture ligand.
In one aspect, the capture ligand provides a coordination atom for
the transition metal. In additional aspects, the capture ligand is
separate from the EAM, such that the electrode comprises a first
species comprising the EAM and a second species comprising a
capture ligand.
[0013] In one aspect, the capture ligand is a protein, including
peptides, or a carbohydrate.
[0014] In an additional aspect, the invention provides methods of
detecting a target analytes comprising contacting a sample with a
composition comprising an electrode as outlined herein. The binding
of the target analyte to the capture ligand alters the E.sup.0 of
the EAM, e.g. creating a second E.sup.0, which is measured to
determine the presence or absence of the target analyte.
[0015] In a further aspect, the invention provides methods of
making a biosensor comprising providing an electrode comprising a
first species (usually a SAM forming species) comprising a first
functional group. The electrode is contacted with a biomolecule
(which will become the capture ligand) comprising a second
functional group to form a covalent bond between the first species
and the biomolecule. The electrode also comprises an electroactive
complex (EAM), to form the biochips of the invention. In some
aspects the functional groups on each molecule are selected from
the group consisting of moieties comprising a maleimide,
imidoester, N-hydroxysuccinimidyl, alkyl halide, aryl halide,
alpha-haloacyl and pryidyl disulfide and cysteines (e.g. the first
functional group comprises a maleimide and the biomolecule is a
protein (e.g. peptide) comprising a cysteine amino acid.
[0016] In an additional aspect, the invention comprises compounds
having the formula:
Anchor-Spacer 1-EAM-(Spacer 2).sub.n--CL
wherein said anchor comprises a cyclic-disulfide group,
[0017] EAM is an electroactive moiety comprises a solvent
accessible redox compound,
[0018] CL is a capture ligand,
[0019] Spacer 1 is a SAM forming species, and
[0020] n=0 or 1.
[0021] In an additional aspect, the invention comprises compounds
having the formula:
Anchor-Spacer 1-EAM-(Spacer 2).sub.n--CL (I)
wherein EAM is an electroactive moiety comprising a transition
metal and at least one charge neutralizing ligand. The charge
neutralizing ligand can be selected from the group consisting of:
dithiocarbamate, benzenedithiolate, a Schiff base, EDTA, DTPA,
carboxylate, amine, thiolate, phosphine, imidazole, pyridine,
bipyridine, terpyridine, tacn, salen, acacen, Cp, pincer,
scorpionates and pentaammine.
BRIEF DESCRIPTION OF THE DRAWINGS
[0022] FIGS. 1A-1C depicts several compounds of the invention. FIG.
1A shows a compound comprising a capture ligand at one end that is
linked to a redox here (here is shown to contain a Ruthenium
example) through a spacer. The compound also comprises an anchor,
through which the compound is attached to the surface of an
electrode. Also shown are insulators (110) that are attached to the
surface of the electrode as well. FIGS. 1B and 1C depicts a
compound comprises multiple metals. The geometries such as the one
shown, where CL is "capture ligand", will attract a single protein
and have it interact with two metal centers simultaneously giving a
larger change in potential.
[0023] FIG. 2 depicts [BIM-Ru(NH3)4L]2+ complexes with BPAI anchors
and [Ru(NH3)5L]2+ complexes with BPA anchors.
[0024] FIG. 3 depicts BIPOD based compounds.
[0025] FIG. 4A depicts [BIM-Ru(NH3)4L].sup.2+ complexes with
alkylthiol anchors. FIG. 4B depicts [Ru(NH3)5L].sup.2+ complexes
with conjugated thiol anchors.
[0026] FIG. 5A depicts new architectures for Ru--N based complexes.
FIG. 5B depicts examples of Ru--N based complexes.
[0027] FIG. 6A schematically depicts modified Prussian blue surface
for detection with amplification. FIG. 6B depicts the use of crown
ether coordination to enhance potential shift.
[0028] FIG. 7 depicts the effect of second-sphere coordination, the
adduct formation between Ru(NH3).sub.5L and 18-C-6.
[0029] FIGS. 8A and 8B depict ligands used in the "single" and
"side-by-side" arrangement when multiple metals are used.
[0030] FIG. 9 depicts some of the building blocks for generating
the compound for detection of analyte.
[0031] FIGS. 10A and 10B depict some exemplary compounds.
[0032] FIG. 11 depicts some exemplary compounds.
[0033] FIGS. 12 and 13 depict several schematics of suitable
geometries of the present invention.
[0034] FIGS. 12A and C depicts the situation where a linker is
attached at one end to the electrode and the other end terminates
in a ligand (L) that provides a coordination atom for the
transition metal (TM). The capture substrate (CS) provides an
additional ligand (not depicted), and a plurality of other ligands
provide the remaining coordination atoms. Upon action by the
enzyme, the capture substrate results in a leaving group (X). It
should be noted that these Figures depicts a situation where the
transition metal utilizes 6 coordination atoms, but other numbers
of coordination atoms can be used, depending on the metal.
Similarly, these Figures depicts the use of ligands that provide a
single coordination atom, but fewer ligands providing multiple
coordination atoms (e.g. multidentate) ligands can be used as well.
FIG. 12B depicts the situation where the capture substrate and the
EAM are attached separately to the electrode. FIG. 12C depicts a
similar situation to FIG. 3A, except the capture substrate does not
provide a coordination atom to the transition metal. It should be
appreciated that solution phase systems can be similar to FIGS. 12
and 14, in that the electrochemical potential of the EAM in
solution can be altered as a result of the enzymatic activity of
the target enzyme.
[0035] FIG. 14 depicts a general scheme for producing the biochips
of the invention.
[0036] FIG. 15 shows a specific example of the production of FIG.
14.
[0037] FIGS. 16A, B, C and D depict some exemplary compounds.
[0038] FIGS. 17 A, B, C and D depict some exemplary compounds.
Similar compounds can be constructed with different anchors, such
as disulfide cyclic anchor groups, for example, or different
spacers.
[0039] FIGS. 18A and B depict some exemplary compounds. Similar
compounds can be constructed with different anchors, such as
disulfide cyclic anchor groups, for example, or different
spacers.
[0040] FIG. 19 depicts a general scheme of synthesis.
[0041] FIG. 20 depicts a general detection scheme.
[0042] FIGS. 21A, B, C, D and E depict some exemplary compounds.
Similar compounds can be constructed with different anchors, such
as disulfide cyclic anchor groups, for example, or different
spacers.
[0043] FIG. 22 depicts a general scheme of synthesis.
[0044] FIG. 23 depicts a general scheme of synthesis for an
assay.
[0045] FIG. 24 depict capture ligands.
[0046] FIGS. 25A, B, C and D depict some exemplary compounds.
Similar compounds can be constructed with different anchors, such
as disulfide cyclic anchor groups, for example, or different
spacers.
[0047] FIGS. 26A, B, C and D depict some exemplary compounds using
ferrocene as the EAM. Similar compounds can be constructed with
different anchors, such as disulfide cyclic anchor groups, for
example, or different spacers.
[0048] FIGS. 27 A and B depict some exemplary compounds. Similar
compounds can be constructed with different anchors, such as
disulfide cyclic anchor groups, for example, or different
spacers.
DETAILED DESCRIPTION OF THE INVENTION
[0049] The present invention is directed to improvements in
electrochemical biosensors that rely on changes in the
reorganization energy, .lamda., upon interaction of the target
analyte and the biosensor, as evidenced by alterations in the
observed E.sup.0. As shown previously, biosensors have been
described that rely on changes in reorganization energy. The
present invention has shown surprising improvements such as
utilizing cyano ligands for the transition metal of the
electroactive moieties (EAMs). The cyano ligands provide a
surprising increase in the change of the E.sup.0; e.g. the delta in
the E.sup.0 is higher than seen for other charged ligands.
I. Overview of Reorganization Energy
[0050] The present invention provides methods and compositions for
the detection of target analytes using changes in the
reorganization energy of redox active molecules upon binding of the
analytes, to facilitate or hinder electron transfer between the
redox active molecule and an electrode. This invention is based on
the fact that when a redox active molecule, such as a transition
metal ion, is either oxidized (losing an electron) or reduced
(gaining an electron), changes occur in the molecular structure as
well as in its immediate solvent environment. These changes in the
molecules structure (bond lengths and angles) and in the
organization of the solvent molecules surrounding the molecule
serve to stabilize the new oxidation state energetically. The sum
of these changes constitute the reorganization energy, .lamda., of
a redox reaction. The intramolecular changes are termed the
inner-sphere reorganization energy, and the changes in the solvent
and environment are termed the outer-sphere or solvent
reorganization energy, .lamda..sub.o.
[0051] For the purposes of this invention, the primary focus is on
changes in the solvent reorganization energy although changes in
the inner-sphere reorganization will also be considered in several
embodiments of the invention. It is the intent of this invention to
capitalize on changes in reorganization energy of a redox reaction
when an electroactive molecule (EAM) is attached to a capture
ligand (CL) which can selectively bind to an analyte of interest
(e.g., proteint or bacteria). Binding of the EAM-CL to the analyte
results in a change in the solvent environment of the EAM so that
the reorganization energy for a redox reaction involving the EAM is
changed. For the case where the redox reaction involves electron
transfer between an electrode and the EAM, the standard potential,
E.sup.0, is changed. Thus, a change in E.sup.0 for an EAM-CL
complex is an indication that it is bound to the anlyte. It is the
intent of this invention to detect the change in E.sup.0 as an
indicator of binding and, consequently, the presentce or absence of
the analyte.
[0052] In conventional methodologies for analyte detection using
electron transfer usually employ the EAM as a label or tag
attaqched to one member of a binding pair (e.g., antibody and
antigen). In these methods, EAM's are chosen in which the outer
sphere solvent effect is minimal, by using electroactive molecules
that have minimal solvent reorganization upon oxidation or
reduction. Such EAMs generally comprise large hydrophobic ligands
which have little interaction with water. Thus, the ligands for the
transition metal ions traditionally used are non-polar and are
generally hydrophobic, frequently containing organic rings (e.g.,
bipyridyl and terpyridyl). Such EAMs are chosen because
conventionally because the magnitude of the total electron transfer
reaction is measured (curent) at a predetermined electrode
potential.
[0053] Without being bound by theory, it is expected that the redox
molecules best suited for this invention will be those whose redox
reaction has a large solvent eorganization energy in aqueous
environments. Solvent reorganization to stabilize an increase or
decrease in charge can be attributed to several phenomena. In polar
solventssuch as water, the charge on a redox molecule is stabilized
by orienation of the polar solvent molecules in the environment
near the redox molecule. Since polar molecules have slight charge
variation on different atoms of the molecule, their orientation
around the redox molecule can help to stabilize it. Further, some
ligands, such as CN--, themselves are polar and have partial
charges on atoms. These polar ligands can themselves induce an
orientation of surrounding solvent molecules. Stabilization (or
destabilization) of charged redox molecules can also occur by
hydrogen bonding of solvent and/or other molecules to the ligands
of the transition metal in the redox molecule. Solvent molecules,
as well as other molecules in the solvent surrounding a redox
molecules can be characterized and compared based on their donor
number or acceptor number (Neyhart et al., J. Am. Chem. Soc 118
(1996) 3724-29, incorporated herein by reference). The use of a
particular solvent or a particular additive to a solvent of a
molecule having a preferred donor or acceptor number would affect
the solvent reorganization energy of a redox reaction. Further, a
change in the charge of a redox molecule is stabilized by charged
ion in the solvent. Thus, changes in solvent reorganization change
upon analyte binding can be maximized by the proper choice of an
electrolyte, considering the charge on the ions, the concentration
of the ions, the size of the ions, and the hydrophobicity of the
ions.
[0054] Without being bound by theory, it is preferred to maximize
the stabilization of the redox molecule (i.e., maximize its solvent
reorganization energy) in the solvent system of choice in order
that the phenomena which stabilize the redox molecule are disruped
upon binding of the redox molecule/capture ligand complex, EAM-CL
to the analyte. Under such conditions, one would expect that the
change in reorganization energy, evidenced by a change in E.sup.0,
would be optimum. It is expected that the binding of the CL to the
analyte will "force" the EAM into an environment on the surface or
in a cleft or pocket of the analyte (e.g., a protein) which will be
less favorable to the optimal organization of the solvent
environment. In one embodiment it is expected that binding would
cause a shedding of water molecules near the EAM because of steric
constraints.
[0055] It should be noted, and not being bound by theory, that
whether the solvent reorganization energy increases or decreases
upon binding (and whether E.sup.0 nives to more positive or to more
negative potentials is dependent upon the particular charge of the
EAM. If the EAM redox reaction being monitored results in an
increaed charge of the EAM, such as EAM.sup.2+ oxidation to
EAM.sup.3+, then the bound environment of the EAM-CL would be less
stabilized by reorganization than the unbound EAM-CL. Hence, one
would expect the EO to move to more positive potentials.
Alternatively, if the EAM redox reaction being monitored results in
a decreased charge of the EAM, such as EAM.sup.2-oxidation to
EAM.sup.-, then the unbound EAM-CL would be less stabilized by
reorganization than the bound EAM-CL. Hence, one would expect the
E.sup.0 to move to less positive potentials.
[0056] Without being bound by theory, there are two general
mechanisms which may be exploited in the present invention. The
first relates to inner sphere change due to the redox label. In
this embodiment, the binding of a target analyte to a capture
ligand which is sterically close to an EAM causes one or more of
the small, polar ligands of the EAM to be replaced by one or more
coordination atoms supplied by the target analyte, causing a change
in the inner-sphere reorganization energy for at least two reasons.
First, the exchange of a small, polar ligand for a putatively
larger ligand will generally exclude more water from the metal,
lowering the required solvent reorganization energy (i.e. an inner
sphere .lamda..sub.i effect). Secondly, the proximity of a
generally large target analyte to the relatively small redox active
molecule will sterically exclude water within the first or second
coordination sphere of the metal ion, also changing the solvent
reorganization energy.
[0057] Alternatively, the invention relies on substitutionally
inert ligand, plus outer sphere effects. In this embodiment
exchange of the polar ligands on the metal ion by a target analyte
coordination atom. Rather, in this embodiment, the polar ligands
are effectively irreversibly bound to the metal ion, and the chznge
in solvent reorganization energy is obtained as a result of the
exclusion of water in the first or second coordination sphere of
the metal ion as a result of the binding of the target analyte;
essentially the water is excluded (i.e. an outer sphere
.lamda..sub.o effect).
[0058] The present invention provides compounds with novel
architecture and methods of using these compounds for detection of
target analytes.
[0059] In some embodiments, the target analyte binds to the capture
ligand. In some embodiments, the target analyte can be an enzyme,
and the change in E.sup.0 is as a result of an enzymatic event, as
described in U.S. Patent Application No. 61/087,094, hereby
incorporated by reference in its entirety.
[0060] In the embodiments of the invention, there is a change in
the E.sup.0, presumably due to a change in the reorganization
energy, upon the introduction of the target analyte. As discussed
more fully below, the change may be either a positive or negative
shift in E.sup.0, depending on a variety of factors. In general,
when cyano ligands are used, the change in E.sup.0 can be a
negative shift in E.sup.0, although depending on the system and the
other ligands used (if any), the effect of interaction of the
target analyte with the capture ligand can result in a positive
shift in E.sup.0. Surprisingly, shifts of greater than about 50 mV,
100 mV, 150 mV, 200 mV, 250 mV and 300 mV can be seen using cyano
ligands.
[0061] CN-- is a good nucleophile and in an example, the Iron-cyano
(-2) complex has a partial charge on the N of a cyano of -0.8767
and has a partial charge on the C of a cyano of 0.5549. That charge
number on the nitrogen is very large that one can consider it
acting like there is a lone pair of electrons. Therefore, the
partial negative charge on the N arranges water molecules with the
protons of water oriented toward the N (the opposite is true for
NH.sub.3 ligands). Since the partial charge on the nitrogen is
high, this local orientation effect is strong and therefore the
delta between water near by (before target capture) and water
excluded (after target capture) is high . . . i.e., the difference
in lambda between the two states is quantitatively higher.
[0062] Unidentate CN-- always binds through the carbonand therefore
that large partial negative charge resides on the N. The larger
that partial negative charge oriented toward the solvent (water)
the larger the observable effect will be. As such, ligands with
partial negative charges on the ligands stabilize high oxidation
state metals, and have a strong impact on the orientation of
water.
[0063] CN being the best because it has the highest net charge on
the N and therefore the strongest interaction with protons of
water:
CN.sup.->NO.sub.2>SO.sub.3.sup.2->NCS.sup.->NO
equiv to NCS.sup.- is SCN.sup.-.
[0064] In general, the more positive the Metal center becomes the
higher the potential of the metal. Accordingly, when most if not
all the negative charges are neutralized by interaction with water,
the metal becomes more positive.
II. Geometries of the Sensors
[0065] The present invention is directed to methods and
compositions for detection of target analytes, based on a change of
electrochemical potential, E.sup.0, of a redox active molecule
either on the surface of an electrode, or in some cases, in
solution (while most of the description herein is directed to solid
phase assays, as will be appreciated by those in the art, the
invention can be used in solution as well, and such description
herein is meant to apply as applicable to solution phase assays as
well).
[0066] In general, the invention can be described as follows. A
redox active molecule, generally comprising a transition metal and
at least one ligand (such as one cyano ligand (or more, as
described herein)) that provide coordination atoms for the
transition metal, is attached to the surface of an electrode,
generally through a linker as described herein. In addition, the
electrode may also optionally comprise a self-assembled monolayer
(SAM) as described herein. In the spatial vicinity of the redox
active molecule, a capture ligand is also attached, generally in
one of three ways, as described herein. Introduction and/or binding
of the target analyte results in a change in the electrochemical
potential of the redox active molecule, which is then detected in a
variety of ways as described herein.
[0067] As depicted in FIGS. 12-14, there are three basic geometries
for the sensor, although the descriptions herein are not meant to
be so limited. In one embodiment, as shown in FIG. 12A, an
electroactive moiety (EAM), comprising a transition metal ion and
ligands that provide coordination atoms for the transition metal
(in some embodiments, at least one of which is a cyano ligand), is
attached to an electrode. In addition, a capture ligand (sometimes
also referred to as a "binding ligand") that will specifically bind
the target analyte is also attached to the electrode. Both species
are generally attached to the electrode using an attachment linker
as described herein. The two species are attached to the electrode
in such a manner that they are spatially close, such that the
E.sup.0 of the EAM is altered upon binding of a target analyte. It
should be noted that a third species, comprising a monolayer
forming species, described below, can also be optionally present on
the electrode. In this embodiment, the EAM species can have the
formula (Ia), the capture ligand species can have the formula (Ib)
and the diluent species can have the formula (Ic):
AG-Spacer 1-EAM (Ia)
AG-Spacer 1-CL (Ib)
AG-Spacer 1-TG.sub.n (Ic)
wherein AG is an anchor group, EAM is an electroactive moiety
comprises a solvent accessible redox complex, spacer 1 is a SAM
forming species described herein, CL is a capture ligand, and TG is
a terminal group, with n being 0 or 1.
[0068] In a second embodiment, as depicted in Figure *XB, one of
the coordination atoms for the transition metal of the EAM is
provided by the capture ligand, forming a "redox active moiety
complex", or ReAMC. In this embodiment, the coordination atom can
be actually part of the capture ligand (e.g. if the capture ligand
is a peptide, an amino group can provide the coordination atom) or
part of a linker used to attach the capture ligand (e.g. a pyridine
linker, etc.). The ReAMC is attached as a single species, and as
above, an additional species, comprising a monolayer forming
species, described below, can also be optionally present on the
electrode. In this embodiment, the present invention provides a
compound having the formula (II):
AG-Spacer 1-EAM-(Spacer 2).sub.n--CL (II)
wherein AG is an anchor group, EAM is an electroactive moiety
comprises a solvent accessible redox complex, CL is a capture
ligand, spacer 1 is a SAM forming species described herein, and
Spacer 2 is a linker, with n=0 or 1.
[0069] In a third embodiment, as depicted in FIG. 12C, there ReAMC
is a single species, but the capture ligand does not provide a
coordination atom; rather, it is spatially close but distinct from
the EAM of the ReAM C. Again, a third species, comprising a
monolayer forming species, described below, can also be optionally
present on the electrode. In this embodiment, the present invention
provides a compound having the formula (III):
##STR00001##
wherein AG is an anchor group, EAM is an electroactive moiety
comprises a solvent accessible redox complex, CL is a capture
ligand, spacer 1 is a SAM forming species described herein, and
S.sub.2 and S.sub.3 are two linkages that link the EAM and CL
together with the AG to form a branched structure. S.sub.2 and
S.sub.3 can be different or the same.
[0070] One example of this configuration is shown below:
##STR00002##
[0071] where M=transitional metal; Ln=coordinating ligand that
covalently connected to the anchor and capture ligand, n=0 or 1;
and L=coordinating ligand.
III. Electrode
[0072] In one aspect, the present invention provides these ligand
architectures attached to an electrode. By "electrode" herein is
meant a composition, which, when connected to an electronic device,
is able to sense a current or charge and convert it to a signal.
Preferred electrodes are known in the art and include, but are not
limited to, certain metals and their oxides, including gold;
platinum; palladium; silicon; aluminum; metal oxide electrodes
including platinum oxide, titanium oxide, tin oxide, indium tin
oxide, palladium oxide, silicon oxide, aluminum oxide, molybdenum
oxide (Mo.sub.2O.sub.6), tungsten oxide (WO.sub.3) and ruthenium
oxides; and carbon (including glassy carbon electrodes, graphite
and carbon paste). Preferred electrodes include gold, silicon,
carbon and metal oxide electrodes, with gold being particularly
preferred.
[0073] The electrodes described herein are depicted as a flat
surface, which is only one of the possible conformations of the
electrode and is for schematic purposes only. The conformation of
the electrode will vary With the detection method used. For
example, flat planar electrodes may be preferred for optical
detection methods, or when arrays of nucleic acids are made, thus
requiring addressable locations for both synthesis and detection.
Alternatively, for single probe analysis, the electrode may be in
the form of a tube, with the components of the system such as SAMs,
EAMs and capture ligands bound to the inner surface. This allows a
maximum of surface area containing the nucleic acids to be exposed
to a small volume of sample.
[0074] The electrodes of the invention are generally incorporated
into biochip cartridges and can take a wide variety of
configurations, and can include working and reference electrodes,
interconnects (including "through board" interconnects), and
microfluidic components. See for example U.S. Pat. No. 7,312,087,
incorporated herein by reference in its entirety.
[0075] The biochip cartridges include substrates comprising the
arrays of biomolecules, and can be configured in a variety of ways.
For example, the chips can include reaction chambers with inlet and
outlet ports for the introduction and removal of reagents. In
addition, the cartridges can include caps or lids that have
microfluidic components, such that the sample can be introduced,
reagents added, reactions done, and then the sample is added to the
reaction chamber comprising the array for detection.
[0076] In a preferred embodiment, the biochips comprise substrates
with a plurality of array locations. By "substrate" or "solid
support" or other grammatical equivalents herein is meant any
material that can be modified to contain discrete individual sites
appropriate of the attachment or association of capture ligands.
Suitable substrates include metal surfaces such as gold, electrodes
as defined below, glass and modified or functionalized glass,
fiberglass, teflon, ceramics, mica, plastic (including acrylics,
polystyrene and copolymers of styrene and other materials,
polypropylene, polyethylene, polybutylene, polyimide,
polycarbonate, polyurethanes, Teflon.TM., and derivatives thereof,
etc.), GETEK (a blend of polypropylene oxide and fiberglass), etc,
polysaccharides, nylon or nitrocellulose, resins, silica or
silica-based materials including silicon and modified silicon,
carbon, metals, inorganic glasses and a variety of other polymers,
with printed circuit board (PCB) materials being particularly
preferred.
[0077] The present system finds particular utility in array
formats, i.e. wherein there is a matrix of addressable detection
electrodes (herein generally referred to "pads", "addresses" or
"micro-locations"). By "array" herein is meant a plurality of
capture ligands in an array format; the size of the array will
depend on the composition and end use of the array. Arrays
containing from about 2 different capture substrates to many
thousands can be made.
[0078] In a preferred embodiment, the detection electrodes are
formed on a substrate. In addition, the discussion herein is
generally directed to the use of gold electrodes, but as will be
appreciated by those in the art, other electrodes can be used as
well. The substrate can comprise a wide variety of materials, as
outlined herein and in the cited references.
[0079] In general, preferred materials include printed circuit
board materials. Circuit board materials are those that comprise an
insulating substrate that is coated with a conducting layer and
processed using lithography techniques, particularly
photolithography techniques, to form the patterns of electrodes and
interconnects (sometimes referred to in the art as interconnections
or leads). The insulating substrate is generally, but not always, a
polymer. As is known in the art, one or a plurality of layers may
be used, to make either "two dimensional" (e.g. all electrodes and
interconnections in a plane) or "three dimensional" (wherein the
electrodes are on one surface and the interconnects may go through
the board to the other side or wherein electrodes are on a
plurality of surfaces) boards. Three dimensional systems frequently
rely on the use of drilling or etching, followed by electroplating
with a metal such as copper, such that the "through board"
interconnections are made. Circuit board materials are often
provided with a foil already attached to the substrate, such as a
copper foil, with additional copper added as needed (for example
for interconnections), for example by electroplating. The copper
surface may then need to be roughened, for example through etching,
to allow attachment of the adhesion layer.
[0080] Accordingly, in a preferred embodiment, the present
invention provides biochips (sometimes referred to herein "chips")
that comprise substrates comprising a plurality of electrodes,
preferably gold electrodes. The number of electrodes is as outlined
for arrays. Each electrode preferably comprises a self-assembled
monolayer as outlined herein. In a preferred embodiment, one of the
monolayer-forming species comprises a capture ligand as outlined
herein. In addition, each electrode has an interconnection, that is
attached to the electrode at one end and is ultimately attached to
a device that can control the electrode. That is, each electrode is
independently addressable.
[0081] Finally, the compositions of the invention can include a
wide variety of additional components, including microfluidic
components and robotic components (see for example U.S. Pat. Nos.
6,942,771 and 7,312,087 and related cases, both of which are hereby
incorporated by reference in its entirety), and detection systems
including computers utilizing signal processing techniques (see for
example U.S. Pat. No. 6,740,518, hereby incorporated by reference
in its entirety)
A. Self Assembled Monolayer Spacers
[0082] In some embodiments, the electrodes optionally further
comprise a SAM. By "monolayer" or "self-assembled monolayer" or
"SAM" herein is meant a relatively ordered assembly of molecules
spontaneously chemisorbed on a surface, in which the molecules are
oriented approximately parallel to each other and roughly
perpendicular to the surface. Each of the molecules includes a
functional group that adheres to the surface, and a portion that
interacts with neighboring molecules in the monolayer to form the
relatively ordered array. A "mixed" monolayer comprises a
heterogeneous monolayer, that is, where at least two different
molecules make up the monolayer. As outlined herein, the use of a
monolayer reduces the amount of non-specific binding of
biomolecules to the surface, and, in the case of nucleic acids,
increases the efficiency of oligonucleotide hybridization as a
result of the distance of the oligonucleotide from the electrode.
Thus, a monolayer facilitates the maintenance of the target enzyme
away from the electrode surface. In addition, a monolayer serves to
keep charge carriers away from the surface of the electrode. Thus,
this layer helps to prevent electrical contact between the
electrodes and the ReAMs, or between the electrode and charged
species within the solvent. Such contact can result in a direct
"short circuit" or an indirect short circuit via charged species
which may be present in the sample. Accordingly, the monolayer is
preferably tightly packed in a uniform layer on the electrode
surface, such that a minimum of "holes" exist. The monolayer thus
serves as a physical barrier to block solvent accesibility to the
electrode.
[0083] In some embodiments, the monolayer comprises conductive
oligomers. By "conductive oligomer" herein is meant a substantially
conducting oligomer, preferably linear, some embodiments of which
are referred to in the literature as "molecular wires". By
"substantially conducting" herein is meant that the oligomer is
capable of transfering electrons at 100 Hz. Generally, the
conductive oligomer has substantially overlapping n-orbitals, i.e.
conjugated 7C-orbitals, as between the monomeric units of the
conductive oligomer, although the conductive oligomer may also
contain one or more sigma (a) bonds. Additionally, a conductive
oligomer may be defined functionally by its ability to inject or
receive electrons into or from an associated EAM. Furthermore, the
conductive oligomer is more conductive than the insulators as
defined herein. Additionally, the conductive oligomers of the
invention are to be distinguished from electroactive polymers, that
themselves may donate or accept electrons.
[0084] A more detailed description of conductive oligomers is found
in WO/1999/57317, herein incorporated by reference in its entirety.
In particular, the conductive oligomers as shown in Structures 1 to
9 on page 14 to 21 of WO/1999/57317 find use in the present
invention. In some embodiments, the conductive oligomer has the
following structure:
##STR00003##
[0085] In addition, the terminus of at least some of the conductive
oligomers in the monolayer is electronically exposed. By
"electronically exposed" herein is meant that upon the placement of
an EAM in close proximity to the terminus, and after initiation
with the appropriate signal, a signal dependent on the presence of
the EAM may be detected. The conductive oligomers may or may not
have terminal groups. Thus, in a preferred embodiment, there is no
additional terminal group, and the conductive oligomer terminates
with a terminal group; for example, such as an acetylene bond.
Alternatively, in some embodiments, a terminal group is added,
sometimes depicted herein as "Q". A terminal group may be used for
several reasons; for example, to contribute to the electronic
availability of the conductive oligomer for detection of EAMs, or
to alter the surface of the SAM for other reasons, for example to
prevent non-specific binding. For example, there may be negatively
charged groups on the terminus to form a negatively charged surface
such that when the target analyte is nucleic acid such as DNA or
RNA, the nucleic acid is repelled or prevented from lying down on
the surface, to facilitate hybridization. Preferred terminal groups
include --NH, --OH, --COOH, and alkyl groups such as --CH.sub.3,
and (poly)alkyloxides such as (poly)ethylene glycol, with
--OCH.sub.2CH.sub.2OH, --(OCH.sub.2CH.sub.2O).sub.2H,
--(OCH.sub.2CH.sub.2O).sub.3H, and --(OCH.sub.2CH.sub.2O).sub.4H
being preferred.
[0086] In one embodiment, it is possible to use mixtures of
conductive oligomers with different types of terminal groups. Thus,
for example, some of the terminal groups may facilitate detection,
and some may prevent non-specific binding.
[0087] In some embodiments, the electrode further comprises a
passivation agent, preferably in the form of a monolayer on the
electrode surface. For some analytes the efficiency of analyte
binding (i.e. hybridization) may increase when the binding ligand
is at a distance from the electrode. In addition, the presence of a
monolayer can decrease non-specific binding to the surface (which
can be further facilitated by the use of a terminal group, outlined
herein. A passivation agent layer facilitates the maintenance of
the binding ligand and/or analyte away from the electrode surface.
In addition, a passivation agent serves to keep charge carriers
away from the surface of the electrode. Thus, this layer helps to
prevent electrical contact between the electrodes and the electron
transfer moieties, or between the electrode and charged species
within the solvent. Such contact can result in a direct "short
circuit" or an indirect short circuit via charged species which may
be present in the sample. Accordingly, the monolayer of passivation
agents is preferably tightly packed in a uniform layer on the
electrode surface, such that a minimum of "holes" exist.
Alternatively, the passivation agent may not be in the form of a
monolayer, but may be present to help the packing of the conductive
oligomers or other characteristics.
[0088] The passivation agents thus serve as a physical barrier to
block solvent accessibility to the electrode. As such, the
passivation agents themselves may in fact be either (1) conducting
or (2) nonconducting, i.e. insulating, molecules. Thus, in one
embodiment, the passivation agents are conductive oligomers, as
described herein, with or without a terminal group to block or
decrease the transfer of charge to the electrode. Other passivation
agents which may be conductive include oligomers of--(CF.sub.2)--,
--(CHF)-- and --(CFR)--. In a preferred embodiment, the passivation
agents are insulator moieties.
[0089] In some embodiments, the monolayers comprise insulators. An
"insulator" is a substantially nonconducting oligomer, preferably
linear. By "substantially nonconducting" herein is meant that the
rate of electron transfer through the insulator is slower than the
rate of electron transfer through the conductive oligomer. Stated
differently, the electrical resistance of the insulator is higher
than the electrical resistance of the conductive oligomer. It
should be noted however that even oligomers generally considered to
be insulators, such as --(CH.sub.2)16 molecules, still may transfer
electrons, albeit at a slow rate.
[0090] In some embodiments, the insulators have a conductivity, S,
of about 10-7.OMEGA.-1 cm.sup.-1 or lower, with less than about
10-8.OMEGA.-1 cm-1 being preferred. Gardner et al., Sensors and
Actuators A 51 (1995) 57-66, incorporated herein by reference.
[0091] Generally, insulators are alkyl or heteroalkyl oligomers or
moieties with sigma bonds, although any particular insulator
molecule may contain aromatic groups or one or more conjugated
bonds. By "heteroalkyl" herein is meant an alkyl group that has at
least one heteroatom, i.e. nitrogen, oxygen, sulfur, phosphorus,
silicon or boron included in the chain. Alternatively, the
insulator may be quite similar to a conductive oligomer with the
addition of one or more heteroatoms or bonds that serve to inhibit
or slow, preferably substantially, electron transfer. Preferably,
the alkyl or heroalkyl chains are from about four to about 18 atoms
in length, and more preferably from about six to about 16 atoms in
length/
[0092] The passivation agents, including insulators, may be
substituted with R groups as defined herein to alter the packing of
the moieties or conductive oligomers on an electrode, the
hydrophilicity or hydrophobicity of the insulator, and the
flexibility, i.e. the rotational, torsional or longitudinal
flexibility of the insulator. For example, branched alkyl groups
may be used. In addition, the terminus of the passivation agent,
including insulators, may contain an additional group to influence
the exposed surface of the monolayer, sometimes referred to herein
as a terminal group ("TG"). For example, the addition of charged,
neutral or hydrophobic groups may be done to inhibit non-specific
binding from the sample, or to influence the kinetics of binding of
the analyte, etc. For example, there may be charged groups on the
terminus to form a charged surface to encourage or discourage
binding of certain target analytes or to repel or prevent from
lying down on the surface.
[0093] The length of the passivation agent will vary as needed.
Generally, the length of the passivation agents is similar to the
length of the conductive oligomers, as outlined above. In addition,
the conductive oligomers may be basically the same length as the
passivation agents or longer than them, resulting in the binding
ligands being more accessible to the solvent.
[0094] The monolayer may comprise a single type of passivation
agent, including insulators, or different types.
[0095] Suitable insulators are known in the art, and include, but
are not limited to, --(CH.sub.2)--, --(CRH)--, and --(CR.sub.2)--,
ethylene glycol or derivatives using other heteroatoms in place of
oxygen, i.e. nitrogen or sulfur (sulfur derivatives are not
preferred when the electrode is gold). Preferably, insulators are
of the form --(CH.sub.2).sub.n-- having a thiol or disulfide
terminus for attachment to gold. Also preferable, the alternate end
of the insulator is terminated in a hydrophylic group such as
oligoethylene glycol, --OH, or --COOH.
[0096] In some embodiments, the electrode is a metal surface and
need not necessarily have interconnects or the ability to do
electrochemistry.
B. Anchor Groups
[0097] The present invention provides compounds comprising an
anchor group. By "anchor" or "anchor group" herein is meant a
chemical group that attaches the compounds of the invention to an
electrode.
[0098] As will be appreciated by those in the art, the composition
of the anchor group will vary depending on the composition of the
surface to which it is attached. In the case of gold electrodes,
both pyridinyl anchor groups and thiol based anchor groups find
particular use.
[0099] The covalent attachment of the conductive oligomer may be
accomplished in a variety of ways, depending on the electrode and
the conductive oligomer used. Generally, some type of linker is
used, as depicted below as "A" in Structure 1, where X is the
conductive oligomer, and the hatched surface is the electrode:
##STR00004##
[0100] In this embodiment, A is a linker or atom. The choice of "A"
will depend in part on the characteristics of the electrode. Thus,
for example, A may be a sulfur moiety when a gold electrode is
used. Alternatively, when metal oxide electrodes are used, A may be
a silicon (silane) moiety attached to the oxygen of the oxide (see
for example Chen et al., Langmuir 10:3332-3337 (1994); Lenhard et
al., J. Electroanal. Chem. 78:195-201 (1977), both of which are
expressly incorporated by reference). When carbon based electrodes
are used, A may be an amino moiety (preferably a primary amine; see
for example Deinhammer et al., Langmuir 10:1306-1313 (1994)). Thus,
preferred A moieties include, but are not limited to, silane
moieties, sulfur moieties (including alkyl sulfur moieties), and
amino moieties.
[0101] In some embodiments, the electrode is a carbon electrode,
i.e. a glassy carbon electrode, and attachment is via a nitrogen of
an amine group. A representative structure is depicted in Structure
15 of US Patent Application Publication No. 20080248592, hereby
incorporated by reference in its entirety but particularly for
Structures as described therein and the description of different
anchor groups and the accompanying text. Again, additional atoms
may be present, i.e. linkers and/or terminal groups.
[0102] In Structure 16 of US Patent Application Publication No.
20080248592, hereby incorporated by reference as above, the oxygen
atom is from the oxide of the metal oxide electrode. The Si atom
may also contain other atoms, i.e. be a silicon moiety containing
substitution groups. Other attachments for SAMs to other electrodes
are known in the art; see for example Napier et al., Langmuir,
1997, for attachment to indium tin oxide electrodes, and also the
chemisorption of phosphates to an indium tin oxide electrode (talk
by H. Holden Thorpe, CHI conference, May 4-5, 1998).
[0103] In one preferred embodiment, indium-tin-oxide (ITO) is used
as the electrode, and the anchor groups are phosphonate-containing
species.
[0104] 1). Pyridinyl Anchor Groups
[0105] In one aspect, the present invention provides the use of
pyridine and derivatives thereof to attach the compounds of the
invention to the surface.
[0106] In some embodiments, the anchor comprises a pyridyl group,
having the structure of formula (II):
##STR00005##
where the carbons on the ring can optionally and independently be
substituted, using R groups as defined herein. Pyridine is a
heterocyclic aromatic organic compound that is structurally related
to benzene, wherein one CH group in the six-membered ring is
replaced by a nitrogen atom. Pyridine can be used as a ligand in
coordination chemistry. As a ligand, it is usually abbreviated as
"py." The invention utilizes the ability of the lone electron pair
on the nitrogen atom of the pyridine to bind to metal surfaces. One
advantage of the pyridine based compounds is that they are air
stable. Curtis et al., Inorg. Chem. 24:385-397 (1985); Callahan et
al., Inorg. Chem. 14:1443-1453 (1975); Lavallee and Fleischer, J.
Am. Chem. Soc. 94:2583-2599 (1972); and Jwo et al., J. Am. Chem.
Soc. 101:6189-6197 (1979), all of which are incorporated by
reference.
[0107] In some embodiments, the pyridyl group comprises a bipyridyl
group (Bispyridylacetylene, BPA), comprising two pyridyl groups
separated by an acetylene group, shown below:
##STR00006##
In this embodiment, the carbons on either ring can be optionally
and independently be substituted, using R groups as defined herein.
One of the rings will contain a linkage to a spacer, as defined
herein, or, as shown in some of the figures, there may be more than
one spacer attached to the pyridyl group (e.g. n=1 or more, with 2
finding particular use in some embodiments).
[0108] 2). Sulfur Anchor Groups
[0109] Although depicted in Structure 1 as a single moiety, the
conductive oligomer may be attached to the electrode with more than
one "A" moiety; the "A" moieties may be the same or different.
Thus, for example, when the electrode is a gold electrode, and "A"
is a sulfur atom or moiety, multiple sulfur atoms may be used to
attach the conductive oligomer to the electrode, such as is
generally depicted below in Structures 2, 3 and 4. As will be
appreciated by those in the art, other such structures can be made.
In Structures 2, 3 and 4 the A moiety is just a sulfur atom, but
substituted sulfur moieties may also be used.
[0110] Thus, for example, when the electrode is a gold electrode,
and "A" is a sulfur atom or moiety, such as generally depicted
below in Structure 6, multiple sulfur atoms may be used to attach
the conductive oligomer to the electrode, such as is generally
depicted below in Structures 2, 3 and 4. As will be appreciated by
those in the art, other such structures can be made. In Structures
2, 3 and 4, the A moiety is just a sulfur atom, but substituted
sulfur moieties may also be used.
##STR00007##
[0111] It should also be noted that similar to Structure 4, it may
be possible to have a conductive oligomer terminating in a single
carbon atom with three sulfur moieties attached to the
electrode.
[0112] In another aspect, the present invention provide anchor
comprise conjugated thiols. Some exemplary complexes with
conjugated thiol anchors are shown in FIG. 4. In some embodiments,
the anchor comprises an alkylthiol group. Some of the examples are
shown in FIGS. 4A and 4B. The two compounds depicts in FIG. 4B are
based on carbene and 4-pyridylalanine, respectively.
[0113] In another aspect, the present invention provides conjugated
multipodal thio-containing compounds that serve as anchoring groups
in the construction of electroactive moieties for analyte detection
on electrodes, such as gold electrodes. That is, spacer groups
(which can be attached to EAMs, ReAMCs, or an "empty" monolayer
forming species) are attached using two or more sulfur atoms. These
mulitpodal anchor groups can be linear or cyclic, as described
herein.
[0114] In some embodiments, the anchor groups are "bipedal",
containing two sulfur atoms that will attach to the gold surface,
and linear, although in some cases it can be possible to include
systems with other multipodalities (e.g. "tripodal"). Such a
multipodal anchoring group display increased stability and/or allow
a greater footprint for preparing SAMs from thiol-containing
anchors with sterically demanding headgroups.
[0115] In some embodiments, the anchor comprises cyclic disulfides
("biped"). Although in some cases it can be possible to include
ring system anchor groups with other multipodalities (e.g.
"tripodal"). The number of the atoms of the ring can vary, for
example from 5 to 10, and also includes multicyclic anchor groups,
as discussed below
[0116] In some embodiments, the anchor groups comprise a
[1,2,5]-dithiazepane unit which is seven membered ring with an apex
nitrogen atom and a intramolecular disulfide bond as shown
below:
##STR00008##
[0117] In Structure (IIIa), it should also be noted that the carbon
atoms of the ring can additionally be substituted. As will be
appreciated by those in the art, other membered rings are also
included. In addition, multicyclic ring structures can be used,
which can include cyclic heteroalkanes such as the
[1,2,5]-dithiazepane shown above substituted with other cyclic
alkanes (including cyclic heteroalkanes) or aromatic ring
structures.
[0118] In some embodiments, the anchor group and part of the spacer
has the structure shown below
##STR00009##
[0119] The "R" group herein can be any substitution group,
including a conjugated oligophenylethynylene unit with terminal
coordinating ligand for the transition metal component of the
EAM.
[0120] The anchors are synthesized from a bipedal intermediate (I)
(the compound as formula III where R=1), which is described in Li
et al., Org. Lett. 4:3631-3634 (2002), herein incorporated by
reference. See also Wei et al, J. Org, Chem. 69:1461-1469 (2004),
herein incorporated by reference.
[0121] The number of sulfur atoms can vary as outlined herein, with
particular embodiments utilizing one, two, and three per
spacer.
C. Electroactive Moieties
[0122] In addition to anchor groups, the present invention provides
compound comprising electroactive moieties. By "electroactive
moiety (EAM)" or "transition metal complex" or "redox active
molecule" or "electron transfer moiety (ETM)" herein is meant a
metal-containing compound which is capable of reversibly or
semi-reversibly transferring one or more electrons. It is to be
understood that electron donor and acceptor capabilities are
relative; that is, a molecule which can lose an electron under
certain experimental conditions will be able to accept an electron
under different experimental conditions.
[0123] It is to be understood that the number of possible
transition metal complexes is very large, and that one skilled in
the art of electron transfer compounds will be able to utilize a
number of compounds in the present invention. By "transitional
metal" herein is meant metals whose atoms have a partial or
completed shell of electrons. Suitable transition metals for use in
the invention include, but are not limited to, cadmium (Cd), copper
(Cu), cobalt (Co), palladium (Pd), zinc (Zn), iron (Fe), ruthenium
(Ru), rhodium (Rh), osmium (Os), rhenium (Re), platinium (Pt),
scandium (Sc), titanium (Ti), Vanadium (V), chromium (Cr),
manganese (Mn), nickel (Ni), Molybdenum (Mo), technetium (Tc),
tungsten (W), and iridium (Jr). That is, the first series of
transition metals, the platinum metals (Ru, Rh, Pd, Os, Jr and Pt),
along with Fe, Re, W, Mo and Tc, find particular use in the present
invention. Particularly preferred are metals that do not change the
number of coordination sites upon a change in oxidation state,
including ruthenium, osmium, iron, platinium and palladium, with
osmium, ruthenium and iron being especially preferred, and osmium
finding particular use in many embodiments. In some embodiments,
iron is not preferred. Generally, transition metals are depicted
herein as TM or M.
[0124] The transitional metal and the coordinating ligands form a
metal complex. By "ligand" or "coordinating ligand" (depicted
herein in the figures as "L") herein is meant an atom, ion,
molecule, or functional group that generally donates one or more of
its electrons through a coordinate covalent bond to, or shares its
electrons through a covalent bond with, one or more central atoms
or ions.
[0125] The other coordination sites of the metal are used for
attachment of the transition metal complex to either a capture
ligand (directly or indirectly using a linker), or to the electrode
(frequently using a spacer, as is more fully described below), or
both. Thus for example, when the transition metal complex is
directly joined to a binding ligand, one, two or more of the
coordination sites of the metal ion may be occupied by coordination
atoms supplied by the binding ligand (or by the linker, if
indirectly joined). In addition, or alternatively, one or more of
the coordination sites of the metal ion may be occupied by a spacer
used to attach the transition metal complex to the electrode. For
example, when the transition metal complex is attached to the
electrode separately from the binding ligand as is more fully
described below, all of the coordination sites of the metal (n)
except 1 (n-1) may contain polar ligands.
[0126] Suitable small polar ligands, generally depicted herein as
"L", fall into two general categories, as is more fully described
herein. In one embodiment, the small polar ligands will be
effectively irreversibly bound to the metal ion, due to their
characteristics as generally poor leaving groups or as good sigma
donors, and the identity of the metal. These ligands may be
referred to as "substitutionally inert". Alternatively, as is more
fully described below, the small polar ligands may be reversibly
bound to the metal ion, such that upon binding of a target analyte,
the analyte may provide one or more coordination atoms for the
metal, effectively replacing the small polar ligands, due to their
good leaving group properties or poor sigma donor properties. These
ligands may be referred to as "substitutionally labile". The
ligands preferably form dipoles, since this will contribute to a
high solvent reorganization energy.
[0127] Some of the structures of transitional metal complexes are
shown below:
##STR00010##
[0128] L are the co-ligands, that provide the coordination atoms
for the binding of the metal ion. As will be appreciated by those
in the art, the number and nature of the co-ligands will depend on
the coordination number of the metal ion. Mono-, di- or polydentate
co-ligands may be used at any position. Thus, for example, when the
metal has a coordination number of six, the L from the terminus of
the conductive oligomer, the L contributed from the nucleic acid,
and r, add up to six. Thus, when the metal has a coordination
number of six, r may range from zero (when all coordination atoms
are provided by the other two ligands) to four, when all the
co-ligands are monodentate. Thus generally, r will be from 0 to 8,
depending on the coordination number of the metal ion and the
choice of the other ligands.
[0129] In one embodiment, the metal ion has a coordination number
of six and both the ligand attached to the conductive oligomer and
the ligand attached to the nucleic acid are at least bidentate;
that is, r is preferably zero, one (i.e. the remaining co-ligand is
bidentate) or two (two monodentate co-ligands are used).
[0130] As will be appreciated in the art, the co-ligands can be the
same or different. Suitable ligands fall into two categories:
ligands which use nitrogen, oxygen, sulfur, carbon or phosphorus
atoms (depending on the metal ion) as the coordination atoms
(generally referred to in the literature as sigma (.sigma.) donors)
and organometallic ligands such as metallocene ligands (generally
referred to in the literature as pi (.pi.) donors, and depicted
herein as Lm). Suitable nitrogen donating ligands are well known in
the art and include, but are not limited to, cyano (C.ident.N),
NH.sub.2; NHR; NRR'; pyridine; pyrazine; isonicotinamide;
imidazole; bipyridine and substituted derivatives of bipyridine;
terpyridine and substituted derivatives; phenanthrolines,
particularly 1,10-phenanthroline (abbreviated phen) and substituted
derivatives of phenanthrolines such as 4,7-dimethylphenanthroline
and dipyridol[3,2-a:2',3'-c]phenazine (abbreviated dppz);
dipyridophenazine; 1,4,5,8,9,12-hexaazatriphenylene (abbreviated
hat); 9,10-phenanthrenequinone diimine (abbreviated phi);
1,4,5,8-tetraazaphenanthrene (abbreviated tap);
1,4,8,11-tetra-azacyclotetradecane (abbreviated cyclam) and
isocyanide. Substituted derivatives, including fused derivatives,
may also be used. In some embodiments, porphyrins and substituted
derivatives of the porphyrin family may be used. See for example,
Comprehensive Coordination Chemistry, Ed. Wilkinson et al.,
Pergammon Press, 1987, Chapters 13.2 (pp 73-98), 21.1 (pp. 813-898)
and 21.3 (pp 915-957), all of which are hereby expressly
incorporated by reference.
[0131] As will be appreciated in the art, any ligand
donor(1)-bridge-donor(2) where donor (1) binds to the metal and
donor(2) is available for interaction with the surrounding medium
(solvent, protein, etc) can be used in the present invention,
especially if donor(1) and donor(2) are coupled through a pi
system, as in cyanos (C is donor(1), N is donor(2), pi system is
the CN triple bond). One example is bipyrimidine, which looks much
like bipyridine but has N donors on the "back side" for
interactions with the medium. Additional co-ligands include, but
are not limited to cyanates, isocyanates (--N.dbd.C.dbd.O),
thiocyanates, isonitrile, N.sub.2, O.sub.2, carbonyl, halides,
alkoxyide, thiolates, amides, phosphides, and sulfur containing
compound such as sulfino, sulfonyl, sulfoamino, and sulfamoyl.
[0132] In some embodiments, multiple cyanos are used as co-ligand
to complex with different metals. For example, seven cyanos bind
Re(III); eight bind Mo(IV) and W(IV). Thus at Re(III) with 6 or
less cyanos and one or more L, or Mo(IV) or W(IV) with 7 or less
cyanos and one or more L can be used in the present invention. The
EAM with W(IV) system has particular advantages over the others
because it is more inert, easier to prepare, more favorable
reduction potential. Generally that a larger CN/L ratio will give
larger shifts.
[0133] Suitable sigma donating ligands using carbon, oxygen, sulfur
and phosphorus are known in the art. For example, suitable sigma
carbon donors are found in Cotton and Wilkenson, Advanced Organic
Chemistry, 5th Edition, John Wiley & Sons, 1988, hereby
incorporated by reference; see page 38, for example. Similarly,
suitable oxygen ligands include crown ethers, water and others
known in the art. Phosphines and substituted phosphines are also
suitable; see page 38 of Cotton and Wilkenson.
[0134] The oxygen, sulfur, phosphorus and nitrogen-donating ligands
are attached in such a manner as to allow the heteroatoms to serve
as coordination atoms.
[0135] In some embodiments, organometallic ligands are used. In
addition to purely organic compounds for use as redox moieties, and
various transition metal coordination complexes with .sigma.-bonded
organic ligand with donor atoms as heterocyclic or exocyclic
substituents, there is available a wide variety of transition metal
organometallic compounds with .pi.-bonded organic ligands (see
Advanced Inorganic Chemistry, 5th Ed., Cotton & Wilkinson, John
Wiley & Sons, 1988, chapter 26; Organometallics, A Concise
Introduction, Elschenbroich et al., 2nd Ed., 1992, VCH; and
Comprehensive Organometallic Chemistry II, A Review of the
Literature 1982-1994, Abel et al. Ed., Vol. 7, chapters 7, 8,10
& 11, Pergamon Press, hereby expressly incorporated by
reference). Such organometallic ligands include cyclic aromatic
compounds such as the cyclopentadienide ion [C.sub.5H.sub.5 (-1)]
and various ring substituted and ring fused derivatives, such as
the indenylide (-1) ion, that yield a class of
bis(cyclopentadieyl)metal compounds, (i.e. the metallocenes); see
for example Robins et al., J. Am. Chem. Soc. 104:1882-1893 (1982);
and Gassman et al., J. Am. Chem. Soc. 108:4228-4229 (1986),
incorporated by reference. Of these, ferrocene
[(C.sub.5H.sub.5).sub.2 Fe] and its derivatives are prototypical
examples which have been used in a wide variety of chemical
(Connelly et al., Chem. Rev. 96:877-910 (1996), incorporated by
reference) and electrochemical (Geiger et al., Advances in
Organometallic Chemistry 23: 1-93; and Geiger et al., Advances in
Organometallic Chemistry 24:87, incorporated by reference) electron
transfer or "redox" reactions. Metallocene derivatives of a variety
of the first, second and third row transition metals are potential
candidates as redox moieties that are covalently attached to either
the ribose ring or the nucleoside base of nucleic acid. Other
potentially suitable organometallic ligands include cyclic arenes
such as benzene, to yield bis(arene)metal compounds and their ring
substituted and ring fused derivatives, of which
bis(benzene)chromium is a prototypical example. Other acyclic
n-bonded ligands such as the allyl(-1) ion, or butadiene yield
potentially suitable organometallic compounds, and all such
ligands, in conduction with other .pi.-bonded and .delta.-bonded
ligands constitute the general class of organometallic compounds in
which there is a metal to carbon bond. Electrochemical studies of
various dimers and oligomers of such compounds with bridging
organic ligands, and additional non-bridging ligands, as well as
with and without metal-metal bonds are potential candidate redox
moieties in nucleic acid analysis.
[0136] When one or more of the co-ligands is an organometallic
ligand, the ligand is generally attached via one of the carbon
atoms of the organometallic ligand, although attachment may be via
other atoms for heterocyclic ligands. Preferred organometallic
ligands include metallocene ligands, including substituted
derivatives and the metalloceneophanes (see page 1174 of Cotton and
Wilkenson, supra). For example, derivatives of metallocene ligands
such as methylcyclopentadienyl, with multiple methyl groups being
preferred, such as pentamethylcyclopentadienyl, can be used to
increase the stability of the metallocene. In a preferred
embodiment, only one of the two metallocene ligands of a
metallocene are derivatized.
[0137] As described herein, any combination of ligands may be used.
Preferred combinations include: a) all ligands are nitrogen
donating ligands; b) all ligands are organometallic ligands; and c)
the ligand at the terminus of the conductive oligomer is a
metallocene ligand and the ligand provided by the nucleic acid is a
nitrogen donating ligand, with the other ligands, if needed, are
either nitrogen donating ligands or metallocene ligands, or a
mixture.
[0138] As a general rule, EAM comprising non-macrocyclic chelators
are bound to metal ions to form non-macrocyclic chelate compounds,
since the presence of the metal allows for multiple proligands to
bind together to give multiple oxidation states.
[0139] In some embodiments, nitrogen donating proligands are used.
Suitable nitrogen donating proligands are well known in the art and
include, but are not limited to, NH2; NHR; NRR'; pyridine;
pyrazine; isonicotinamide; imidazole; bipyridine and substituted
derivatives of bipyridine; terpyridine and substituted derivatives;
phenanthrolines, particularly 1,10-phenanthroline (abbreviated
phen) and substituted derivatives of phenanthrolines such as
4,7-dimethylphenanthroline and dipyridol[3,2-a:2',3' c] phenazine
(abbreviated dppz); dipyridophenazine;
1,4,5,8,9,12-hexaazatriphenylene (abbreviated hat);
9,10-phenanthrenequinone diimine (abbreviated phi);
1,4,5,8-tetraazaphenanthrene (abbreviated tap);
1,4,8,11-tetra-azacyclotetradecane (abbreviated cyclam) and
isocyanide. Substituted derivatives, including fused derivatives,
may also be used. It should be noted that macrocylic ligands that
do not coordinatively saturate the metal ion, and which require the
addition of another proligand, are considered non-macrocyclic for
this purpose. As will be appreciated by those in the art, it is
possible to covalent attach a number of "non-macrocyclic" ligands
to form a coordinatively saturated compound, but that is lacking a
cyclic skeleton.
[0140] In some embodiments, a mixture of monodentate (e.g. at least
one cyano ligand), bi-dentate, tridentate, and polydentate ligands
(till to saturate) can be used in the construction of EAMs
[0141] Generally, it is the composition or characteristics of the
ligands that determine whether a transition metal complex is
solvent accessible. By "solvent accessible transition metal
complex" or grammatical equivalents herein is meant a transition
metal complex that has at least one, preferably two, and more
preferably three, four or more small polar ligands. The actual
number of polar ligands will depend on the coordination number (n)
of the metal ion. Preferred numbers of polar ligands are (n-1) and
(n-2). For example, for hexacoordinate metals, such as Fe, Ru, and
Os, solvent accessible transition metal complexes preferably have
one to five small polar ligands, with two to five being preferred,
and three to five being particularly preferred, depending on the
requirement for the other sites, as is more fully described below.
Tetracoordinate metals such as Pt and Pd preferably have one, two
or three small polar ligands.
[0142] It should be understood that "solvent accessible" and
"solvent inhibited" are relative terms. That is, at high applied
energy, even a solvent accessible transition metal complex may be
induced to transfer an electron.
[0143] Some examples of EAMs are described herein.
[0144] 1) Cyano-Based Complexes
[0145] In one aspect, the present invention provides EAMs with a
transition metal and at least one cyano (--C.dbd.N) ligand.
Depending on the valency of the metal and the configuration of the
system (e.g. capture ligand contributing a coordination atom,
etc.), 1, 2, 3, 4 or 5 cyano ligands can be used. In general,
embodiments which use the most cyano ligands are preferred; again,
this depends on the configuration of the system. For example, as
depicted in FIG. 15, an EAM using a hexadentate metal such as
osmium, separately attached from the capture ligand, allows 5 cyano
ligands, with the 6th coordination site being occupied by the
terminus of the attachment linker. When a hexadentate metal has
both an attachment linker and a capture ligand providing
coordination atoms, there can be four cyano ligands.
[0146] In some embodiments, such as depicted in the Figures, the
attachment linker and/or the capture ligand can provide more than a
single coordination atom. Thus, for example, in FIG. 17, the
attachment linker comprises a bipyridine which contributes two
coordination atoms.
[0147] In some embodiments, ligands other than cyano ligands are
used in combination with at least one cyano ligand.
[0148] 2). Ru--N Based Complexes
[0149] In one aspect, the resent invention provides new
architectures for Ru--N based complexes, where the coordination
could be monodentate, bidentate, tridentate, or multidendate. Thus
the number of coordination ligand L (which covalently connected to
the anchor and capture ligand) can be 1, 2, 3, or 4. Some of the
examples are shown in FIG. 5A.
[0150] The charge-neutralizing ligands can be any suitable ligand
known in the art, such as dithiocarbamate, benzenedithiolate, or
Schiff base as described herein. The capture ligand and the anchor
can be on the same framework or separate.
[0151] In another aspect of the present invention, each component
of the EAM ligand architecture is connected through covalent bonds
rather than Ru coordination chemistry. The construction of the
architectures provide herein relies on modern synthetic organic
chemical methodology. An important design consideration includes
the necessary orthogonal reactivity of the functional groups
present in the anchor and capture ligand component versus the
coordinating ligand component. Preferably, the entire compound can
be synthesized and the redox active transitional metal coordinated
to the ligand near the last step of the synthesis. The coordinating
ligands provided herein rely on well-established inorganic
methodologies for ruthenium pentaamine precursors. See Gerhardt and
Week, J. Org. Chem. 71:6336-6341 (2006); Sizova et al., Inorg.
Chim. Acta, 357:354-360 (2004); and Scott and Nolan, Eur. J. Inorg.
Chem. 1815-1828 (2005), all herein incorporated by reference. Some
examples of EAM architectures with Ru-pentaamine complexes are
shown bellow in FIG. 5B.
[0152] As can be understood by those skilled in the art, the anchor
components of the compounds provided herein could be interchanged
between alkyl and multipodal-based thiols.
[0153] 3). Ferrocene-Based EAMs
[0154] In some embodiments, the EAMs comprise substituted
ferrocenes. Ferrocene is air-stable. It can be easily substituted
with both capture ligand and anchoring group. Upon binding of the
target protein to the capture ligand on the ferrocene which will
not only change the environment around the ferrocene, but also
prevent the cyclopentadienyl rings from spinning, which will change
the energy by approximately 4kJ/mol. W0/1998/57159; Heinze and
Schlenker, Eur. J. Inorg. Chem. 297 4-2988 (2004); Heinze and
Schlenker, Eur. J. Inorg. Chem. 66-71 (2005); and Holleman-Wiberg,
Inorganic Chemistry, Academic Press 34th Ed, at 1620, all
incorporated by reference.
##STR00011##
[0155] In some embodiments the anchor and capture ligands are
attached to the same ligand for easier synthesis. In some
embodiments the anchor and capture ligand are attached to different
ligands.
[0156] There are many ligands that can be used to build the new
architecture disclosed herein. They include but not limited to
carboxylate, amine, thiolate, phosphine, imidazole, pyridine,
bipyridine, terpyridine, tacn (1,4,7-Triazacyclononane), salen
(N,N'-bis(salicylidene) ethylenediamine), acacen
(N,N'Ethylenebis(acetylacetoniminate(-)), EDTA (ethylenediamine
tetraacetic acid), DTPA (diethylene triamine pentaacetic acid), Cp
(cyclopentadienyl), pincer ligands, and scorpionates. In some
embodiments, the preferred ligand is pentaamine.
[0157] Pincer ligands are a specific type of chelating ligand. A
pincer ligand wraps itself around the metal center to create bonds
on opposite sides of the metal as well as one in between. The
effects pincer ligand chemistry on the metal core electrons is
similar to amines, phosphines, and mixed donor ligands. This
creates a unique chemical situation where the activity of the metal
can be tailored. For example, since there is such a high demand on
the sterics of the complex in order to accommodate a pincer ligand,
the reactions that the metal can participate in is limited and
selective.
[0158] Scorpionate ligand refers to a tridentate ligand which would
bind to a metal in a fac manner. The most popular class of
scorpionates are the tris(pyrazolyl)hydroborates or Tp ligands. A
Cp ligand is isolobal to Tp
[0159] In some embodiments, the following restraints are desirable:
the metal complex should have small polar ligands that allow close
contact with the solvent.
[0160] 4). Charge-Neutralizing Ligands
[0161] In another aspect, the present invention provides
compositions having metal complexes comprising charged ligands. The
reorganization energy for a system that changes from neutral to
charged or from charged to neutral (e.g.
M(L).sub.n.sup.+<->M(L)2;
M(L).sub.n-<->)M(L).sub.n.sup.2+ may be larger than that for
a system in which the charge simply changes (e.g.
M(L).sub.n.sup.2+<->M(L).sub.n.sup.3+) because the water
molecules and surrounding ions have to "reorganize" more to
accommodate the change to or from an uncharged state.
[0162] In some embodiments, charged ligand anionic compounds can be
used to attach the anchor and the capture ligand to the metal
center. A metal complex containing a halide ion X in the inner
complex sphere reacts with charged ligands, including but not
limited to, thiols (R--SH), thiolates (RS-E; E=leaving group, i.e.,
trimethylsilyl-group), carbonic acids, dithiols, carbonates,
acetylacetonates, salicylates, cysteine,
3-mercapto-2-(mercaptomethyl) propanoic acid. The driving force for
this reaction is the formation of HX or EX. If the anionic ligand
contains both capture ligand and anchor, one substitution reaction
is required, and therefore the metal complex, with which it is
reacted, needs to have one halide ligand in the inner sphere. If
the anchor and capture ligand are introduced separately the
starting material generally needs to contain two halide in the
inner coordination sphere. Seidel et al., Inorg. Chem. 37:6587-6596
(1998); Kathari and Busch, Inorg. Chem. 8:2276-2280 (1978); Isied
and Kuehn J. Am. Chem. Soc. 100:6752-6754; and Volkers et al., Eur.
J. Inorg. Chem. 4793-4799 (2006), all herein incorporated by
reference.
[0163] Examples for suitable metal complexes are the following (it
should be noted that the structures depicted below show multiple
unidentate ligands, and multidentate ligands can be substituted for
or combined with unidentate ligands such as cyano ligands):
##STR00012##
[0164] In some embodiments, dithiocarbamate is used as a
charge-neutralizing ligand, such as the following example:
##STR00013##
[0165] In some embodiments, benzenedithiolate is used as
charge-neutralizing ligand, such as the following example:
##STR00014##
[0166] In the above depicted structures, Ln is coordinate ligand
and n=0 or 1.
[0167] In some embodiments, the EAM comprises Schiff base type
complexes. By "Schiff base" or "azomethine" herein is meant a
functional group that contains a carbon-nitrogen double bond with
thenitrogen atom connected to an aryl or alkyl group--but not
hydrogen. Schiff bases are of the general formula
R.sub.1R.sub.2C.dbd.N--R.sub.3, where R.sub.3 is a phenyl or alkyl
group that makes the Schiff base a stable imine. Schiff bases can
be synthesized from an aromatic amine and a carbonyl compound by
nucleophilic addition forming a hemiaminal, followed by a
dehydration to generate an imine.
[0168] Acacen is a small planar tetradentate ligand that can form
hydrogen bonds to surrounding water molecules through its nitrogen
and oxygen atoms, which would enhance the reorganization energy
effect. It can be modified with many functionalities, including but
not limited to, carboxylic acid and halides, which can be used to
couple the acacen-ligand to the capture ligand and to the anchoring
group. This system allows a large variety of different metal
centers to be utilized in the EAMs. Since the ligand binds with its
two oxygen and two nitrogen atoms, only four coordination sites are
occupied. This leaves two additional coordination sites open,
depending on the metal center. These coordination sites can be
occupied by a large variety of organic and inorganic ligands. These
additional open sites can be used for inner-sphere substution (e.g.
labile H.sub.20 or NH.sub.3 can be displaced by protein binding) or
outer-sphere influence (e.g. CO, CN can for H-bonds) to optimize
the shift of potentials upon binding of the capture ligand to the
target. WO/1998/057158, WO/1997/21431, Louie et al., PNAS
95:6663-6668 (1999), and Bottcher et al., Inorg. Chem. 36:2498-2504
(1997), herein all incorporated by reference.
[0169] In some embodiments, salen-complexes are used as well.
Syamal et al., Reactive and Functional Polymers 39:27-35
(1999).
[0170] The structures of some acacen-based complexes and
salen-based complexes are shown below, where positions on the
ligand that are suitable for functionalization with the capture
ligand and/or the anchor are marked with an asterisk.
##STR00015##
[0171] One example of using acacen as ligand to form a cobalt
complex is the following: wherein
##STR00016##
wherein is A and Bare substitute groups, Ln is coordinating ligand
and n=0 or 1, and Y is a counterion.
[0172] 5). Sulfate Ligands
[0173] In some embodiments, the EAM comprises sulfate complexes,
including but not limited to, [LRu(III)(NH.sub.3).sub.4SO.sub.4
(and [L-Ru(III)(NH.sub.3).sub.4SO2.sub.2].sup.2+. The
SO.sub.4--Ru(III)-complexes are air stable. The ligand L comprises
a capture ligand and anchor. The sulfate ligand is more polar than
amine and negatively charged. The surface complexes therefore will
have a larger reorganization energy contribution from surrounding
water molecules than both the [L-Ru(NH3).sub.4-L'] and
[L-Ru(NH.sub.3).sub.5].sup.2+. Isied and Taube, Inorg. Chem.
13:1545-1551 (1974), herein incorporated by reference.
##STR00017##
[0174] 6). EAM With Multiple Metals
[0175] In one aspect of the present invention multiple metal
centers are incorporated to a single ligand complex and thereby
increases the signal. This arrangement increases the ratio of
metals per target, resulting in a higher sensitivity.
[0176] In some embodiments, multiple metal centers are present
close to the capture ligand of an anchoring moiety to enable larger
interaction with the analyte of interest (target). Having more than
one reporter metal per analyte could boost the signal to noise
ratio, increasing the sensitivity of the device. One of such
examples is shown in FIG. 19.
[0177] In some embodiments Prussian blue (PB) is used. Prussian
blue is an inorganic, three dimensional polymer (see below) that
can be formed chemically or electrochemically from simple iron
cyanide precursors. Other metals such as Mn and V and Ru have also
been incorporated into PB-like films. Films of 50-100 nm thickness
are formed quickly. An iron (or other similar metal) complex with a
capture ligand can be incorporated on the surface of the film by
combining this complex with the precursors during the formation of
the film:
FE(H.sub.2O).sub.6.sup.3++FE(CL)H.sub.2O).sub.5.sup.3++FE(CN).sub.6.sup.-
4-.fwdarw.PB with Fe--Cl on surface
[0178] When the target analyte (such as a protein) binds, the
hydrogen bonding of water to cyano groups and other water molecules
on the surface will be disrupted, and will affect more metals than
just the one with the capture ligand. The electrochemical signal
will be drastically changed due to this amplification. See FIG. 6A.
In some embodiments a background subtraction of the signal before
protein binding may be advantageous.
##STR00018##
[0179] In the example shown above, the axial positions on the iron
metal are functionalized with capture ligands arranged orthogonal
to the surface. The binding of a single target to the
functionalized surface will impact the metal that is directly
attached as well as adjacent metal centers.
[0180] The Fe--CL complex may be added after initial formation of
the film so that it will be incorporated on the surface only, and
not cause excessive defects. The film thickness can be controlled
by the time the chemical reaction is allowed to proceed or by how
much current is applied to the solution if formed
electrochemically.
[0181] Alternatively, islands of PB can be grown between areas of
alkane or conjugated SAMs with or without the capture ligand. This
would require nanopatterning and would help prevent electrochemical
signals from extraneous species in the sample solution.
[0182] The metal can be used include, but not limited to,
ruthenium, iron, rhenium, and osmium, with the appropriate ligand
structure associated with each.
[0183] When there are multiple metals in the same complex the
connectivity between the multiple metal centers generally should
not allow "cross-talk" between the metals; but should rather be
insulating.
[0184] 7). Crown Ether Ligands
[0185] In one aspect, the present invention provides compositions
where polar groups, such as crown ethers (CEs), are introduced in
the vicinity to the metal center. This could increase the potential
shift upon binding of a target analyte (e.g. a protein) to an EAM
and therefore increase the sensitivity of the probe.
[0186] Crown ethers are heterocyclic chemical compounds that, in
their simplest form, are cyclic oligomers of ethylene oxide. The
essential repeating unit of any simple crown ether is ethyleneoxy,
i.e., --CH.sub.2CH.sub.2O--, which repeats twice in dioxane and six
times in 18-crown-6. In general, macrocycles of the
(CH.sub.2CH.sub.2O--) n type in which n>4 are referred to as
"crown" ethers rather than by their lengthier systematic names: for
instance, the systematic name of 18-crown-6 is "1, 4, 7, 10, 13, 16
hexaoxacyclooctadecane." The first number in a crown ether's name
refers to the number of atoms in the cycle, and the second number
refers to the number of those atoms which are oxygen.
[0187] Also envisioned by the present invention are crown ether
derivatives.
[0188] This embodiment of the is based on having a second-sphere
moiety bound to the ruthenium center of the EAM prior to the
protein binding event. It has been shown that having a crown ether
hydrogen bonded to pentaammine ruthenium complexes shifts the redox
potential significantly (up to -100 mV) negative in acetonitrile.
See Ando, Coordination Chemistry Reviews, 248:185-203 (2004), and
references therein; Ando et al., Polyhedron, 11:2335-2340 (1992);
Zang et al., Inorg. Chem., 4738-4743 (1994); Todd et al. Inorg.
Chem., 32:2001-2001 (1993); Dong et al., J. Am. Chem. Soc., 115,
4379-4380 (1993), all herein incorporated by reference.
[0189] The applicants have observed a positive shift in redox
potential upon protein binding to the EAM provided herein, thus the
use of crown ether would amplify this effect. By having some
electron donating moiety (i.e. crown ether) bound to the metal
center prior to protein binding "stacks the deck" for us by moving
our initial potential more negative such that upon protein binding
the crown ether is displaced (changing the second sphere
coordination) giving a larger positive potential shift.
[0190] Without being bound by theory, the reason for the increased
potential shift is likely the following: CEs form hydrogen bonds to
surrounding water molecules. CEs are known to bind to alkali metal
ions (e.g. Na.sup.+, K.sup.+ in electrolyte) which bind to the
oxygen atoms of the CE. In water, the CE, the ion and the
counterion (e.g. Cr) are hydrated with surrounding water molecules.
Upon binding of the target to the capture ligand the water
molecules surrounding the transition metal complex are replaced as
well as the water molecules hydrating the CE, the alkali metal ion
and the counterion of the alkali metal ion. See FIGS. 6A and 6B.
The fact that many more water molecules are replaced will increase
the shift in potential observed in a binding event. In some cases
the change in environment from hydrophilic to more hydrophobic
actually expels the alkali metal salt (such as K.sup.+ and Na.sup.+
ions) from the CE as well as the water molecules, and a potential
shift of as much as 1.0V can be expected. Electrochimica acta 2001,
2733, herein incorporated by reference. See e.g. FIG. 7. Some of
the examples are:
##STR00019##
wherein S.sup.1 and S.sup.2 are spacers, CL=capture ligand and
AG=anchoring group.
[0191] 8). Pyridine-Thioether/ether--Ligands
[0192] In some embodiments, pyridine-thioether/ether-ligands are
used in the synthesis of EAM. These ligand systems will be able to
bind to various metal centers via the pyridine-nitrogen and the
thioether/ether functionality. Without being bound by the theory,
there is the possibility that upon binding of the EAM to the
target, the metal-thioether/ether bond is getting cleaved and e.g.
halide binds to the metal center, which would be an inner-sphere
effect, leading to a large shift in the electrochemical
potential.
[0193] One of the examples for such complexes is shown bellow:
##STR00020##
where Ln=coordinate ligand of metal center, L=0 or 1, and X.dbd.O
or S;
[0194] In some embodiments, bipyridines and other
multidentate-nitrogen-based ligands, such as 1,10 phenanthrolines
or terpyridines, are used. Examples for these type of ligands are
shown bellow:
##STR00021##
D. Spacer Groups
[0195] In some embodiments, the EAM or ReAMC is covalently attached
to the anchor group (which is attached to the electrode) via an
attachment linker or spacer ("Spacer 1"), that further generally
includes a functional moiety that allows the association of the
attachment linker to the electrode. See for example U.S. Pat. No.
7,384,749, incorporated herein by reference in its entirety and
specifically for the discussion of attachment linkers). It should
be noted in the case of a gold electrode, a sulfur atom can be used
as the functional group (this attachment is considered covalent for
the purposes of this invention). By "spacer" or "attachment linker"
herein is meant a moiety which holds the redox active complex off
the surface of the electrode. In some embodiments, the spacer is a
conductive oligomer as outlined herein, although suitable spacer
moieties include passivation agents and insulators as outlined
below. In some cases, the spacer molecules are SAM forming species.
The spacer moieties may be substantially non-conductive, although
preferably (but not required) is that the electron coupling between
the redox active molecule and the electrode (HAs) does not limit
the rate in electron transfer.
[0196] In addition, attachment linkers can be used to between the
coordination atom of the capture ligand and the capture ligand
itself, in the case when ReAMCs are utilized. Similarly, attachment
linkers can be branched, such as shown in FIGS. 12-14. In addition,
attachment linkers can be used to attach capture ligands to the
electrode when they are not associated in a ReAMC.
[0197] One end of the attachment linker is linked to the
EAM/ReAMC/capture ligand, and the other end (although as will be
appreciated by those in the art, it need not be the exact terminus
for either) is attached to the electrode.
[0198] The covalent attachment of the conductive oligomer
containing the redox active molecule (and the attachment of other
spacer molecules) may be accomplished in a variety of ways,
depending on the electrode and the conductive oligomer used. See
for example Structures 12-19 and the accompanying text in U.S.
Patent Publication No. 20020009810, hereby incorporated by
reference in its entirety.
[0199] In general, the length of the spacer is as outlined for
conductive polymers and passivation agents in U.S. Pat. Nos.
6,013,459, 6,013,170, and 6,248,229, as well as 7,384,749 all
herein incorporated by reference in their entireties. As will be
appreciated by those in the art, if the spacer becomes too long,
the electronic coupling between the redox active molecule and the
electrode will decrease rapidly.
E. Capture Ligands
[0200] A variety of molecules can be used in the present invention
as capture ligands. By "capture ligand" or "binding ligand" or
"capture binding ligand" or "capture binding species" or "capture
probe" herein is meant a compound that is used to probe for the
presence of the target analyte that will bind to the target
analyte. Generally, the capture ligand allows the attachment of a
target analyte to the electrode, for the purposes of detection. As
is more fully outlined below, attachment of the target analyte to
the capture probe may be direct (i.e. the target analyte binds to
the capture ligand) or indirect (one or more capture extender
ligands are used). By "covalently attached" herein is meant that
two moieties are attached by at least one bond, including sigma
bonds, pi bonds and coordination bonds.
[0201] In some embodiments, the binding is specific, and the
capture ligand is part of a binding pair. By "specifically bind"
herein is meant that the ligand binds the analyte, with specificity
sufficient to differentiate between the analyte and other
components or contaminants of the test sample. However, as will be
appreciated by those in the art, it will be possible to detect
analytes using binding which is not highly specific; for example,
the systems may use different capture ligands, for example an array
of different ligands, and detection of any particular analyte is
via its "signature" of binding to a panel of binding ligands,
similar to the manner in which "electronic noses" work. This finds
particular utility in the detection of chemical analytes. The
binding should be sufficient to remain bound under the conditions
of the assay, including wash steps to remove non-specific binding.
This binding should be sufficient to remain bound under the
conditions of the assay, including wash steps to remove
non-specific binding. Generally, the disassociation constants of
the analyte to the binding ligand will be in the range of at least
10.sup.-4-10.sup.-6 M.sup.-1, with a preferred range being
10.sup.-5 to 10.sup.-9 M.sup.-1 and a particularly preferred range
being 10.sup.-7-10.sup.-9 M.sup.-1
[0202] As will be appreciated by those in the art, the composition
of the capture ligand will depend on the composition of the target
analyte. Capture ligands to a wide variety of analytes are known or
can be readily found using known techniques. For example, when the
analyte is a single-stranded nucleic acid, the capture ligand may
be a complementary nucleic acid. Similarly, the analyte may be a
nucleic acid binding protein and the capture binding ligand is
either single-stranded or double stranded nucleic acid;
alternatively, the binding ligand may be a nucleic acid-binding
protein when the analyte is a single or double-stranded nucleic
acid. When the analyte is a protein, the binding ligands include
proteins or small molecules. Preferred binding ligand proteins
include peptides. For example, when the analyte is an enzyme,
suitable binding ligands include substrates and inhibitors. As will
be appreciated by those in the art, any two molecules that will
associate may be used, either as an analyte or as the binding
ligand. Suitable analyte/binding ligand pairs include, but are not
limited to, antibodies/antigens, receptors/ligands,
proteins/nucleic acid, enzymes/substrates and/or inhibitors,
carbohydrates (including glycoproteins and glycolipids)/lectins,
proteins/proteins, proteins/small molecules; and carbohydrates and
their binding partners are also suitable analyte-binding ligand
pairs. These may be wild-type or derivative sequences. In a
preferred embodiment, the binding ligands are portions
(particularly the extracellular portions) of cell surface receptors
that are known to multimerize, such as the growth hormone receptor,
glucose transporters (particularly GLUT 4 receptor), transferrin
receptor, epidermal growth factor receptor, low density lipoprotein
receptor, high density lipoprotein receptor, epidermal growth
factor receptor, leptin receptor, interleukin receptors including
IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-11, IL-12,
IL-13, IL-15, and IL-17 receptors, human growth hormone receptor,
VEGF receptor, PDGF receptor, EPO receptor, TPO receptor, ciliary
neurotrophic factor receptor, prolactin receptor, and T-cell
receptors.
[0203] As described herein, the capture ligand can be attached to
the coordinating ligand and/or anchor via a covalent bond. The
method of attachment of the capture binding ligand will generally
be done as is known in the art, and will depend on the composition
of the attachment linker and the capture binding ligand. In
general, the capture binding ligands are attached to the attachment
linker through the use of functional groups on each that can then
be used for attachment. Preferred functional groups for attachment
are amino groups, carboxy groups, oxo groups and thiol groups.
These functional groups can then be attached, either directly or
through the use of a linker, sometimes depicted herein as "Z".
Linkers are known in the art; for example, homo- or
hetero-bifunctional linkers as are well known (see 1994 Pierce
Chemical Company catalog, technical section on cross-linkers, pages
155-200, incorporated herein by reference). Preferred Z linkers
include, but are not limited to, alkyl groups (including
substituted alkyl groups and alkyl groups containing heteroatom
moieties), with short alkyl groups, esters, amide, amine, epoxy
groups and ethylene glycol and derivatives being preferred. Z may
also be a sulfone group, forming sulfonamide.
[0204] In this way, capture binding ligands comprising proteins,
lectins, nucleic acids, small organic molecules, carbohydrates,
etc. can be added.
[0205] In some embodiment, antibodies or a fragment thereof are
used as capture ligands. By "antibody" herein is meant a member of
a family of glycosylated proteins called immunoglobulins, which can
specifically combine with an antigen. The term "antibody" includes
full-length as well antibody fragments, as are known in the art,
including Fab, Fab2, single chain antibodies (Fv for example),
chimeric antibodies, humanized and human antibodies, etc., either
produced by the modification of whole antibodies or those
synthesized de novo using recombinant DNA technologies, and
derivatives thereof.
[0206] However, in some embodiments, whole antibodies are not
preferred. This is because antibodies could be too bulky, leads to
interference with transducer. Thus in some embodiments, antibody
fragments and mimitopes are used as capture ligands.
[0207] By "epitope" herein is meant the actual site of antibody
recognition of the antigen. The term is also used interchangeably
with "antigenic determinant" or "antigenic determinant site".
[0208] By "mimitopes" or "mimotope" herein is meant a peptide which
has the spatial structure of a biologically important site, e.g.,
an epitope, or an enzyme active site, or a receptor binding
site.
[0209] In some embodiments, the capture ligand comprises antibody
alternatives, including but not limited to avimer. By "avimer"
herein is meant proteins that are evolved from a large family of
human extracellular receptor domains by in vitro exon shuffling and
phage display. It is generally a multidomain protein with binding
and inhibitory properties. See Silverman et al., Nature
Biotechnology 23:1556-1561 (2005), herein incorporated by
reference.
[0210] In some embodiments, the capture ligand comprises oligomeric
peptides. These peptides can be obtained using techniques known in
the art, including but not limited to phage display, Sidhu et al.,
Methods Enzymol., 328, 333-363 (2000), and one bead one peptide.
For example, the peptide can be obtained using Biopanning. Giodano
et al., Nat. Med. 7:1249-53 (2001); herein incorporated by
reference.
[0211] The capture ligand may be nucleic acid, when the target
analyte is a nucleic acid or nucleic acid binding proteins;
alternatively, as is generally described in U.S. Pat. Nos.
5,270,163, 5,475,096, 5,567,588, 5,595,877, 5,637,459, 5,683,867,
5,705,337, and related patents, hereby incorporated by reference,
nucleic acid "aptamers" can be developed for binding to virtually
any target analyte. Similarly, there is a wide body of literature
relating to the development of binding partners based on
combinatorial chemistry methods. In this embodiment, when the
capture ligand is a nucleic acid, preferred compositions and
techniques are outlined in PCT US97/20014, hereby incorporated by
reference.
[0212] In some embodiments, the capture ligand comprises an
aptamer. By "aptamer" herein is meant a single-stranded, partially
single-stranded, partially double-stranded or double-stranded
nucleotide sequence, advantageously a replicatable nucleotide
sequence, capable of specifically recognizing a selected
nonoligonucleotide molecule or group of molecules by a mechanism
other than Watson-Crick base pairing or triplex formation. Aptamers
disclosed herein include, without limitation, defined sequence
segments and sequences comprising nucleotides, ribonucleotides,
deoxyribonucleotides, nucleotide analogs, modified nucleotides and
nucleotides comprising backbone modifications, branchpoints and non
nucleotide residues, groups or bridges. Aptamers of the invention
include partially and fully single stranded and double-stranded
nucleotide molecules and sequences, synthetic RNA, DNA and chimeric
nucleotides, hybrids, duplexes, heteroduplexes, and any
ribonucleotide, deoxyribonucleotide or chimeric counterpart thereof
and/or corresponding complementary sequence, promoter or primer
annealing sequence needed to amplify, transcribe or replicate all
or part of the a pta mer molecule or sequence. Aptamers can
specifically bind to soluble, insoluble or immobilized selected
molecules (e.g., ligands, receptors and effector molecules).
Alternatively, the term "aptamer" includes nucleotides capable of
shape-specific recognition of chemically bland surfaces by a
mechanism distinctly different from specific binding. Aptamers of
the instant invention may be selected to specifically recognize a
structural shape or surface feature comprising a chemically bland
surface (e.g., a silicon chip or carbon nanostructure) rather than
the chemical identity of a selected target molecule (e.g., a ligand
or receptor). An aptamer may be a molecule unto itself or a
sequence segment comprising a nucleotide molecule or group of
molecules, e.g., a defined sequence segment or aptameric sequence
comprising a synthetic heteropolymer, multivalent heteropolymeric
hybrid structure or aptameric multimolecular device.
[0213] IV. Method of Making the Compositions of the Invention
[0214] As will be appreciated by those in the art, the compositions
can be made using a variety of techniques known in the art. See for
example the disclosures of U.S. Pat. Nos. 6,013,459, 6,248,229,
7,018,523, 7,267,939, U.S. patent application Ser. No. 09/096,593
and Ser. No. 60/980,733, and U.S. Provisional Application titled
"Electrochemical Assay for the Detection of Enzymes" which is filed
concurrently with the present application, particularly for
teachings associated with synthesis.
[0215] In one embodiment, the compositions of the invention are
made as depicted in FIG. 3. In this embodiment, the electrodes
comprising a species including a functional group for the
attachment of the capture ligand is used, and after the composition
is made, a capture ligand with a complementary functional group is
added, resulting in essentially spontaneous addition of the capture
ligand to the surface. As will be appreciated by those in the art,
there are a wide variety of functional groups/complementary
functional groups that can be used. Suitable functional groups
include, but are not limited to, maleimide, imidoesters,
N-hydroxysuccinimidyls, alkyl halides, aryl halides,
alpha-haloacyls and pryidyl disulfides. In general, the
corresponding/complementary functional groups sulfhydryls, amines,
amines, sulfhydryls, sulfhydryls, sulfhydryls and sulfhydryls,
respectively. As will be appreciated by those in the art, it is
also possible to switch the orientation of these functional groups,
e.g. the sulfhydryl is present on the attachment linker and the
maleimide is added to the biomolecule to be used as the capture
ligand.
[0216] As noted herein, the methods of attaching are dependent upon
the reactive groups present on the two components. In an exemplary
embodiment, the reactive functional group of the haptens of the
invention and the functional group of the reactive part comprise
electrophiles and nucleophiles that can generate a covalent linkage
between them. Alternatively, the reactive functional group
comprises a photoactivatable group, which becomes chemically
reactive only after illumination with light of an appropriate
wavelength. Typically, the conjugation reaction between the
reactive functional group and the reactive partner results in one
or more atoms of the reactive functional group or the reactive
partner being incorporated into a new linkage attaching the two
components. Selected examples of functional groups and linkages are
shown in Table 1, where the reaction of an electrophilic group and
a nucleophilic group yields a covalent linkage.
TABLE-US-00001 TABLE 1 Examples of some routes to useful covalent
linkages with electrophile and nucleophile reactive groups
Electrophilic Group Nucleophilic Group Resulting Covalent Linkage
activated esters* amines/anilines carboxamides acyl azides**
amines/anilines carboxamides acyl halides amines/anilines
carboxamides acyl halides alcohols/phenols esters acyl nitriles
alcohols/phenols esters acyl nitriles amines/anilines carboxamides
aldehydes amines/anilines imines aldehydes or ketones hydrazines
hydrazones aldehydes or ketones hydroxylamines oximes alkyl halides
amines/anilines alkyl amines alkyl halides carboxylic acids esters
alkyl halides thiols thioethers alkyl halides alcohols/phenols
ethers alkyl sulfonates thiols thioethers alkyl sulfonates
carboxylic acids esters alkyl sulfonates alcohols/phenols ethers
anhydrides alcohols/phenols esters anhydrides amines/anilines
carboxamides aryl halides thiols thiophenols aryl halides amines
aryl amines aziridines thiols thioethers boronates glycols boronate
esters carboxylic acids amines/anilines carboxamides carboxylic
acids alcohols esters carboxylic acids hydrazines hydrazides
carbodiimides carboxylic acids N-acylureas or anhydrides
diazoalkanes carboxylic acids esters epoxides thiols thioethers
haloacetamides thiols thioethers halotriazines amines/anilines
aminotriazines halotriazines alcohols/phenols triazinyl ethers
imido esters amines/anilines amidines isocyanates amines/anilines
ureas isocyanates alcohols/phenols urethanes isothiocyanates
amines/anilines thioureas maleimides thiols thioethers
phosphoramidites alcohols phosphite esters silyl halides alcohols
silyl ethers sulfonate esters amines/anilines alkyl amines
sulfonate esters thiols thioethers sulfonate esters carboxylic
acids esters sulfonate esters alcohols ethers sulfonyl halides
amines/anilines sulfonamides sulfonyl halides phenols/alcohols
sulfonate esters *Activated esters, as understood in the art,
generally have the formula --CO.OMEGA., where .OMEGA. is a good
leaving group (e.g. oxysuccinimidyl (--OC.sub.4H.sub.4O.sub.2)
oxysulfosuccinimidyl (--OC.sub.4H.sub.3O.sub.2--SO.sub.3H),
-1-oxybenzotriazolyl (--OC.sub.6H.sub.4N.sub.3); or an aryloxy
group or aryloxy substituted one or more times by electron
withdrawing substituents such as nitro, fluoro, chloro, cyano, or
trifluoromethyl, or combinations thereof, used to form activated
aryl esters; or a carboxylic acid activated by a carbodiimide to
form an anhydride or mixed anhydride --OCOR.sup.a or
--OCNR.sup.aNHR.sup.b, where R.sup.a and R.sup.b, which may be the
same or different, are C.sub.1-C.sub.6 alkyl, C.sub.1-C.sub.6
perfluoroalkyl, or C.sub.1-C.sub.6 alkoxy; or cyclohexyl,
3-dimethylaminopropyl, or N-morpholinoethyl). **Acyl azides can
also rearrange to isocyanates.
[0217] The functional groups and complementary functional groups
can also include linkers, for flexibility or steric rigidity as the
case may be, or other reasons.
[0218] It should be noted that while the figures depict the
presence of a functional group and the complementary functional
group, in some cases the addition results in the loss of atoms from
these groups, and thus this is not meant to depict a situation when
the entire functional group and complementary functional group is
present in the final composition.
[0219] In addition, the figures depict the use of "monofunctional"
linkers, e.g. a maleimide. It is also possible to include
additional steps that utilize either homo- or heterobifunctional
groups, (see 1994 Pierce Chemical Company catalog, technical
section on cross linkers, pages 155-200, incorporated herein by
reference). For example, an attachment linker comprising a sulfur
atom on one terminus and an amino group on the other end could be
reacted with a bifunctional linker that reacts with amines, and
then subsequently a capture ligand comprising an amino group can be
added.
[0220] In another embodiment, the compositions of the invention are
made by synthesizing each component and adding them to the
electrode, generally simultaneously. That is, in the embodiment of
FIG. 12A, for example, the REAMC comprising the attachment linker
(with the attachment functional moiety such as a sulfur atom), the
ligands, the transition metal and the binding ligand is made, and
added (optionally with a SAM forming species) to the electrode.
Similarly, a two or three component system is done in FIG. 1B, with
a first species comprising the EAM with the attachment linker and
attachment functional group, a second species comprising an
attachment linker with the capture ligand, and the optional third
species of a SAM forming species, which are added, against
generally simultaneously, to the electrode. In some cases, the
components can be added sequentially, and in some cases, a post
synthesis step done of adding extra SAM forming species (and/or
other components) with optional heating can be done to ensure good
packing on the electrode.
[0221] In some embodiments, the ligands can have functionalities
that allow the anchor and capture ligand to be added to it after
the metal complex is formed.
[0222] In some embodiments, the compound is synthesized stepwise.
Thus, the capture ligand and the anchor are added to the ligand of
the EAM sequentially.
[0223] In some embodiments, the capture ligand and the anchor are
added to the EAM concomitantly.
[0224] In some embodiments, "clip" are added to the EAM first and
the capture ligand and anchor groups are added to the "clips"
later. By "clips" herein is meant a group or moiety that can be
attached to an EAM covalently, and on to which the capture ligand
and/or the anchor group could be added.
[0225] One of the clips is shown below:
##STR00022##
wherein PG=protection group.
[0226] In some embodiments, wherein pentaammine is used as
coordinating ligands, the capture ligand can be added first, and
the anchor group is added to the capture ligand.
[0227] The compositions of the present invention may be used in a
variety of research, clinical, quality control, or field testing
settings.
[0228] The examples provided herein are for illustration purposes
only and are in no means to limit the scope the present invention.
Further, all references cited herein are incorporated by reference
for all the relevant contents therein.
[0229] V. Method of Using the Composition of the Invention
A. Target Analyte and Sample
[0230] In one aspect, the present invention provides methods and
compositions useful in the detection of target analytes. By "target
analyte" or "analyte" or grammatical equivalents herein is meant
any molecule or compound to be detected and that can bind to a
binding species, e.g. a capture ligand, defined below. Suitable
analytes include, but not limited to, small chemical molecules such
as environmental or clinical chemical or pollutant or biomolecule,
including, but not limited to, pesticides, insecticides, toxins,
therapeutic and abused drugs, hormones, antibiotics, antibodies,
organic materials, etc. Suitable biomolecules include, but are not
limited to, proteins (including enzymes, immunoglobulins and
glycoproteins), nucleic acids, lipids, lectins, carbohydrates,
hormones, whole cells (including prokaryotic (such as pathogenic
bacteria) and eucaryotic cells, including mammalian tumor cells),
viruses, spores, etc. Particularly preferred analytes are proteins
including enzymes; drugs, cells; antibodies; antigens; cellular
membrane antigens and receptors (neural, hormonal, nutrient, and
cell surface receptors) or their ligands.
[0231] In some embodiments, the target analyte is cytochrome P450,
avidin/streptavdin, SEB, PSA (protease), tryprin/chymotrypin
(protease), anthrax spore and E. coli. O157:H7.
[0232] In some embodiments, the target analyte is a protein. As
will be appreciated by those in the art, there are a large number
of possible proteinaceous target analytes that may be detected
using the present invention. By "proteins" or grammatical
equivalents herein is meant proteins, oligopeptides and peptides,
derivatives and analogs, including proteins containing
non-naturally occurring amino acids and amino acid analogs, and
peptidomimetic structures. The side chains may be in either the (R)
or the (S) configuration. In a preferred embodiment, the amino
acids are in the (S) or L-configuration. As discussed below, when
the protein is used as a capture ligand, it may be desirable to
utilize protein analogs to retard degradation by sample
contaminants.
[0233] Suitable protein target analytes include, but are not
limited to, (1) immunoglobulins, particularly IgEs, IgGs and IgMs,
and particularly therapeutically or diagnostically relevant
antibodies, including but not limited to, for example, antibodies
to human albumin, apolipoproteins (including apolipoprotein E),
human chorionic gonadotropin, cortisol, a-fetoprotein, thyroxin,
thyroid stimulating hormone (TSH), antithrombin, antibodies to
pharmaceuticals (including antieptileptic drugs (phenyloin,
primidone, carbariezepin, ethosuximide, valproic acid, and
phenobarbital), cardioactive drugs (digoxin, lidocaine,
procainamide, and disopyramide), bronchodilators (theophylline),
antibiotics (chloramphenicol, sulfonamides), antidepressants,
immunosuppresants, abused drugs (amphetamine, methamphetamine,
cannabinoids, cocaine and opiates) and antibodies to any number of
viruses (including orthomyxoviruses, (e.g. influenza virus),
paramyxoviruses (e.g respiratory syncytial virus, mumps virus,
measles virus), adenoviruses, rhinoviruses, coronaviruses,
reoviruses, togaviruses (e.g. rubella virus), parvoviruses,
poxviruses (e.g. variola virus, vaccinia virus), enteroviruses
(e.g. poliovirus, coxsackievirus), hepatitis viruses (including A,
Band C), herpesviruses (e.g. Herpes simplex virus, varicella-zoster
virus, cytomegalovirus, Epstein-Ban virus), rotaviruses, Norwalk
viruses, hantavirus, arenavirus, rhabdovirus (e.g. rabies virus),
retroviruses (including HIV, HTLV-I and -II), papovaviruses (e.g.
papillomavirus), polyomaviruses, and picornaviruses, and the like),
and bacteria (including a wide variety of pathogenic and
non-pathogenic prokaryotes of interest including Bacillus; Vibrio,
e.g. V. cholerae; Escherichia, e.g. Enterotoxigenic E. coli,
Shigella, e.g. S. dysenteriae; Salmonella, e.g. S. typhi;
Mycobacterium e.g. M. tuberculosis, M. leprae; Clostridium, e.g. C.
botulinum, C. tetani, C. difficile, C. perfringens;
Cornyebacterium, e.g. C. diphtheriae; Streptococcus, S. pyogenes,
S. pneumoniae; Staphylococcus, e.g. S. aureus; Haemophilus, e.g. H.
influenzae; Neisseria, e.g. N. meningitidis, N. gonorrhoeae;
Yersinia, e.g. G. lamblia Y. pestis, Pseudomonas, e.g. P.
aeruginosa, P. putida; Chlamydia, e.g. C. trachomatis; Bordetella,
e.g. B. pertussis; Treponema, e.g. T. palladium; and the like); (2)
enzymes (and other proteins), including but not limited to, enzymes
used as indicators of or treatment for heart disease, including
creatine kinase, lactate dehydrogenase, aspartate amino
transferase, troponin T, myoglobin, fibrinogen, cholesterol,
triglycerides, thrombin, tissue plasminogen activator (tPA);
pancreatic disease indicators including amylase, lipase,
chymotrypsin and trypsin; liver function enzymes and proteins
including cholinesterase, bilirubin, and alkaline phosphatase;
aldolase, prostatic acid phosphatase, terminal deoxynucleotidyl
transferase, and bacterial and viral enzymes such as HIV protease;
(3) hormones and cytokines (many of which serve as ligands for
cellular receptors) such as erythropoietin (EPO), thrombopoietin
(TPO), the interleukins (including IL-1 through IL-17), insulin,
insulin-like growth factors (including IGF-1 and -2), epidermal
growth factor (EGF), transforming growth factors (including
TGF-.alpha. and TGF(3), human growth hormone, transferrin,
epidermal growth factor (EGF), low density lipoprotein, high
density lipoprotein, leptin, VEGF, PDGF, ciliary neurotrophic
factor, prolactin, adrenocorticotropic hormone (ACTH), calcitonin,
human chorionic gonadotropin, cotrisol, estradiol, follicle
stimulating hormone (FSH), thyroid-stimulating hormone (TSH),
leutinzing hormone (LH), progeterone, testosterone,and (4) other
proteins (including .alpha.-fetoprotein, carcinoembryonic antigen
CEA.
[0234] In addition, any of the biomolecules for which antibodies
may be detected may be detected directly as well; that is,
detection of virus or bacterial cells, therapeutic and abused
drugs, etc., may be done directly.
[0235] Suitable target analytes include carbohydrates, including
but not limited to, markers for breast cancer (CA15-3, CA 549, CA
27.29), mucin-like carcinoma associated antigen (MCA), ovarian
cancer (CA 125), pancreatic cancer (DE-PAN-2), and colorectal and
pancreatic cancer (CA 19, CA 50, CA242).
[0236] As will be appreciated by those in the art, a large number
of analytes may be detected using the present methods; basically,
any target analyte for which a binding ligand, described below, may
be made may be detected using the methods of the invention.
[0237] In some embodiments, the target analyte is a protein related
to MRSA. Methicillin-resistant Staphylococcus aureus (MRSA) (also
be referred to as multiple-resistant Staphylococcus aureus or
oxacillin-resistant Staphylococcus aureus (ORSA)) is responsible
for difficult-to-treat infections in humans. MRSA is a strain of
Staphylococcus aureus that is resistant to a large group of
antibiotics called the betalactams, which include the penicillins
and the cephalosporins.
[0238] The organism is often sub-categorized as
Community-Associated MRSA (CA-MRSA) or Health Care-Associated MRSA
(HA-MRSA) although this distinction is complex. Some have defined
CA-MRSA by criteria related to patients suffering from an MRSA
infection while other authors have defined CAMRSA by genetic
characteristics of the bacteria themselves. CA-MRSA strains were
first reported in the late 1990s; these cases were defined by a
lack of exposure to the health care setting. In the next several
years, it became clear that CA-MRSA infections were caused by
strains of MRSA that differed from the older and better studied
healthcare-associated strains. The new CA-MRSA strains have rapidly
spread in the United States to become the most common cause of
cultured skin infections among individuals seeking medical care for
these infections at emergency rooms in cities. These strains also
commonly cause skin infections in athletes, jail and prison
detainees, soldiers, Native Alaskans and Native Americans, and
children in the inner city.
[0239] MRSA is a resistant variation of the common bacterium
Staphylococcus aureus. It has evolved an ability to survive
treatment with beta-lactamase resistant beta-lactam antibiotics,
including methicillin, dicloxacillin, nafcillin, and oxacillin.
MRSA is especially troublesome in hospital-associated (nosocomial)
infections. In hospitals, patients with open wounds, invasive
devices, and weakened immune systems are at greater risk for
infection than the general public. Hospital staff who do not follow
proper sanitary procedures may transfer bacteria from patient to
patient. Visitors to patients with MRSA infections or MRSA
colonization are advised to follow hospital isolation protocol by
using the provided gloves, gowns, and masks if indicated. Visitors
who do not follow such protocols are capable of spreading the
bacteria to cafeterias, bathrooms, and elevators.
[0240] In some embodiment, the MRSA related protein is penicillin
binding protein 2a (PBP2a). PBP2' is a protein coded by the mecA
gene and is present in the membranes of methicillin resistant
Staphylococcus aureus and coagulase-negative staphylococci. The
preparation of PBP2' can be carried out using methods known in the
art, such as the protocol described in the MRSA Latex Test for
PBP2' kit distributed by Hardy Diagnostics (Santa Maria,
Calif.).
[0241] In some embodiments, the target is the PBP2a protein of
MRSA, and the capture ligand is a moiety that is capable of binding
to PBP2a.
[0242] By "nucleic acid" or "oligonucleotide" or grammatical
equivalents herein is meant at least two nucleotides covalently
linked together. A nucleic acid of the present invention will
generally contain phosphodiester bonds, although in some cases, as
outlined below, nucleic acid analogs are included that may have
alternate backbones, comprising, for example, phosphoramide
(Beaucage et al., Tetrahedron 49(10): 1925 (1993) and references
therein; Letsinger, J. Org. Chem. 35:3800 (1970); Sprinzl et al.,
Eur. J. Biochem. 81:579 (1977); Letsinger et al., Nucl. Acids Res.
14:3487 (1986); Sawai et al, Chem. Lett. 805 (1984), Letsinger et
al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al., Chemica
Scripta 26:141 91986)), phosphorothioate (Mag et al., Nucleic Acids
Res. 19:1437 (1991); and U.S. Pat. No. 5,644,048),
phosphorodithioate (Briu et al., J. Am. Chem. Soc. 111:2321 (1989),
0-methylphosphoroamidite linkages (see Eckstein, Oligonucleotides
and Analogues: A Practical Approach, Oxford University Press), and
peptide nucleic acid backbones and linkages (see Egholm, J. Am.
Chem. Soc. 114:1895 (1992); Meier et al., Chem. Int. Ed. Engl.
31:1008 (1992); Nielsen, Nature, 365:566 (1993); Carlsson et al.,
Nature 380:207 (1996), all of which are incorporated by reference).
Other analog nucleic acids include those with positive backbones
(Denpcy et al., Proc. Natl. Acad. Sci. USA 92:6097 (1995);
non-ionic backbones (U.S. Pat. Nos. 5,386,023, 5,637,684,
5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew. Chem.
Inti. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem.
Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide
13:1597 (1994); Chapters 2 and 3, ASC Symposium Series 580,
"Carbohydrate Modifications in Antisense Research", Ed. Y. S.
Sanghui and P. Dan Cook; Mesmaeker et al., Bioorganic &
Medicinal Chem. Lett. 4:395 (1994); Jeffs et al., J. Biomolecular
NMR 34:17 (1994); Tetrahedron Lett. 37:743 (1996)) and non-ribose
backbones, including those described in U.S. Pat. Nos. 5,235,033
and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580,
"Carbohydrate Modifications in Antisense Research", Ed. Y. S.
Sanghui and P. Dan Cook. Nucleic acids containing one or more
carbocyclic sugars are also included within the definition of
nucleic acids (see Jenkins et al., Chem. Soc. Rev. (1995) pp
169-176). Several nucleic acid analogs are described in Rawls, C
& E News Jun. 2, 1997 page 35. All of these references are
hereby expressly incorporated by reference. These modifications of
the ribose-phosphate backbone may be done to facilitate the
addition of ETMs, or to increase the stability and half-life of
such molecules in physiological environments.
[0243] As will be appreciated by those in the art, all of these
nucleic acid analogs may find use in the present invention. In
addition, mixtures of naturally occurring nucleic acids and analogs
can be made; for example, at the site of conductive oligomer or EAM
attachment, an analog structure may be used. Alternatively,
mixtures of different nucleic acid analogs, and mixtures of
naturally occurring nucleic acids and analogs may be made.
[0244] As will be appreciated by those in the art, all of these
nucleic acid analogs may find use in the present invention. In
addition, mixtures of naturally occurring nucleic acids and analogs
can be made; for example, at the site of conductive oligomer or EAM
attachment, an analog structure may be used. Alternatively,
mixtures of different nucleic acid analogs, and mixtures of
naturally occurring nucleic acids and analogs may be made.
[0245] The nucleic acids may be single stranded or double stranded,
as specified, or contain portions of both double stranded or single
stranded sequence. The nucleic acid may be DNA, both genomic and
cDNA, RNA or a hybrid, where the nucleic acid contains any
combination of deoxyribo- and ribonucleotides, and any combination
of bases, including uracil, adenine, thymine, cytosine, guanine,
inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc. A
preferred embodiment utilizes isocytosine and isoguanine in nucleic
acids designed to be complementary to other probes, rather than
target sequences, as this reduces non-specific hybridization, as is
generally described in U.S. Pat. No. 5,681,702. As used herein, the
term "nucleoside" includes nucleotides as well as nucleoside and
nucleotide analogs, and modified nucleosides such as amino modified
nucleosides. In addition, "nucleoside" includes normaturally
occurring analog structures. Thus for example the individual units
of a peptide nucleic acid, each containing a base, are referred to
herein as a nucleoside.
[0246] In some embodiments, nucleic acid target analytes are not
preferred.
[0247] In general, a sample is added to the compositions of the
invention. In one aspect, the present invention provides a method
of detecting a target enzyme in a sample. By "sample" or "test
sample" herein is meant a composition that contains the analyte or
analytes to be detected. The sample can be heterogeneous,
containing a variety of components, i.e. different proteins.
Alternatively, the sample can be homogenous, containing one
component. The sample can be naturally occurring, a biological
material, or man-made material. The material can be in a native or
denatured form. The sample can be a single cell or a plurality of
cells, a blood sample, a tissue sample, a skin sample, a urine
sample, a water sample, or a soil sample. In some embodiments, the
sample comprises the contents of a single cell, or the contents of
a plurality of cells. The sample can be from a living organism,
such as a eukaryote, prokaryote, mammal, human, yeast, or
bacterium, or the sample can be from a virus. The samples can be
used without any treatment, or with treatment if desired.
[0248] In some embodiments, the target analyte, contained within a
test sample, is added to the compositions of the invention, under
conditions that if present, the target analyte binds to the capture
binding ligand. These conditions are generally physiological
conditions. Generally a plurality of assay mixtures is run in
parallel with different concentrations to obtain a differential
response to the various concentrations. Typically, one of these
concentrations serves as a negative control, i.e., at zero
concentration or below the level of detection. In addition, any
variety of other reagents may be included in the screening assay.
These include reagents like salts, neutral proteins, e.g. albumin,
detergents, etc which may be used to facilitate optimal binding
and/or reduce non-specific or background interactions. Also
reagents that otherwise improve the efficiency of the assay, such
as protease inhibitors, nuclease inhibitors, anti-microbial agents,
etc., may be used. The mixture of components may be added in any
order that provides for the requisite binding.
[0249] As will be appreciated by those in the art, a large number
of analytes may be detected using the present methods; basically,
any target analyte for which a capture ligand, described below, may
be made may be detected using the methods of the invention.
[0250] In addition, those in the art will appreciate that it is
also possible to use the compositions of the invention in assays
that rely on a loss of signal. For example, a first measurement is
taken when the redox active molecule is inhibited, and then the
system is changed as a result of the introduction of a target
analyte, causing the solvent inhibited molecule to become solvent
accessible, resulting in a loss of signal. This may be done in
several ways, as will be appreciated by those in the art.
[0251] In some embodiments, a first measurement is taken when the
target analyte is present. The target analyte is then removed, for
example by the use of high salt concentrations or thermal
conditions, and then a second measurement is taken. The
quantification of the loss of the signal can serve as the basis of
the assay.
[0252] Alternatively, the target analyte may be an enzyme. In this
embodiment, the redox active molecule is made solvent inhibited by
the presence of an enzyme substrate or analog, preferably, but not
required to be covalently attached to the redox active molecule,
preferably as one or more ligands. Upon introduction of the target
enzyme, the enzyme associates with the substrate to cleave or
otherwise sterically alter the substrate such that the redox active
molecule is made solvent accessible. This change can then be
detected. This embodiment is advantageous in that it results in an
amplification of the signal, since a single enzyme molecule can
result in multiple solvent accessible molecules. This may find
particular use in the detection of bacteria or other pathogens that
secrete enzymes, particularly scavenger proteases or
carbohydrases.
[0253] In some embodiments, the target analyte is a protease.
Proteases are classified into six groups: serine proteases,
threonine proteases, cysteine proteases, aspartic acid proteases,
metalloproteases, and glutamic acid proteases. In general, protease
can either break specific peptide bonds (e.g. specific segments for
limited proteolysis), depending on the amino acid sequence of a
protein, or break down a complete protein to amino acids (unlimited
proteolysis). The activity can be a destructive change, abolishing
a protein's function or digesting it to its principal components;
it can be an activation of a function, or it can be a signal in a
signaling pathway.
[0254] In some embodiments, the target enzyme is an endopeptidase.
By "endopeptidase" herein is meant peptidases that break peptide
bonds within a protein substrate, in contrast to exopeptidases,
which break peptide bonds from one or both termini of the protein
substrate. Endopeptidases are divided into subclasses on the basis
of catalytic mechanism: the serine endopeptidases, cysteine
endopeptidases, aspartic endopeptidases, metalloendopeptidases, and
other endopeptidases.
[0255] (1). Serine Endopeptidases
[0256] This class comprises two distinct families. The chymotrypsin
family which includes the mammalian enzymes such as chymotrypsin,
trypsin or elastase or kallikrein and the substilisin family which
include the bacterial enzymes such as subtilisin. The general three
dimensional (3D) structure is different in the two families but
they have the same active site geometry and the catalysis proceeds
via the same mechanism. The serine endopeptidases exhibit different
substrate specificities which are related to amino acid
substitutions in the various enzyme subsites interacting with the
substrate residues. Some enzymes have an extended interaction site
with the substrate whereas others have a specificity restricted to
the P1 substrate residue.
[0257] (2). Cysteine Endopeptidases
[0258] This family includes the plant proteases such as papain,
actinidin or bromelain, several mammalian cathepsins, including
lysosomal cathepsins and cathepsin B, L, S, H, J, N and O; the
cytosolic calpains (calcium-activated) as well as several parasitic
proteases (e.g., Trypanosoma, Schistosoma) and caspases, including
interleukin converting enzyme (ICE).
[0259] (3). Aspartic Endopeptidases
[0260] Most of aspartic endopeptidases belong to the pepsin family.
The pepsin family includes digestive enzymes such as pepsin and
chymosin as well as lysosomal cathepsins D and processing enzymes
such as renin, and certain fungal proteases (penicillopepsin,
rhizopuspepsin, endothiapepsin). A second family comprises viral
endopeptidases such as the protease from the AIDS virus (HIV) also
called retropepsin.
[0261] In contrast to serine and cysteine proteases, catalysis by
aspartic endopeptidases do not involve a covalent intermediate
though a tetrahedral intermediate exists. The nucleophilic attack
is achieved by two simultaneous proton transfer: one from a water
molecule to the diad of the two carboxyl groups and a second one
from the diad to the carbonyl oxygen of the substrate with the
concurrent CO--NH bond cleavage.
[0262] (4). Metallo Endopeptidases
[0263] The metallo endopeptidases are found in bacteria, fungi as
well as in higher organisms. They differ widely in their sequences
and their structures but the great majority of enzymes contain a
zinc atom which is catalytically active. In some cases, zinc may be
replaced by another metal such as cobalt or nickel without loss of
the activity. Bacterial thermolysin has been well characterized and
its crystallographic structure indicates that zinc is bound by two
histidines and one glutamic acid. Many enzymes contain the sequence
HEXXH, which provides two histidine ligands for the zinc whereas
the third ligand is either a glutamic acid (thermolysin,
neprilysin, alanyl aminopeptidase) or a histidine (astacin). Other
families exhibit a distinct mode of binding of the Zn atom. The
catalytic mechanism leads to the formation of a non covalent
tetrahedral intermediate after the attack of a zinc-bound water
molecule on the carbonyl group of the scissile bond. This
intermediate is further decomposed by transfer of the glutamic acid
proton to the leaving group.
[0264] Of particular interest are metalloenzymes including
adenosine deaminase, angiotensin converting enzyme, calcineurin,
metallo-beta-lactamase, PDE3, PDE4, PDE5, renal dipeptidase, and
urease.
[0265] In one embodiment, the metallo endopeptidase is a matrix
metalloproteinase, including MMP-1 through MMP-1 0, particularly
MMP-1, MMP-2, MMP-7 and MMP-9.
[0266] (5). Bacterial/Toxin Endopeptidases
[0267] Toxin endopeptidases, usually of bacterial origin, can have
a devastating and sometime lethal impact on host organisms. Some of
the better known bacterial endopeptidase toxins are listed below in
Table 1.
TABLE-US-00002 TABLE 1 Bacterial Endopeptidases Organism/Toxin Mode
of Action Target (Cleavage Site) Disease B. anthracis/lethal
Metalloprotease MAPKK1/MAPKK2 Anthrax factor (multiple) C.
botulinum/neurotxin Zinc- SNAP-25 (ANQ/RAT) Botulism A
Metalloprotease C. botulinum/neurotxin Zinc- VAMP/synaptobrevin
Botulism B Metalloprotease (ASQ/FET) C. botulinum/neurotxin Zinc-
Syntaxin (TKK/AVK) Botulism C Metalloprotease C.
botulinum/neurotxin Zinc- VAMP/synaptobrevin Botulism D
Metalloprotease (DQK/LSE) C. botulinum/neurotxin Zinc- SNAP-25
(IDR/IME) Botulism E Metalloprotease C. botulinum/neurotxin Zinc-
VAMP/synaptobrevin Botulism F Metalloprotease C.
botulinum/neurotxin Zinc- VAMP/synaptobrevin Botulism G
Metalloprotease (TSA/AKL) Yersinia virulence Cysteine Unknown
factor YopJ protease Yersinia virulence Cysteine Prenylated
cysteine factor YopT protease Salmonella virulence Unknown Unknown
Salmonellosis factor AvrA Clostridium tetani/ Zinc-
VAMP/synaptobrevin Tetanus tetanus toxin metalloprotease
(ASQ/FET)
[0268] The C. botulinum neurotoxins (BoNTs, serotypes A-G) and the
C. tetani tetanus neurotoxin (TeNT) are two examples of bacterial
toxins that are endopeptidases. BoNTs are most commonly associated
with infant and food-borne botulism and exist in nature as large
complexes comprised of the neurotoxin and one or more associated
proteins believed to provide protection and stability to the toxin
molecule while in the gut. TeNT, which is synthesized from
vegetative C. tetani in wounds, does not appear to form complexes
with any other protein components.
[0269] BoNTs are highly specific, zinc-dependent endoproteases that
specifically cleave small proteins which control the docking of
synaptic vesicles with the neural synaptic membrane. BoNT A and
BoNT E specifically cleave the 25-kD synaptosomal-associated
protein (SNAP-25) with BoNT A cleaves between residues Q197 and R
198. SNAP-25 is a presynaptic plasma membrane protein involved in
the regulation of neurotransmitter release. Two alternative
transcript variants encoding different protein isoforms have been
described for this gene in human, SNAP25A (GenBank Accession No.
NP.sub.--003072) and SNAP25B (GenBank Accession No. NP 570824).
BoNT C cleaves the membrane protein syntaxin and SNAP-25. BoNT B,
D, F and G are specific for the intracellular vesicle-associated
membrane-associated protein (VAMP, also termed synaptobrevin). See
Schiavo et al., JBC 266:23784-87 (1995); Schiavo et al., FEBS
Letters 335:99-103 (1993), herein are incorporated by reference in
their entireties.
[0270] Several in vitro assays have been developed based on the
cleavage of immobilized synthetic peptide substrates. Halls et al.,
J Clin Microbial 34:1934-8 (1996); Witcome et al., Appl Environ
Microbial 65:3787-92 (1999), and Anne et al., Ana Biochem
291:253-61 (2001).
[0271] The BeNTs and TeNT are either plasmid encoded (TeNT,
BeNTs/A, G, and possibly B) or bacteriophage encoded (BoNTs/C, D,
E, F), and the neurotoxins are synthesized as inactive polypeptides
of 150 kDa. BeNTs and TeNT are released from lysed bacterial cells
and then activated by the proteolytic cleavage of an exposed loop
in the neurotoxin polypeptide. Each active neurotoxin molecule
consists of a heavy (100 kDa) and light chain (50 kDa) linked by a
single interchain disulphide bond. The heavy chains of both the
BeNTs and TeNT contain two domains: a region necessary for toxin
translocation located in the N-terminal half of the molecule, and a
cell-binding domain located within the C-terminus of the heavy
chain. The light chains of both the BeNTs and TeNT contain
zinc-binding motifs required for the zinc-dependent protease
activities of the molecules.
[0272] The cellular targets of the BeNTs and TeNT are a group of
proteins required for docking and fusion of synaptic vesicles to
presynaptic plasma membranes and therefore essential for the
release of neurotransmitters. The BeNTs bind to receptors on the
presynaptic membrane of motor neurons associated with the
peripheral nervous system. Proteolysis of target proteins in these
neurons inhibits the release of acetylcholine, thereby preventing
muscle contraction. BoNTs/B, D, F, and G cleave the
vesicleassociated membrane protein and synaptobrevin, BoNT/A and E
target the synaptosomal-associated protein SNAP-25, and BoNT/C
hydrolyzes syntaxin and SNAP-25. TeNT affects the central nervous
system and does so by entering two types of neurons. TeNT initially
binds to receptors on the presynaptic membrane of motor neurons but
then migrates by retrograde vesicular transport to the spinal cord,
where the neurotoxin can enter inhibitory interneurons. Cleavage of
the vesicle-associated membrane protein and synaptobrevin in these
neurons disrupts the release of glycine and gamma-aminobutyric
acid, which, in turn, induces muscle contraction. The contrasting
clinical manifestations of BoNT or TeNT intoxication (flaccid and
spastic paralysis, respectively) are the direct result of the
specific neurons affected and the type of neurotransmitters
blocked.
[0273] Of particular interest is BoNT/LC (serotype C), and
specifically BoNTC/LC (as compared to other LC serotypes). First,
BoNTC/LC poses a particularly significant bioterror threat because
it has a long half-life inside human neuronal cells. Second, an in
vitro assay for BoNTC/LC does not currently exist, probably because
this LC protease appears to require membranes to function. In the
neuronal cell environment, BoNTC/LC cleaves syntaxin, a membrane
protein required for synaptic vesicle fusion to the presynaptic
membrane.
[0274] Other examples include the Yersinia virulence factors YopJ
and YopT, as well as Salmonella AvrA.
[0275] Other target analytes include, but are not limited to:
coagulation factor levels (hemorrhagic or thrombotic conditions),
fecal elastase (exocrine activity of the pancreas, e.g. in cystic
fibrosis or chronic pancreatitis), PSA, VEGF and EGFR (tumor
response in rectal cancer), MMP-9 (tumor marker of esophageal
cancer and early stroke marker), MMP-13 (early stroke marker),
cathepsin B (cancer), cathepsin G (emphysema, rheumatoid arthritis,
inflammation), plasminogen activator (thrombosis, chronic
inflammation, cancer), urokinase (cancer).
[0276] In some embodiments the target analyte is troponin (cardiac
troponin I and T). Troponin is a complex of three regulatory
proteins that is integral to muscle contraction in skeletal and
cardiac muscle, but not smooth muscle. Troponin is found in both
skeletal muscle and cardiac muscle, but the specific versions of
troponin differ between types of muscle. Two subtypes of troponin
(cardiac troponin I and T) are very sensitive and specific
indicators of damage to the heart muscle (myocardium). They are
measured in the blood to differentiate between unstable angina and
myocardial infarction (heart attack) in patients with chest pain. A
patient who had suffered from a myocardial infarction would have an
area of damaged heart muscle and so would have elevated cardiac
troponin levels in the blood.
[0277] Similarly, another embodiment utilizes competition-type
assays. In this embodiment, the binding ligand is the same as the
actual molecule for which detection is desired; that is, the
binding ligand is actually the target analyte or an analog. A
binding partner of the binding ligand is added to the surface, such
that the redox active molecule becomes solvent inhibited, electron
transfer occurs and a signal is generated. Then the actual test
sample, containing the same or similar target analyte which is
bound to the electrode, is added. The test sample analyte will
compete for the binding partner, causing the loss of the binding
partner on the surface and a resulting decrease in the signal.
[0278] A similar embodiment utilizes a target analyte (or analog)
is covalently attached to a preferably larger moiety (a "blocking
moiety"). The analyte-blocking moiety complex is bound to a binding
ligand that binds the target analyte, serving to render the redox
active molecule solvent inhibited. The introduction of the test
sample target analyte serves to compete for the analyte-blocking
moiety complex, releasing the larger complex and resulting in a
more solvent accessible molecule.
[0279] The present invention further provides apparatus for the
detection of analytes using AC detection methods. The apparatus
includes a test chamber which has at least a first measuring or
sample electrode, and a second measuring or counter electrode.
Three electrode systems are also useful. The first and second
measuring electrodes are in contact with a test sample receiving
region, such that in the presence of a liquid test sample, the two
electrodes may be in electrical contact.
[0280] In yet another embodiment, the first measuring electrode
comprises a redox active complex, covalently attached via a spacer,
and preferably via a conductive oligomer, such as are described
herein. Alternatively, the first measuring electrode comprises
covalently attached redox active molecules and binding ligands.
[0281] The apparatus further comprises a voltage source
electrically connected to the test chamber; that is, to the
measuring electrodes. Preferably, the voltage source is capable of
delivering AC and DC voltages, if needed.
[0282] In a embodiment, the apparatus further comprises a processor
capable of comparing the input signal and the output signal. The
processor is coupled to the electrodes and configured to receive an
output signal, and thus detect the presence of the target
analyte.
B. Initiation
[0283] In one aspect, the present invention provides methods of
detecting target analyte.
[0284] The target analyte, contained within a test sample, is added
to the electrode containing either a solvent accessible redox
active complex or a mixture of solvent accessible redox active
molecules and capture ligands, under conditions that if present,
the target analyte will bind to the capture ligand. These
conditions are generally physiological conditions. Generally a
plurality of assay mixtures is run in parallel with different
concentrations to obtain a differential response to the various
concentrations. Typically, one of these concentrations serves as a
negative control, i.e., at zero concentration or below the level of
detection. In addition, any variety of other reagents may be
included in the screening assay. These include reagents like salts,
neutral proteins, e.g. albumin, detergents, etc which may be used
to facilitate optimal binding and/or reduce non-specific or
background interactions. Also reagents that otherwise improve the
efficiency of the assay, such as protease inhibitors, nuclease
inhibitors, anti-microbial agents, etc., may be used. The mixture
of components may be added in any order that provides for the
requisite binding.
[0285] In some embodiments, the target analyte will bind the
capture ligand reversibly, i.e. non-covalently, such as in
protein-protein interactions of antigens-antibodies,
enzyme-substrate (or some inhibitors) or receptor-ligand
interactions.
[0286] In a preferred embodiment, the target analyte will bind the
binding ligand irreversibly, for example covalently. For example,
some enzyme-inhibitor interactions are considered irreversible.
Alternatively, the analyte initially binds reversibly, with
subsequent manipulation of the system which results in covalent
attachment. For example, chemical cross-linking after binding may
be done, as will be appreciated by those in the art. For example,
peptides may be cross-linked using a variety of bifunctional
agents, such as maleimidobenzoic acid, methyldithioacetic acid,
mercaptobenzoic acid, S-pyridyl dithiopropionate, etc.
Alternatively, functionally reactive groups on the target analyte
and the binding ligand may be induced to form covalent
attachments.
[0287] Upon binding of the analyte to the binding moiety, the
solvent accessible redox active molecule becomes solvent inhibited.
By "solvent inhibited redox active molecule" herein is meant the
solvent reorganization energy of the solvent inhibited redox active
molecule is less than the solvent reorganization energy of the
solvent accessible redox active molecule. As noted above, this may
occur in several ways. In some embodiments, the target analyte
provides a coordination atom, such that the solvent accessible
redox active molecule loses at least one, and preferably several,
of its small polar ligands. Alternatively, in some embodiments, the
proximity of the target analyte to the redox active molecule does
not result in ligand exchange, but rather excludes solvent from the
area surrounding the metal ion (i.e. the first or second
coordination sphere) thus effectively lowering the required solvent
reorganization energy.
[0288] In some embodiments, the required solvent reorganization
energy decreases sufficiently to result in a decrease in the E0 of
the redox active molecule by at about 100 mV, with at least about
200 mV being preferred, and at least about 300-500 mV being
particularly preferred.
[0289] In some embodiments, the required solvent reorganization
energy decreases by at least 100 mV, with at least about 200 mV
being preferred, and at least about 300-500 mV being particularly
preferred.
[0290] In some embodiments, the required solvent reorganization
energy decreases sufficiently to result in a rate change of
electron transfer (kET) between the solvent inhibited redox active
molecule and the electrode relative to the rate of electron
transfer between the solvent accessible redox active molecule and
the electrode. In a embodiment, this rate change is greater than
about a factor of 3, with at least about a factor of 10 being
preferred and at least about a factor of 100 or more being
particularly preferred.
[0291] The determination of solvent reorganization energy will be
done as is appreciated by those in the art. Briefly, as outlined in
Marcus theory, the electron transfer rates (kET) are determined at
a number of different driving forces (or free energy,
-.DELTA.G.degree.); the point at which the rate equals the free
energy is the .lamda.. This may be treated in most cases as the
equivalent of the solvent reorganization energy; see Gray et al.
Ann. Rev. Biochem. 65:537 (1996), hereby incorporated by
reference.
[0292] The solvent inhibited redox active molecule, indicating the
presence of a target analyte, is detected by initiating electron
transfer and detecting a signal characteristic of electron transfer
between the solvent inhibited redox active molecule and the
electrode.
[0293] Electron transfer is generally initiated electronically,
with voltage being preferred. A potential is applied to a sample
containing modified nucleic acid probes. Precise control and
variations in the applied potential can be via a potentiostat and
either a three electrode system (one reference, one sample and one
counter electrode) or a two electrode system (one sample and one
counter electrode). This allows matching of applied potential to
peak electron transfer potential of the system which depends in
part on the choice of redox active molecules and in part on the
conductive oligomer used.
[0294] Preferably, initiation and detection is chosen to maximize
the relative difference between the solvent reorganization energies
of the solvent accessible and solvent inhibited redox active
molecules.
C. Detection
[0295] Electron transfer between the redox active molecule and the
electrode can be detected in a variety of ways, with electronic
detection, including, but not limited to, amperommetry,
voltammetry, capacitance and impedance being preferred. These
methods include time or frequency dependent methods based on AC or
DC currents, pulsed methods, lock-in techniques, and filtering
(high pass, low pass, band pass). In some embodiments, all that is
required is electron transfer detection; in others, the rate of
electron transfer may be determined.
[0296] In some embodiments, electronic detection is used, including
amperommetry, voltammetry, capacitance, and impedance. Suitable
techniques include, but are not limited to, electrogravimetry;
coulometry (including controlled potential coulometry and constant
current coulometry); voltametry (cyclic voltametry, pulse
voltametry (normal pulse voltametry, square wave voltametry,
differential pulse voltametry, Osteryoung square wave voltametry,
and coulostatic pulse techniques); stripping analysis (aniodic
stripping analysis, cathiodic stripping analysis, square wave
stripping voltammetry); conductance measurements (electrolytic
conductance, direct analysis); time-dependent electrochemical
analyses (chronoamperometry, chronopotentiometry, cyclic
chronopotentiometry and amperometry, AC polography,
chronogalvametry, and chronocoulometry); AC impedance measurement;
capacitance measurement; AC voltametry, and
photoelectrochemistry.
[0297] In some embodiments, monitoring electron transfer is via
amperometric detection. This method of detection involves applying
a potential (as compared to a separate reference electrode) between
the electrode containing the compositions of the invention and an
auxiliary (counter) electrode in the test sample. Electron transfer
of differing efficiencies is induced in samples in the presence or
absence of target analyte.
[0298] The device for measuring electron transfer amperometrically
involves sensitive current detection and includes a means of
controlling the voltage potential, usually a potentiostat. This
voltage is optimized with reference to the potential of the redox
active molecule.
[0299] In some embodiments, alternative electron detection modes
are utilized. For example, potentiometric (or voltammetric)
measurements involve non-faradaic (no net current flow) processes
and are utilized traditionally in pH and other ion detectors.
Similar sensors are used to monitor electron transfer between the
redox active molecules and the electrode. In addition, other
properties of insulators (such as resistance) and of conductors
(such as conductivity, impedance and capicitance) could be used to
monitor electron transfer between the redox active molecules and
the electrode. Finally, any system that generates a current (such
as electron transfer) also generates a small magnetic field, which
may be monitored in some embodiments.
[0300] In some embodiments, the system may be calibrated to
determine the amount of solvent accessible redox active molecules
on an electrode by running the system in organic solvent prior to
the addition of target. This is quite significant to serve as an
internal control of the sensor or system. This allows a preliminary
measurement, prior to the addition of target, on the same molecules
that will be used for detection, rather than rely on a similar but
different control system. Thus, the actual molecules that will be
used for the detection can be quantified prior to any experiment.
Running the system in the absence of water, i.e. in organic solvent
such as acetonitrile, will exclude the water and substantially
negate any solvent reorganization effects. This will allow a
quantification of the actual number of molecules that are on the
surface of the electrode. The sample can then be added, an output
signal determined, and the ratio of bound/unbound molecules
determined. This is a significant advantage over prior methods.
[0301] It should be understood that one benefit of the fast rates
of electron transfer observed in the compositions of the invention
is that time resolution can greatly enhance the signal-to-noise
results of monitors based on electronic current. The fast rates of
electron transfer of the present invention result both in high
signals and stereotyped delays between electron transfer initiation
and completion. By amplifying signals of particular delays, such as
through the use of pulsed initiation of electron transfer and
"lock-in" amplifiers of detection, orders of magnitude improvements
in signal-to-noise may be achieved.
[0302] Without being bound by theory, it appears that target
analytes, bound to an electrode, may respond in a manner similar to
a resistor and capacitor in series. Also, the E0 of the redox
active molecule can shift as a result of the target analyte
binding. Furthermore, it may be possible to distinguish between
solvent accessible and solvent inhibited redox active molecules on
the basis of the rate of electron transfer, which in turn can be
exploited in a number of ways for detection of the target analyte.
Thus, as will be appreciated by those in the art, any number of
initiation-detection systems can be used in the present
invention.
[0303] In some embodiments, electron transfer is initiated and
detected using direct current (DC) techniques. As noted above, the
E.degree. of the redox active molecule can shift as a result of the
change in the solvent reorganization energy upon target analyte
binding. Thus, measurements taken at the E.degree. of the solvent
accessible redox active molecule and at the E.degree. of the
solvent inhibited molecule will allow the detection of the analyte.
As will be appreciated by those in the art, a number of suitable
methods may be used to detect the electron transfer.
[0304] In some embodiments, electron transfer is initiated using
alternating current (AC) methods. A first input electrical signal
is applied to the system, preferably via at least the sample
electrode (containing the complexes of the invention) and the
counter electrode, to initiate electron transfer between the
electrode and the second electron transfer moiety. Three electrode
systems may also be used, with the voltage applied to the reference
and working electrodes. In this embodiment, the first input signal
comprises at least an AC component. The AC component may be of
variable amplitude and frequency. Generally, for use in the present
methods, the AC amplitude ranges from about 1 mV to about 1.1 V,
with from about 10 mV to about 800 mV being preferred, and from
about 10 mV to about 500 mV being especially preferred. The AC
frequency ranges from about 0.01 Hz to about 10 MHz, with from
about 1 Hz to about 1 MHz being preferred, and from about 1 Hz to
about 100 kHz being especially preferred
[0305] In some embodiments, the first input signal comprises a DC
component and an AC component. That is a DC offset voltage between
the sample and counter electrodes is swept through the
electrochemical potential of the second electron transfer moiety.
The sweep is used to identify the DC voltage at which the maximum
response of the system is seen. This is generally at or about the
electrochemical potential of the redox active molecule. Once this
voltage is determined, either a sweep or one or more uniform DC
offset voltages may be used. DC offset voltages of from about -1 V
to about +1.1 V are preferred, with from about -500 mV to about
+800 mV being especially preferred, and from about -300 mV to about
500 mV being particularly preferred. On top of the DC offset
voltage, an AC signal component of variable amplitude and frequency
is applied. If the redox active molecule has a low enough solvent
reorganization energy to respond to the AC perturbation, an AC
current will be produced due to electron transfer between the
electrode and the redox active molecule.
[0306] In some embodiments, the AC amplitude is varied. Without
being bound by theory, it appears that increasing the amplitude
increases the driving force. Thus, higher amplitudes, which result
in higher overpotentials give faster rates of electron transfer.
Thus, generally, the same system gives an improved response (i.e.
higher output signals) at any single frequency through the use of
higher overpotentials at that frequency. Thus, the amplitude may be
increased at high frequencies to increase the rate of electron
transfer through the system, resulting in greater sensitivity. In
addition, as noted above, it may be possible to distinguish between
solvent accessible and solvent inhibited redox active molecules on
the basis of the rate of electron transfer, which in turn can be
used either to distinguish the two on the basis of frequency or
overpotential.
[0307] In some embodiments, measurements of the system are taken at
least two separate amplitudes or overpotentials, with measurements
at a plurality of amplitudes being preferred. As noted above,
changes in response as a result of changes in amplitude may form
the basis of identification, calibration and quantification of the
system.
[0308] In some embodiments, the AC frequency is varied. At
different frequencies, different molecules respond in different
ways. As will be appreciated by those in the art, increasing the
frequency generally increases the output current. However, when the
frequency is greater than the rate at which electrons may travel
between the electrode and the redox active molecules, higher
frequencies result in a loss or decrease of output signal. At some
point, the frequency will be greater than the rate of electron
transfer through even solvent inhibited redox active molecules, and
then the output signal will also drop.
[0309] In addition, the use of AC techniques allows the significant
reduction of background signals at any single frequency due to
entities other than the covalently attached nucleic acids, i.e.
"locking out" or "filtering" unwanted signals. That is, the
frequency response of a charge carrier or redox active molecule in
solution will be limited by its diffusion coefficient. Accordingly,
at high frequencies, a charge carrier may not diffuse rapidly
enough to transfer its charge to the electrode, and/or the charge
transfer kinetics may not be fast enough. This is particularly
significant in embodiments that do not utilize a passivation layer
monolayer or have partial or insufficient monolayers, i.e. where
the solvent is accessible to the electrode. As outlined above, in
DC techniques, the presence of "holes" where the electrode is
accessible to the solvent can result in solvent charge carriers
"short circuiting" the system. However, using the present AC
techniques, one or more frequencies can be chosen that prevent a
frequency response of one or more charge carriers in solution,
whether or not a monolayer is present. This is particularly
significant since many biological fluids such as blood contain
significant amounts of redox active molecules which can interfere
with amperometric detection methods.
[0310] In some embodiments, measurements of the system are taken at
least two separate frequencies, with measurements at a plurality of
frequencies being preferred. A plurality of frequencies includes a
scan. In a preferred embodiment, the frequency response is
determined at least two, preferably at least about five, and more
preferably at least about ten frequencies.
D. Signal Processing
[0311] After transmitting the input signal to initiate electron
transfer, an output signal is received or detected. The presence
and magnitude of the output signal will depend on the
overpotential/amplitude of the input signal; the frequency of the
input AC signal; the composition of the intervening medium, i.e.
the impedance, between the electron transfer moieties; the DC
offset; the environment of the system; and the solvent. At a given
input signal, the presence and magnitude of the output signal will
depend in general on the solvent reorganization energy required to
bring about a change in the oxidation state of the metal ion. Thus,
upon transmitting the input signal, comprising an AC component and
a DC offset, electrons are transferred between the electrode and
the redox active molecule, when the solvent reorganization energy
is low enough, the frequency is in range, and the amplitude is
sufficient, resulting in an output signal.
[0312] In some embodiments, the output signal comprises an AC
current. As outlined above, the magnitude of the output current
will depend on a number of parameters. By varying these parameters,
the system may be optimized in a number of ways.
[0313] In general, AC currents generated in the present invention
range from about 1 femptoamp to about 1 milliamp, with currents
from about 50 femptoamps to about 100 microamps being preferred,
and from about 1 picoamp to about 1 microamp being especially
preferred.
EXAMPLES
Example 1
Synthesis of Compounds
[0314] Compound 200
##STR00023##
[0315] To a 100 mL round bottom flask was added 1-undecanethiol
(1.4973 g, 7.95 mmol) and dry methanol (30 mL). Dry dichloromethane
(5 mL) was added to aid in dissolution. 2,2-dithiodipyridine (1.754
7 g, 7.96 mmol) was added as a powder followed by triethylamine
(1.15 mL, 8.27 mmol). The reaction mixture was deoxygenated with
argon then set to stir at room temperature under a positive
pressure of argon for 24 hours. The reaction contents were dried on
a rotary evaporator and purified by silica gel column
chromatography using ethyl acetate/hexanes (1:1) as the eluent to
yield compound 200 (1.8494 g, 78%).
[0316] Compound 201
##STR00024##
[0317] To a 100 mL Schlenk flask was added 200 (1.8528 g, 6.23
mmol) with dry tetrahydrofuran (30 mL). 1-mercaptoudecanoic acid
(1.5108 g, 6.92 mmol) and 4-dimethylaminopyridine (0.7710 g, 6.31
mmol) were added as solids to the reaction flask then additional
tetrahydrofuran (20 mL). The reaction contents were deoxygenated
with argon then set to stir at room temperature under a positive
pressure of argon for 16 hours. The reaction contents were dried on
a rotary evaporator and purified by silica gel column
chromatography using methanol I dichloromethane (1:9) as the eluent
to yield compound 201 (1.0207 g, 40%).
[0318] Compound 202
##STR00025##
[0319] To a 250 mL round bottom flask was added
N-hydroxysuccinimide (0.1435 g, 1.25 mmol) with dry dichloromethane
(100 mL). The contents were briefly placed in a sonication bath to
aid in dissolution then compound 201 (0.5078 g, 1.25 mmol) was
added at once as a dichloromethane solution (10 mL). A
dichloromethane solution (10 mL) of dicyclohexylcarbodiimide
(0.2876 g, 1.39 mmol) was added drop wise over 23 min., followed by
deoxygenation with bubbling argon for 30 min. The contents were set
to stir at room temperature under a positive pressure of argon for
17 hours. The reaction contents were filtered to remove the
dicyclohexylurea precipitate, concentrated on a rotary evaporator
to 20-25 mL, then purified by silica gel column chromatography
using methanol (2.5%) in dichlormethane as the eluent to provide
compound 202 (0.3892 g, 62%).
[0320] Compound 203
##STR00026##
[0321] To a 25 mL round bottom flask was added
Boc-D-2,4-diaminobutyric acid (0.3080 g, 1.41 mmol) and maleic
anhydride (0.1415 g, 1.44 mmol) with glacial acetic acid (8 mL).
The reaction contents were set to stir at room temperature under a
positive pressure of argon for 4.5 hours. The reaction contents
were dried on a vacuum line to remove all volatiles to yield
compound 203 (0.4490 g). The material was used as-is without
further purification; estimated purity is 65% based on .sup.1H NMR
data.
[0322] Compound 204
##STR00027##
[0323] To a 100 mL Schlenk flask was added 203 (0.2919 g, 0.92
mmol) with dry toluene (40 mL) and triethylamine (400 .mu.L, 2.89
mmol). The flask was fitted with a Dean-Stark apparatus and the
side arm filled with dry toluene. The entire setup was flushed with
argon and the flask brought to a vigorous reflux for 4.5 hours. The
reaction contents were dried on a rotary evaporator to provide a
tan/brownish oil. This oil was dissolved in water (20 mL) and
acidified with citric acid (50 mL aqueous). Extraction of the crude
product was accomplished with dichloromethane/methanol (9:1). The
organic solution was concentrated on a rotary evaporator then
purified by silica gel column chromatography using ethyl
acetate/methanol (4:1)+trace acetic acid as the eluent to provide
compound 204 (0.2647 g, 96%).
[0324] Compound 205
##STR00028##
[0325] To a 25 mL round bottom flask was added HCl (10 mL of 4M in
dioxane; 40 mmol) under argon. The contents were cooled in an ice
water bath then transferred to a pre-cooled 25 mL round bottom
flask containing compound 204. The contents were stirred at
0.degree. C. under argon for 45 min. then warmed to room
temperature and stirred for an additional 2 hours. All solvent and
excess HCl was removed on a vacuum line and the crude residue
passed through a Dowex 1.times.2-100 anion exchange resin using
water as the eluent to provide compound 205 (0.2004 g, 98%)
[0326] Compound 206
##STR00029##
[0327] To a 50 mL Schlenk flask was added 202 (0.0220 g, 0.044
mmol) and dry acetonitrile (6 mL). 203 (0.01 05 g, 0.045 mmol) and
diisopropylethylamine (8.5 .mu.L, 0.049 mmol) were added in
sequence and the heterogeneous contents set to stir under argon at
room temperature. After 30 min. additional diisopropylethylamine
(8.5 .mu.L, 0.049 mmol) was added to the reaction mixture to aid in
the dissolution of 203. Dimethylacetamide (1.5 mL) was added drop
wise to provide a homogeneous solution; the contents were flushed
with argon and set to stir at room temperature for 17 hours. The
reaction contents were pumped to dryness on a vacuum line then
dissolved in dichloromethane and washed with aqueous citric acid.
Extraction with dichloromethane (4.times.20 mL), followed by silica
gel column chromatography using methanol/dichloromethane (1:9)
yielded compound 206 (0.0114 g, 45%).
[0328] Compound 207
##STR00030##
[0329] To a 15 mL quartz Schlenk tube was added potassium
hexacyanoosmate (0.3052 g, 0.61 mmol) and sodium nitrite (0.8138 g,
11.8 mmol) with water (10 mL; pH=4, acetic acid) to give a
homogeneous solution. The reaction contents were deoxygenated with
argon for 20 minutes then sealed with a Teflon screwcap. The quartz
tube was placed in a Rayonet photoreactor equipped with (14) 254 nm
bulbs and irradiated for 17 hours. The reaction contents were
transferred to a 50 mL round bottom flask and concentrated on a
rotary evaporator to yield a yellow solid. The crude reaction
mixture was purified on a Sephadex G-15 column using water as the
eluent to provide compound 207 (0.1567 g, 65%).
[0330] Compound 208
##STR00031##
[0331] To a 50 mL round bottom flask was added compound 207
(0.1567, 0.40 mmol) and water (2 mL) to give a homogeneous
solution. 4-aminomethylpyridine (0.4320 g, 4.0 mmol) was added as a
liquid then aqueous sodium hydroxide (7 mL of 3 M, 21 mmol). The
reaction mixture was deoxygenated with argon and heated to
65.degree. C. for 72 hours. The reaction contents were cool to room
temperature then neutralized by the slow addition of 1 M HCl. The
solvent was removed on a rotary evaporator and the crude material
purified on a Sephadex G-15 column using water as the eluent to
provide compound 208 (0.0922 g, 47%).
[0332] Compound 209
##STR00032##
[0333] To a 50 mL Schlenk flask will be added 206 (0.0114 g, 0.044
mmol), 2-succinimido-1, 1,3,3-tetramethyluronium tetrafluoroborate
(0.0140 g, 0.047 mmol), and N,Ndimethylformamide (5 mL). The
contents will be stirred under argon, followed by the addition of
diisopropylethylamine (7.8 .mu.L, 0.045 mmol). After stirring at
room temperature for 1 hour, the solvent will be removed on a
rotary evaporator, then the residue dissolved in dry methanol (5
mL). Compound 208 (0.0219 g, 0.044 mmol) will be added as a solid
and the contents stirred at room temperature for 18 hours. The
solvent will be removed on a rotary evaporator and the residue
purified by chromatography on an LH-20 column using methanol as the
eluent to provide compound 209.
Example 2
Pentacyanoosmate Branched Molecular Wire Complex
[0334] General Considerations. All synthetic manipulations (Schemes
S1) were performed under a dry argon atmosphere using standard
Schlenk techniques, unless otherwise noted. For reaction media,
solvents were dried over neutral alumina via the Dow-Grubbs solvent
system 1 acquired from Glass Contours (Laguna Beach, Calif.). These
solvents were degassed with argon prior to use.
[0335] Materials. Compound 101,
1-ethynyl-4-(trimethylsilylethynyl)benzene,
5-(4-iodophenylethynyl)[1,2,5] dithiazepane, and compound 208 were
synthesized as described previously. .sup.2,3,4,5 All other
reagents were purchased from commercial sources and used without
further purification unless otherwise noted. Reactions were
monitored by TLC (aluminum backed silica gel sheets 60 F254; EMD
Chemicals, Inc., Gibbstown, N.J.) and spots were visualized by
fluorescence quenching upon exposure to UV light.
[0336] Experimental Methods:
##STR00033## ##STR00034## ##STR00035##
[0337] Compound 102. Compound 101 (1.44 g, 3.55 mmol),
1-ethynyl-4(trimethylsilylethynyl)benzene (0.705 g, 3.55 mmol),
Pd(PPh.sub.3).sub.2Cl.sub.2 (0.062 g, 0.089 mmol), and CuI (0.017
g, 0.089 mmol) were combined in THF (15 mL). TEA (2.5 mL) was added
and the reaction was set to stir at r.t. for 2.5 h under an
atmosphere of Ar. The reaction mixture was concentrated in vacuo
and the crude residue was purified by column chromatography on
silica gel (1:1:5, EtOAC:DCM:hexanes) to yield the pure product as
a flaky yellow solid (1.51 g, 3.17 mmol, 89%). ESI-MS (positive,
MeOH:DCM) m/z: 498.10 (M+Na). .sup.1H NMR was consistent with the
structure of 102.
[0338] Compound 103. Compound 102 (1.44 g, 3.03 mmol) in THF (50
mL) was cooled to ca.-15.degree. C. in an acetonitrile/N.sub.2(l)
bath. TBAF (1.0 M in THF, 4.5 mL, 4.5 mmol) was added dropwise via
syringe. After 20 min, water (2 mL) was added to quench the
reaction and the volatiles were removed in vacuo. The crude orange
oil was dissolved in EtOAc (200 mL) and washed with water
(3.times.100 mL), dried over Na.sub.2SO.sub.4, filtered, and
concentrated to a crude residue that was purified by column
chromatography on silica gel (1:1:3, EtOAc:DCM:hexanes) to yield
the pure product as an off-white solid (1.22 g, 3.02 mmol, 99%).
.sup.1H NMR was consistent with the structure of 103.
[0339] Compound 104. Compound 103 (0.533 g, 1.32 mmol),
5-(4-iodophenylethynyl)-[1,2,5] dithiazepane (0.445 g, 1.32 mmol),
Pd(PPh.sub.3).sub.2Cl.sub.2 (0.046 g, 0.066 mmol), and CuI (0.006
g, 0.033 mmol) were combined in THF (5 mL). TEA (1.0 mL) was added
and the reaction was heated to 50.degree. C. under an atmosphere of
Ar. After 22 h the volatiles were removed in vacuo and the crude
residue was purified by column chromatography on silica gel
(0.2:0.8:4, EtOAc:hexanes:DCM) to yield the pure product as a
greenish yellow solid (0.285 g, 0.470 mmol, 36%). .sup.1H NMR was
consistent with the structure of 104.
[0340] Compound 105. Compound 104 (0.072 g, 0.12 mmol) was
dissolved in dioxane (3 mL) and anisole (0.5 mL). HCl (4.0 M in
dioxane, 3 mL) was added dropwise and the reaction stirred at r.t.
for 1 h. The volatiles were removed in vacuo and the crude yellow
solid was used without further purification.
NHS-3-maleimidopropionate (MPS) (0.034 g, 0.13 mmol),
N,N-dimethylacetamide (4 mL), and TEA (50 1-JL) were added and the
reaction stirred at r.t. overnight. After 15 h, the reaction
mixture was poured into water (75 mL) and extracted with DCM
(4.times.50 mL). The organic phase was dried over Na.sub.2SO.sub.4,
filtered, and concentrated to a crude residue that was purified by
column chromatography on silica gel (1:2:2, diethyl
ether:EtOAc:DCM) to yield the pure product as a yellow solid (0.040
g, 0.060 mmol, 50%). 1H NMR was consistent with the structure of
105.
[0341] Compound 106. Compound 105 (0.031 g, 0.047 mmol) and ultra
dry Lil (0.045 g, 0.34 mmol) were refluxed in dry EtOAc (3 mL) for
24 h in the dark. The reaction mixture was poured into HCl.sub.(aq)
(0.1M, 10 mL) with EtOAc (100 mL). The organic phase was washed
with HCl.sub.(aq) (0.1 M, 2.times.50 mL), dried over
Na.sub.2SO.sub.4, filtered, and concentrated to a crude residue
that was purified by column chromatography on silica gel
(0.1:0.5:9.4, acetic acid:MeOH:DCM) to yield the pure product as a
yellow solid (0.020 g, 0.031 mmol, 66%). ESI-MS (negative, MeOH)
m/z: 684.39 (M+Cl) .sup.1H NMR was consistent with the structure of
106.
[0342] Compound 107. Compound 106 (0.007 g, 0.011 mmol) and
compound 208 (0.006 g, 0.013 mmol) are suspended in MeOH (2.5 mL)
and THF (0.5 mL). The flask is sonicated and the mixture cooled to
4.degree. C. in an ice bath. 1-Hydroxybenzotriazole (0.1 equiv with
respect to 106) in THF (0.5 mL) is added followed by
N-(3-dimethylaminopropyl)-N-ethylcarbodiimide.HCl (0.002 g, 0.011
mmol) and TEA (3 .mu.L) and the reaction stirred allow to warm to
r.t. overnight. The solvent will be removed in vacuo and the
residue purified by chromatography on an LH-20 column using
methanol as the eluent to provide compound 107.
Sequence CWU 1
1
618PRTArtificial SequenceSynthetic 1Ala Thr Tyr Pro Leu Pro Ile Arg
1 5 27PRTArtificial SequenceSynthetic 2Tyr Tyr Trp Leu His His Cys
1 5 316PRTArtificial SequenceSynthetic 3Leu His Ile His Arg Thr Leu
Ser Ile Gln Gly Gly Gly Gly Ser Cys 1 5 10 15 47PRTArtificial
SequenceSynthetic 4His Ser Ser Lys Leu Gln Cys 1 5 57PRTArtificial
SequenceSynthetic 5Tyr Tyr Trp Leu His His Cys 1 5 68PRTArtificial
SequenceSynthetic 6Ala Thr Tyr Pro Leu Pro Ile Arg 1 5
* * * * *