U.S. patent application number 14/678685 was filed with the patent office on 2015-07-30 for method and apparatus for match quality analysis of analyte binding.
The applicant listed for this patent is INTEL CORPORATION. Invention is credited to Brandon BARNETT, Hernan CASTRO, Gordon HOLT.
Application Number | 20150212032 14/678685 |
Document ID | / |
Family ID | 42934715 |
Filed Date | 2015-07-30 |
United States Patent
Application |
20150212032 |
Kind Code |
A1 |
HOLT; Gordon ; et
al. |
July 30, 2015 |
METHOD AND APPARATUS FOR MATCH QUALITY ANALYSIS OF ANALYTE
BINDING
Abstract
Described are devices and methods for detecting the match
quality and concentration of analytes binding to an electrode
surface. The devices utilize a clock to measure capacitance change
as a function of time and a temperature controller to measure the
capacitance change as a function of temperature.
Inventors: |
HOLT; Gordon; (Beaverton,
OR) ; CASTRO; Hernan; (Shingle Springs, CA) ;
BARNETT; Brandon; (Beaverton, OR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
INTEL CORPORATION |
Santa Clara |
CA |
US |
|
|
Family ID: |
42934715 |
Appl. No.: |
14/678685 |
Filed: |
April 3, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
11646615 |
Dec 28, 2006 |
8999724 |
|
|
14678685 |
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Current U.S.
Class: |
506/39 ;
422/69 |
Current CPC
Class: |
G01N 27/22 20130101;
G01N 27/3276 20130101; G01N 27/227 20130101 |
International
Class: |
G01N 27/22 20060101
G01N027/22 |
Claims
1. A device comprising; a surface; a detector configured to detect
changes in capacitance on the surface; and a clock configured to
keep track of the time as changes in capacitance on the surface
occur; and a processor configured to correlate the change in
capacitance on the surface with the concentration of the
analyte.
2. The device of claim 1, wherein the capacitance change is
measured utilizing an integrating charge amplifier.
3. The device of claim 1, wherein the capacitance change is caused
by DNA hybridization, peptide/protein binding, peptide
phosphorylation, or aptamer/protein binding.
4. The device of claim 1, wherein the analyte is in a conductive
solution.
5. The device of claim 1, wherein the analyte is in an aqueous
solution or conductive gel.
6. The device of claim 1, wherein the surface is an electrode
surface.
7. The device of claim 6, wherein the electrode is part of an array
of electrodes fabricated on a single substrate.
8. A device comprising: a substrate; a functionalized surface
configured to bind to selected analytes; a heater configured to
heat the surface after one or more selected analytes have bound to
the surface; and a detector configured to detect capacitance
changes on the surface.
9. The device of claim 8, wherein the binding characteristic is the
match quality of the analyte and a probe molecule attached to the
surface.
10. The device of claim 9, wherein the probe is a DNA molecule.
11. The device of claim 8, wherein the detector comprises an
integrating charge amplifier.
12. The device of claim 8, wherein the capacitance change is caused
by DNA hybridization, peptide/protein binding, peptide
phosphorylation, or aptamer/protein binding.
13. The device of claim 8, wherein the surface is an electrode
surface.
14. The device of claim 8, wherein the electrode is part of an
array of electrodes fabricated on a single substrate.
Description
RELATED APPLICATIONS
[0001] This application is a Continuation of U.S. patent
application Ser. No. 11/646,615 filed Dec. 28, 2006; which is
related to U.S. patent application Ser. No. 11/646,600 filed Dec.
28, 2006 and U.S. patent application Ser. No. 11/646,602 filed Dec.
28, 2006, all of which are incorporated herein by reference.
FIELD OF INVENTION
[0002] The embodiments of the invention relate to devices and
methods for detecting the match quality and concentration of
analytes binding to an electrode surface. The invention transcends
several scientific disciplines such as polymer chemistry,
biochemistry, molecular biology, medicine and medical
diagnostics.
BACKGROUND
[0003] Molecular recognition (also called a binding event) is
fundamental to every cellular event: transcription, translation,
signal transduction, viral and bacterial infection and immune
response are all mediated by selective recognition events. Thus,
developing a better understanding of detecting the binding events
of molecules is of significant importance.
[0004] Typical methods for carrying out on-chip analyte detections
include: optical tagging (fluorescence, visible, IR, Raman),
radiometric (various radioactive tag), and indirect electrochemical
methods of detection (tagging with enzymes that generate charges
that can be measured).
[0005] In addition, on-chip manufacturing of polymer arrays also
offers the ability to create huge arrays of bio-polymers quickly
and efficiently. These arrays offer huge potential in advancing the
capabilities of bio-pharmaceutical drug discovery and basic
academic bioresearch.
BRIEF DESCRIPTION OF THE DRAWINGS
[0006] FIG. 1 is a schematic of an exposed electrode array
including large area drive electrodes and micron or sub-micron
scale sense and reference electrodes.
[0007] FIG. 2 is a schematic of exposed electrode array with
attachment chemistry and affinity probes attached to the sense and
reference electrodes.
[0008] FIG. 3 is a schematic showing analyte (e.g. complementary
sequence DNA) bound to affinity probe on a sense electrode.
[0009] FIG. 4 is a schematic of a device operating in differential
detection mode with key elements and electrical connections
shown.
[0010] FIG. 5 is a schematic of device operating in absolute
detection mode with key elements and electrical connections
shown.
[0011] FIG. 6 is a circuit schematic of a detection device showing
connection of the sense and reference electrode capacitors,
internal switches, etc.
[0012] FIG. 7 is a circuit schematic of the device showing
connection of the addressing circuits and attached amplifiers.
[0013] FIG. 8 is an image of a completed device prototype according
to the invention.
[0014] FIG. 9 is a graph showing how the device operates to detect
analyte binding.
[0015] FIG. 10 is a schematic of a device in electrochemical
synthesis of polymer affinity probe operation.
[0016] FIG. 11 is an alternative configuration of a device in
electrochemical synthesis of polymer affinity probe operation.
[0017] FIG. 12 is an image of an electrode pattern in which
concentric rings are used to more effectively confine the acid/base
field.
[0018] FIG. 13 is a graph of capacitance change as a function of
the number of replicated targets.
[0019] FIG. 14 is a graph of capacitance change as a function of
DNA binding to DNA that had been attached to an electrode on a
chip.
[0020] FIG. 15 is a graph showing the timing and extent of
capacitance change as a function of the concentration of added DNA
that is binding to probe DNA attached to an electrode.
[0021] FIG. 16 is a graph of capacitance change as a function of
the concentration and type of added DNA binding to probe DNA.
[0022] FIG. 17 is an image of a known Peltier thermoelectric
controller for precisely controlling the temperature of a chip over
time.
[0023] FIG. 18 is a schematic showing the base pairing and hydrogen
bonding rules for DNA hybridization.
[0024] FIG. 19 includes graphs of capacitance changes as a function
of heating of electrodes bearing different types of DNA hybridized
to probe DNA.
DETAILED DESCRIPTION
[0025] As used in the specification and claims, the singular forms
"a", "an" and "the" include plural references unless the context
clearly dictates otherwise. For example, the term "an array" may
include a plurality of arrays unless the context clearly dictates
otherwise.
[0026] An "array" is an intentionally created collection of
molecules which can be prepared either synthetically or
biosynthetically. The molecules in the array can be identical or
different from each other. The array can assume a variety of
formats, e.g., libraries of soluble molecules; libraries of
compounds tethered to resin beads, silica chips, or other solid
supports. The array could either be a macroarray or a microarray,
depending on the size of the sample spots on the array. A
macroarray generally contains sample spot sizes of about 300
microns or larger and can be easily imaged by gel and blot
scanners. A microarray would generally contain spot sizes of less
than 300 microns.
[0027] "Solid support," "support," and "substrate" refer to a
material or group of materials having a rigid or semi-rigid surface
or surfaces. In some aspects, at least one surface of the solid
support will be substantially flat, although in some aspects it may
be desirable to physically separate synthesis regions for different
molecules with, for example, wells, raised regions, pins, etched
trenches, or the like. In certain aspects, the solid support(s)
will take the form of beads, resins, gels, microspheres, or other
geometric configurations.
[0028] The term "probe" or "probe molecule" refers to a molecule
attached to the substrate of the array, which is typically cDNA or
pre-synthesized polynucleotide deposited on the array. Probes
molecules are biomolecules capable of undergoing binding or
molecular recognition events with target molecules. (In some
references, the terms "target" and "probe" are defined opposite to
the definitions provided here.) The polynucleotide probes require
only the sequence information of genes, and thereby can exploit the
genome sequences of an organism. In cDNA arrays, there could be
cross-hybridization due to sequence homologies among members of a
gene family. Polynucleotide arrays can be specifically designed to
differentiate between highly homologous members of a gene family as
well as spliced forms of the same gene (exon-specific).
Polynucleotide arrays of the embodiment of this invention could
also be designed to allow detection of mutations and single
nucleotide polymorphism.
[0029] The term "target" or "target molecule" refers to a small
molecule, biomolecule, or nanomaterial such as but not necessarily
limited to a small molecule that is biologically active, nucleic
acids and their sequences, peptides and polypeptides, as well as
nanostructure materials chemically modified with biomolecules or
small molecules capable of binding to molecular probes such as
chemically modified carbon nanotubes, carbon nanotube bundles,
nanowires and nanoparticles. The target molecule may be
fluorescently labeled DNA or RNA.
[0030] The terms "die," "polymer array chip," "DNA array," "array
chip," "DNA array chip," "bio-chip" or "chip" are used
interchangeably and refer to a collection of a large number of
probes arranged on a shared substrate which could be a portion of a
silicon wafer, a nylon strip or a glass slide.
[0031] The term "molecule" generally refers to a macromolecule or
polymer as described herein. However, arrays comprising single
molecules, as opposed to macromolecules or polymers, are also
within the scope of the embodiments of the invention.
[0032] "Predefined region" or "spot" or "pad" refers to a localized
area on a solid support which is, was, or is intended to be used
for formation of a selected molecule and is otherwise referred to
herein in the alternative as a "selected" region. The predefined
region may have any convenient shape, e.g., circular, rectangular,
elliptical, wedge-shaped, etc. For the sake of brevity herein,
"predefined regions" are sometimes referred to simply as "regions"
or "spots." In some embodiments, a predefined region and,
therefore, the area upon which each distinct molecule is
synthesized is smaller than about 1 cm.sup.2 or less than 1
mm.sup.2, and still more preferably less than 0.5 mm.sup.2. In most
preferred embodiments the regions have an area less than about
10,000 .mu.m.sup.2 or, more preferably, less than 100 .mu.m.sup.2.
Additionally, multiple copies of the polymer will typically be
synthesized within any preselected region. The number of copies can
be in the thousands to the millions. More preferably, a die of a
wafer contains at least 400 spots in, for example, an at least
20.times.20 matrix. Even more preferably, the die contains at least
2048 spots in, for example, an at least 64.times.32 matrix, and
still more preferably, the die contains at least 204,800 spots in,
for example, an at least 640.times.320 array. A spot could contain
an electrode to generate an electrochemical reagent, a working
electrode to synthesize a polymer and a confinement electrode to
confine the generated electrochemical reagent. The electrode to
generate the electrochemical reagent could be of any shape,
including, for example, circular, flat disk shaped and hemisphere
shaped.
[0033] An "electrode" is a body or a location at which an
electrochemical reaction occurs. The term "electrochemical" refers
to an interaction or interconversion of electric and chemical
phenomena.
[0034] A "functionalized electrode" is an electrode of a microchip
array having a probe molecule that has a specific chemical affinity
to a target molecule. An "unfunctionalized electrode" is an
electrode of a microchip array having no probe molecule or having a
probe molecule that has no specific chemical affinity to a target
molecule.
[0035] The electrodes used in embodiments of the invention may be
composed of, but are not limited to, metals such as iridium and/or
platinum, and other metals, such as, palladium, gold, silver,
copper, mercury, nickel, zinc, titanium, tungsten, aluminum, as
well as alloys of various metals, and other conducting materials,
such as, carbon, including glassy carbon, reticulated vitreous
carbon, basal plane graphite, edge plane graphite and graphite.
Doped oxides such as indium tin oxide, and semiconductors such as
silicon oxide and gallium arsenide are also contemplated.
Additionally, the electrodes may be composed of conducting
polymers, metal doped polymers, conducting ceramics and conducting
clays. Among the metals, platinum and palladium are especially
preferred because of the advantageous properties associated with
their ability to absorb hydrogen, i.e., their ability to be
"preloaded" with hydrogen before being used in the methods of the
invention.
[0036] The electrodes may be connected to an electric source in any
known manner. Preferred ways of connecting the electrodes to the
electric source include CMOS (complementary metal oxide
semiconductor) switching circuitry, radio and microwave frequency
addressable switches, light addressable switches, direct connection
from an electrode to a bond pad on the perimeter of a semiconductor
chip, and combinations thereof. CMOS switching circuitry involves
the connection of each of the electrodes to a CMOS transistor
switch. The switch could be accessed by sending an electronic
address signal down a common bus to SRAM (static random access
memory) circuitry associated with each electrode. When the switch
is "on", the electrode is connected to an electric source. Radio
and microwave frequency addressable switches involve the electrodes
being switched by a RF or microwave signal. This allows the
switches to be thrown both with and/or without using switching
logic. The switches can be tuned to receive a particular frequency
or modulation frequency and switch without switching logic. Light
addressable switches are switched by light. In this method, the
electrodes can also be switched with and without switching logic.
The light signal can be spatially localized to afford switching
without switching logic. This could be accomplished, for example,
by scanning a laser beam over the electrode array; the electrode
being switched each time the laser illuminates it.
[0037] In some aspects, a predefined region can be achieved by
physically separating the regions (i.e., beads, resins, gels, etc.)
into wells, trays, etc.
[0038] A "protecting group" is a moiety which is bound to a
molecule and designed to block one reactive site in a molecule, but
may be spatially removed upon selective exposure to an activator or
a deprotecting reagent. Several examples of protecting groups are
known in the literature. The proper selection of protecting group
(also known as protective group) for a particular synthesis would
be governed by the overall methods employed in the synthesis.
Activators include, for example, electromagnetic radiation, ion
beams, electric fields, magnetic fields, electron beams, x-ray, and
the like. A deprotecting reagent could include, for example, an
acid, a base or a free radical. Protective groups are materials
that bind to a monomer, a linker molecule or a pre-formed molecule
to protect a reactive functionality on the monomer, linker molecule
or pre-formed molecule, which may be removed upon selective
exposure to an activator, such as an electrochemically generated
reagent. Protective groups that may be used in accordance with an
embodiment of the invention preferably include all acid and base
labile protecting groups. For example, peptide amine groups are
preferably protected by t-butyloxycarbonyl (BOC) or
benzyloxycarbonyl (CBZ), both of which are acid labile, or by
9-fluorenylmethoxycarbonyl (FMOC), which is base labile.
Additionally, hydroxyl groups on phosphoramidites may be protected
by dimethoxytrityl (DMT), which is acid labile. Exocyclic amine
groups on nucleosides, in particular on phosphoramidites, are
preferably protected by dimethylformamidine on the adenosine and
guanosine bases, and isobutyryl on the cytidine bases, both of
which are base labile protecting groups. This protection strategy
is known as fast oligonucleotide deprotection (FOD).
[0039] Any unreacted deprotected chemical functional groups may be
capped at any point during a synthesis reaction to avoid or to
prevent further bonding at such molecule. Capping groups "cap"
deprotected functional groups by, for example, binding with the
unreacted amino functions to form amides. Capping agents suitable
for use in an embodiment of the invention include: acetic
anhydride, n-acetylimidizole, isopropenyl formate, fluorescamine,
3-nitrophthalic anhydride and 3-sulfoproponic anhydride. Of these,
acetic anhydride and n-acetylimidizole are preferred.
[0040] Additional protecting groups that may be used in accordance
with an embodiment of the invention include acid labile groups for
protecting amino moieties: tertbutyloxycarbonyl,
-tert-amyloxycarbonyl, adamantyloxycarbonyl,
1-methylcyclobutyloxycarbonyl, 2-(p-biphenyl)propyl(2)oxycarbonyl,
2-(p-phenylazophenylyl)propyl(2)oxycarbonyl,
.alpha.,.alpha.-dimethyl-3,5-dimethyloxybenzyloxy-carbonyl,
2-phenylpropyl(2)oxycarbonyl, 4-methyloxybenzyloxycarbonyl,
benzyloxycarbonyl, furfuryloxycarbonyl, triphenylmethyl(trityl),
p-toluenesulfenylaminocarbonyl, dimethylphosphinothioyl,
diphenylphosphinothioyl, 2-benzoyl-1-methylvinyl,
o-nitrophenylsulfenyl, and 1-naphthylidene; as base labile groups
for protecting amino moieties: 9-fluorenylmethyloxycarbonyl,
methylsulfonylethyloxycarbonyl, and
5-benzisoazolylmethyleneoxycarbonyl; as groups for protecting amino
moieties that are labile when reduced: dithiasuccinoyl, p-toluene
sulfonyl, and piperidino-oxycarbonyl; as groups for protecting
amino moieties that are labile when oxidized: (ethylthio)carbonyl;
as groups for protecting amino moieties that are labile to
miscellaneous reagents, the appropriate agent is listed in
parenthesis after the group: phthaloyl(hydrazine),
trifluoroacetyl(piperidine), and chloroacetyl(2-aminothiophenol);
acid labile groups for protecting carboxylic acids: tert-butyl
ester; acid labile groups for protecting hydroxyl groups:
dimethyltrityl; and basic labile groups for protecting
phosphotriester groups: cyanoethyl.
[0041] An "electrochemical reagent" refers to a chemical generated
at a selected electrode by applying a sufficient electrical
potential to the selected electrode and is capable of
electrochemically removing a protecting group from a chemical
functional group. The chemical group would generally be attached to
a molecule. Removal of a protecting group, or "deprotection," in
accordance with the invention, preferably occurs at a particular
portion of a molecule when a chemical reagent generated by the
electrode acts to deprotect or remove, for example, an acid or base
labile protecting group from the molecule. This electrochemical
deprotection reaction may be direct, or may involve one or more
intermediate chemical reactions that are ultimately driven or
controlled by the imposition of sufficient electrical potential at
a selected electrode.
[0042] Electrochemical reagents that can be generated
electrochemically at an electrode fall into two broad classes:
oxidants and reductants. Oxidants that can be generated
electrochemically, for example, include iodine, iodate, periodic
acid, hydrogen peroxide, hypochlorite, metavanadate, bromate,
dichromate, cerium (IV), and permanganate ions. Reductants that can
be generated electrochemically, for example, include chromium (II),
ferrocyanide, thiols, thiosulfate, titanium (III), arsenic (III)
and iron (II) ions. The miscellaneous reagents include bromine,
chloride, protons and hydroxyl ions. Among the foregoing reagents,
protons, hydroxyl, iodine, bromine, chlorine and thiol ions are
preferred.
[0043] The generation of and electrochemical reagent of a desired
type of chemical species requires that the electric potential of
the electrode that generates the electrochemical reagent have a
certain value, which may be achieved by specifying either the
voltage or the current. There are two ways to achieve the desired
potential at this electrode: either the voltage may be specified at
a desired value or the current can be determined such that it is
sufficient to provide the desired voltage. The range between the
minimum and maximum potential values could be determined by the
type of electrochemical reagent chosen to be generated.
[0044] An "activating group" refers to those groups which, when
attached to a particular chemical functional group or reactive
site, render that site more reactive toward covalent bond formation
with a second chemical functional group or reactive site.
[0045] A "polymeric brush" ordinarily refers to polymer films
comprising chains of polymers that are attached to the surface of a
substrate. The polymeric brush could be a functionalized polymer
films which comprise functional groups such as hydroxyl, amino,
carboxyl, thiol, amide, cyanate, thiocyanate, isocyanate and
isothio cyanate groups, or a combination thereof, on the polymer
chains at one or more predefined regions. The polymeric brushes of
the embodiment of the invention are capable of attachment or
stepwise synthesis of macromolecules thereon.
[0046] A "linker" molecule refers to any of those molecules
described supra and preferably should be about 4 to about 40 atoms
long to provide sufficient exposure. The linker molecules may be,
for example, aryl acetylene, ethylene glycol oligomers containing
2-10 monomer units, diamines, diacids, amino acids, among others,
and combinations thereof. Alternatively, the linkers may be the
same molecule type as that being synthesized (i.e., nascent
polymers), such as polynucleotides, oligopeptides, or
oligosaccharides.
[0047] The linker molecule or substrate itself and monomers used
herein are provided with a functional group to which is bound a
protective group. Generally, the protective group is on the distal
or terminal end of a molecule. Preferably, the protective group is
on the distal or terminal end of the linker molecule opposite the
substrate. The protective group may be either a negative protective
group (i.e., the protective group renders the linker molecules less
reactive with a monomer upon exposure) or a positive protective
group (i.e., the protective group renders the linker molecules more
reactive with a monomer upon exposure). In the case of negative
protective groups, there could be an additional step of
reactivation. In some embodiments, this will be done by
heating.
[0048] The polymer brush or the linker molecule may be provided
with a cleavable group at an intermediate position, which group can
be cleaved with an electrochemically generated reagent. This group
is preferably cleaved with a reagent different from the reagent(s)
used to remove the protective groups. This enables removal of the
various synthesized polymers or nucleic acid sequences following
completion of the synthesis. The cleavable group could be acetic
anhydride, n-acetylimidizole, isopropenyl formate, fluorescamine,
3-nitrophthalic anhydride and 3-sulfoproponic anhydride. Of these,
acetic anhydride and n-acetylimidizole are preferred.
[0049] The polymer brush or the linker molecule could be of
sufficient length to permit polymers on a completed substrate to
interact freely with binding entities (monomers, for example)
exposed to the substrate. The polymer brush or the linker molecule,
when used, could preferably be long enough to provide sufficient
exposure of the functional groups to the binding entity. The linker
molecules may include, for example, aryl acetylene, ethylene glycol
oligomers containing from 2 to 20 monomer units, diamines, diacids,
amino acids, and combinations thereof. Other linker molecules may
be used in accordance with the different embodiments of the present
invention and will be recognized by those skilled in the art in
light of this disclosure. In one embodiment, derivatives of the
acid labile 4,4'-dimethyoxytrityl molecules with an exocyclic
active ester can be used in accordance with an embodiment of the
invention. More preferably,
N-succinimidyl-4[bis-(4-methoxyphenyl)-chloromethyl]-benzoate is
used as a cleavable linker molecule during DNA synthesis.
Alternatively, other manners of cleaving can be used over the
entire array at the same time, such as chemical reagents, light or
heat.
[0050] A "free radical initiator" or "initiator" is a compound that
can provide a free radical under certain conditions such as heat,
light, or other electromagnetic radiation, which free radical can
be transferred from one monomer to another and thus propagate a
chain of reactions through which a polymer may be formed. Several
free radical initiators are known in the art, such as azo,
nitroxide, and peroxide types, or those comprising multi-component
systems.
[0051] "Living free radical polymerization" is defined as a living
polymerization process wherein chain initiation and chain
propagation occur without significant chain termination reactions.
Each initiator molecule produces a growing monomer chain which
continuously propagates until all the available monomer has been
reacted. Living free radical polymerization differs from
conventional free radical polymerization where chain initiation,
chain propagation and chain termination reactions occur
simultaneously and polymerization continues until the initiator is
consumed. Living free radical polymerization facilitates control of
molecular weight and molecular weight distribution. Living free
radical polymerization techniques, for example, involve reversible
end capping of growing chains during polymerization. One example is
atom transfer radical polymerization (ATRP).
[0052] A "radical generation site" is a site on an initiator
wherein free radicals are produced in response to heat or
electromagnetic radiation.
[0053] A "polymerization terminator" is a compound that prevents a
polymer chain from further polymerization. These compounds may also
be known as "terminators," or "capping agents" or "inhibitors."
Various polymerization terminators are known in the art. In one
aspect, a monomer that has no free hydroxyl groups may act as a
polymerization terminator.
[0054] The term "capable of supporting polymer array synthesis"
refers to any body on which polymer array synthesis can be carried
out, e.g., a polymeric brush that is functionalized with functional
groups such as hydroxyl, amino, carboxyl etc. These functional
groups permit macromolecular synthesis by acting as "attachment
points."
[0055] The monomers in a given polymer or macromolecule can be
identical to or different from each other. A monomer can be a small
or a large molecule, regardless of molecular weight. Furthermore,
each of the monomers may be protected members which are modified
after synthesis.
[0056] "Monomer" as used herein refers to those monomers that are
used to a form a polymer. However, the meaning of the monomer will
be clear from the context in which it is used. The monomers for
forming the polymers of the embodiments of the invention, e.g., a
polymeric brush or a linker molecule, have for example the general
structure:
##STR00001##
[0057] wherein R.sub.1 is hydrogen or lower alkyl; R.sub.2 and
R.sub.3 are independently hydrogen, or --Y--Z, wherein Y is lower
alkyl, and Z is hydroxyl, amino, or C(O)--R, where R is hydrogen,
lower alkoxy or aryloxy.
[0058] The term "alkyl" refers to those groups such as methyl,
ethyl, propyl, butyl etc, which may be linear, branched or
cyclic.
[0059] The term "alkoxy" refers to groups such as methoxy, ethoxy,
propoxy, butoxy, etc., which may be linear, branched or cyclic.
[0060] The term "lower" as used in the context of lower alkyl or
lower alkoxy refers to groups having one to six carbons.
[0061] The term "aryl" refers to an aromatic hydrocarbon ring to
which is attached an alkyl group. The term "aryloxy" refers to an
aromatic hydrocarbon ring to which is attached an alkoxy group. One
of ordinary skill in the art would readily understand these
terms.
[0062] Other monomers for preparing macromolecules of the
embodiments of the invention are well-known in the art. For
example, when the macromolecule is a peptide, the monomers include,
but are not restricted to, for example, amino acids such as the
L-amino acids, the D-amino acids, the synthetic and/or natural
amino acids. When the macromolecule is a nucleic acid, or
polynucleotide, the monomers include any nucleotide. When the
macromolecule is a polysaccharide, the monomers can be any pentose,
hexose, heptose, or their derivatives.
[0063] A "monomer addition cycle" is a cycle comprising the
chemical reactions necessary to produce covalent attachment of a
monomer to a nascent polymer or linker, such as to elongate the
polymer with the desired chemical bond (e.g., 5'-3' phosphodiester
bond, peptide bond, etc.). For example, and not to limit the
invention, the following steps typically comprise a monomer
addition cycle in phosphoramidite-based polynucleotide synthesis:
(1) deprotection, comprising removal of the DMT group from a
5'-protected nucleoside (which may be part of a nascent
polynucleotide) wherein the 5'-hydroxyl is blocked by covalent
attachment of DMT, such deprotection is usually done with a
suitable deprotection reagent (e.g., a protic acid: trichloroacetic
acid or dichloroacetic acid), and may include physical removal
(e.g., washing, such as with acetonitrile) of the removed
protecting group (e.g., the cleaved dimethyltrityl group), (2)
coupling, comprising reacting a phosphoramidite nucleoside(s),
often activated with tetrazole, with the deprotected nucleoside,
(3) optionally including capping, to truncate unreacted nucleosides
from further participation in subsequent monomer addition cycles,
such as by reaction with acetic anhydride and N-methylimidazole to
acetylate free 5'-hydroxyl groups, and (4) oxidation, such as by
iodine in tetrahydrofuran/water/pyridine, to convert the trivalent
phosphite triester linkage to a pentavalent phosphite triester,
which in turn can be converted to a phosphodiester via reaction
with ammonium hydroxide. Thus, with respect to phosphoramidite
synthesis of polynucleotides, the following reagents are typically
necessary for a complete monomer addition cycle: trichloroacetic
acid or dichloroacetic acid, a phosphoramidite nucleoside, an
oxidizing agent, such as iodine (e.g., iodine/water/THF/pyridine),
and optionally N-methylimidazole for capping.
[0064] A "macromolecule" or "polymer" comprises two or more
monomers covalently joined. The monomers may be joined one at a
time or in strings of multiple monomers, ordinarily known as
"oligomers." Thus, for example, one monomer and a string of five
monomers may be joined to form a macromolecule or polymer of six
monomers. Similarly, a string of fifty monomers may be joined with
a string of hundred monomers to form a macromolecule or polymer of
one hundred and fifty monomers. The term polymer as used herein
includes, for example, both linear and cyclic polymers of nucleic
acids, polynucleotides, polynucleotides, polysaccharides,
oligosaccharides, proteins, polypeptides, peptides, phospholipids
and peptide nucleic acids (PNAs). The peptides include those
peptides having either .alpha.-, .beta.-, or .omega.-amino acids.
In addition, polymers include heteropolymers in which a known drug
is covalently bound to any of the above, polyurethanes, polyesters,
polycarbonates, polyureas, polyamides, polyethyleneimines,
polyarylene sulfides, polysiloxanes, polyimides, polyacetates, or
other polymers which will be apparent upon review of this
disclosure.
[0065] A "nanomaterial" as used herein refers to a structure, a
device or a system having a dimension at the atomic, molecular or
macromolecular levels, in the length scale of approximately 1-100
nanometer range. Preferably, a nanomaterial has properties and
functions because of the size and can be manipulated and controlled
on the atomic level.
[0066] A "carbon nanotube" refers to a fullerene molecule having a
cylindrical or toroidal shape. A "fullerene" refers to a form of
carbon having a large molecule consisting of an empty cage of sixty
or more carbon atoms.
[0067] The term "nucleotide" includes deoxynucleotides and analogs
thereof. These analogs are those molecules having some structural
features in common with a naturally occurring nucleotide such that
when incorporated into a polynucleotide sequence, they allow
hybridization with a complementary polynucleotide in solution.
Typically, these analogs are derived from naturally occurring
nucleotides by replacing and/or modifying the base, the ribose or
the phosphodiester moiety. The changes can be tailor-made to
stabilize or destabilize hybrid formation, or to enhance the
specificity of hybridization with a complementary polynucleotide
sequence as desired, or to enhance stability of the
polynucleotide.
[0068] The term "polynucleotide" or "nucleic acid" as used herein
refers to a polymeric form of nucleotides of any length, either
ribonucleotides or deoxyribonucleotides, that comprise purine and
pyrimidine bases, or other natural, chemically or biochemically
modified, non-natural, or derivatized nucleotide bases.
Polynucleotides of the embodiments of the invention include
sequences of deoxyribopolynucleotide (DNA), ribopolynucleotide
(RNA), or DNA copies of ribopolynucleotide (cDNA) which may be
isolated from natural sources, recombinantly produced, or
artificially synthesized. A further example of a polynucleotide of
the embodiments of the invention may be polyamide polynucleotide
(PNA). The polynucleotides and nucleic acids may exist as
single-stranded or double-stranded. The backbone of the
polynucleotide can comprise sugars and phosphate groups, as may
typically be found in RNA or DNA, or modified or substituted sugar
or phosphate groups. A polynucleotide may comprise modified
nucleotides, such as methylated nucleotides and nucleotide analogs.
The sequence of nucleotides may be interrupted by non-nucleotide
components. The polymers made of nucleotides such as nucleic acids,
polynucleotides and polynucleotides may also be referred to herein
as "nucleotide polymers.
[0069] An "oligonucleotide" is a polynucleotide having 2 to 20
nucleotides. Phosphoramidites protected in this manner are known as
FOD phosphoramidites.
[0070] Analogs also include protected and/or modified monomers as
are conventionally used in polynucleotide synthesis. As one of
skill in the art is well aware, polynucleotide synthesis uses a
variety of base-protected nucleoside derivatives in which one or
more of the nitrogens of the purine and pyrimidine moiety are
protected by groups such as dimethoxytrityl, benzyl, tert-butyl,
isobutyl and the like.
[0071] For instance, structural groups are optionally added to the
ribose or base of a nucleoside for incorporation into a
polynucleotide, such as a methyl, propyl or allyl group at the 2'-O
position on the ribose, or a fluoro group which substitutes for the
2'-O group, or a bromo group on the ribonucleoside base.
2'-O-methyloligoribonucleotides (2'-O-MeORNs) have a higher
affinity for complementary polynucleotides (especially RNA) than
their unmodified counterparts. Alternatively, deazapurines and
deazapyrimidines in which one or more N atoms of the purine or
pyrimidine heterocyclic ring are replaced by C atoms can also be
used.
[0072] The phosphodiester linkage, or "sugar-phosphate backbone" of
the polynucleotide can also be substituted or modified, for
instance with methyl phosphonates, O-methyl phosphates or
phosphororthioates. Another example of a polynucleotide comprising
such modified linkages for purposes of this disclosure includes
"peptide polynucleotides" in which a polyamide backbone is attached
to polynucleotide bases, or modified polynucleotide bases. Peptide
polynucleotides which comprise a polyamide backbone and the bases
found in naturally occurring nucleotides are commercially
available.
[0073] Nucleotides with modified bases can also be used in the
embodiments of the invention. Some examples of base modifications
include 2-aminoadenine, 5-methylcytosine, 5-(propyn-1-yl)cytosine,
5-(propyn-1-yl)uracil, 5-bromouracil, 5-bromocytosine,
hydroxymethylcytosine, methyluracil, hydroxymethyluracil, and
dihydroxypentyluracil which can be incorporated into
polynucleotides in order to modify binding affinity for
complementary polynucleotides.
[0074] Groups can also be linked to various positions on the
nucleoside sugar ring or on the purine or pyrimidine rings which
may stabilize the duplex by electrostatic interactions with the
negatively charged phosphate backbone, or through interactions in
the major and minor groves. For example, adenosine and guanosine
nucleotides can be substituted at the N.sup.2 position with an
imidazolyl propyl group, increasing duplex stability. Universal
base analogues such as 3-nitropyrrole and 5-nitroindole can also be
included. A variety of modified polynucleotides suitable for use in
the embodiments of the invention are described in the
literature.
[0075] When the macromolecule of interest is a peptide, the amino
acids can be any amino acids, including .alpha., .beta., or
.omega.-amino acids. When the amino acids are .alpha.-amino acids,
either the L-optical isomer or the D-optical isomer may be used.
Additionally, unnatural amino acids, for example, .beta.-alanine,
phenylglycine and homoarginine are also contemplated by the
embodiments of the invention. These amino acids are well-known in
the art.
[0076] A "peptide" is a polymer in which the monomers are amino
acids and which are joined together through amide bonds and
alternatively referred to as a polypeptide. In the context of this
specification it should be appreciated that the amino acids may be
the L-optical isomer or the D-optical isomer. Peptides are two or
more amino acid monomers long, and often more than 20 amino acid
monomers long.
[0077] A "protein" is a long polymer of amino acids linked via
peptide bonds and which may be composed of two or more polypeptide
chains. More specifically, the term "protein" refers to a molecule
composed of one or more chains of amino acids in a specific order;
for example, the order as determined by the base sequence of
nucleotides in the gene coding for the protein. Proteins are
essential for the structure, function, and regulation of the body's
cells, tissues, and organs, and each protein has unique functions.
Examples are hormones, enzymes, and antibodies.
[0078] The term "sequence" refers to the particular ordering of
monomers within a macromolecule and it may be referred to herein as
the sequence of the macromolecule.
[0079] The term "hybridization" refers to the process in which two
single-stranded polynucleotides bind non-covalently to form a
stable double-stranded polynucleotide; triple-stranded
hybridization is also theoretically possible. The resulting
(usually) double-stranded polynucleotide is a "hybrid." The
proportion of the population of polynucleotides that forms stable
hybrids is referred to herein as the "degree of hybridization." For
example, hybridization refers to the formation of hybrids between a
probe polynucleotide (e.g., a polynucleotide of the invention which
may include substitutions, deletion, and/or additions) and a
specific target polynucleotide (e.g., an analyte polynucleotide)
wherein the probe preferentially hybridizes to the specific target
polynucleotide and substantially does not hybridize to
polynucleotides consisting of sequences which are not substantially
complementary to the target polynucleotide. However, it will be
recognized by those of skill that the minimum length of a
polynucleotide desired for specific hybridization to a target
polynucleotide will depend on several factors: G/C content,
positioning of mismatched bases (if any), degree of uniqueness of
the sequence as compared to the population of target
polynucleotides, and chemical nature of the polynucleotide (e.g.,
methylphosphonate backbone, phosphorothiolate, etc.), among
others.
[0080] Methods for conducting polynucleotide hybridization assays
have been well developed in the art. Hybridization assay procedures
and conditions will vary depending on the application and are
selected in accordance with the general binding methods known in
the art.
[0081] It is appreciated that the ability of two single stranded
polynucleotides to hybridize will depend upon factors such as their
degree of complementarity as well as the stringency of the
hybridization reaction conditions.
[0082] As used herein, "stringency" refers to the conditions of a
hybridization reaction that influence the degree to which
polynucleotides hybridize. Stringent conditions can be selected
that allow polynucleotide duplexes to be distinguished based on
their degree of mismatch. High stringency is correlated with a
lower probability for the formation of a duplex containing
mismatched bases. Thus, the higher the stringency, the greater the
probability that two single-stranded polynucleotides, capable of
forming a mismatched duplex, will remain single-stranded.
Conversely, at lower stringency, the probability of formation of a
mismatched duplex is increased.
[0083] The appropriate stringency that will allow selection of a
perfectly-matched duplex, compared to a duplex containing one or
more mismatches (or that will allow selection of a particular
mismatched duplex compared to a duplex with a higher degree of
mismatch) is generally determined empirically. Means for adjusting
the stringency of a hybridization reaction are well-known to those
of skill in the art.
[0084] A "ligand" is a molecule that is recognized by a particular
receptor. Examples of ligands that can be investigated by this
invention include, but are not restricted to, agonists and
antagonists for cell membrane receptors, toxins and venoms, viral
epitopes, hormones, hormone receptors, peptides, enzymes, enzyme
substrates, cofactors, drugs (e.g. opiates, steroids, etc.),
lectins, sugars, polynucleotides, nucleic acids, oligosaccharides,
proteins, and monoclonal antibodies.
[0085] A "receptor" is molecule that has an affinity for a given
ligand. Receptors may-be naturally-occurring or manmade molecules.
Also, they can be employed in their unaltered state or as
aggregates with other species. Receptors may be attached,
covalently or noncovalently, to a binding member, either directly
or via a specific binding substance. Examples of receptors which
can be employed by this invention include, but are not restricted
to, antibodies, cell membrane receptors, monoclonal antibodies and
antisera reactive with specific antigenic determinants (such as on
viruses, cells or other materials), drugs, polynucleotides, nucleic
acids, peptides, cofactors, lectins, sugars, polysaccharides,
cells, cellular membranes, and organelles. Receptors are sometimes
referred to in the art as anti-ligands. As the term receptors is
used herein, no difference in meaning is intended. A "Ligand
Receptor Pair" is formed when two macromolecules have combined
through molecular recognition to form a complex. Other examples of
receptors which can be investigated by this invention include but
are not restricted to:
[0086] a) Microorganism receptors: Determination of ligands which
bind to receptors, such as specific transport proteins or enzymes
essential to survival of microorganisms, is useful in developing a
new class of antibiotics. Of particular value would be antibiotics
against opportunistic fungi, protozoa, and those bacteria resistant
to the antibiotics in current use.
[0087] b) Enzymes: For instance, one type of receptor is the
binding site of enzymes such as the enzymes responsible for
cleaving neurotransmitters; determination of ligands which bind to
certain receptors to modulate the action of the enzymes which
cleave the different neurotransmitters is useful in the development
of drugs which can be used in the treatment of disorders of
neurotransmission.
[0088] c) Antibodies: For instance, the invention may be useful in
investigating the ligand-binding site on the antibody molecule
which combines with the epitope of an antigen of interest;
determining a sequence that mimics an antigenic epitope may lead to
the development of vaccines of which the immunogen is based on one
or more of such sequences or lead to the development of related
diagnostic agents or compounds useful in therapeutic treatments
such as for auto-immune diseases (e.g., by blocking the binding of
the "anti-self" antibodies).
[0089] d) Nucleic Acids: Sequences of nucleic acids may be
synthesized to establish DNA or RNA binding sequences.
[0090] e) Catalytic Polypeptides: Polymers, preferably
polypeptides, which are capable of promoting a chemical reaction
involving the conversion of one or more reactants to one or more
products. Such polypeptides generally include a binding site
specific for at least one reactant or reaction intermediate and an
active functionality proximate to the binding site, which
functionality is capable of chemically modifying the bound
reactant.
[0091] f) Hormone receptors: Examples of hormones receptors
include, e.g., the receptors for insulin and growth hormone.
Determination of the ligands which bind with high affinity to a
receptor is useful in the development of, for example, an oral
replacement of the daily injections which diabetics take to relieve
the symptoms of diabetes. Other examples are the vasoconstrictive
hormone receptors; determination of those ligands which bind to a
receptor may lead to the development of drugs to control blood
pressure.
[0092] g) Opiate receptors: Determination of ligands which bind to
the opiate receptors in the brain is useful in the development of
less-addictive replacements for morphine and related drugs.
[0093] The term "complementary" refers to the topological
compatibility or matching together of interacting surfaces of a
ligand molecule and its receptor. Thus, the receptor and its ligand
can be described as complementary, and furthermore, the contact
surface characteristics are complementary to each other.
[0094] A "scribe line" is typically an "inactive" area between the
active dies that provide area for separating the die (usually with
a saw). Often, metrology and alignment features populate this
area.
[0095] A "via" refers to a hole etched in the interlayer of a
dielectric which is then filled with an electrically conductive
material, preferably tungsten, to provide vertical electrical
connection between stacked up interconnect metal lines that are
capable of conducting electricity.
[0096] "Metal lines" within a die are interconnect lines. Metal
interconnect lines do not typically cross the scribe line boundary
to electrically connect two dies or, as in the some embodiments of
this invention, a multitude of die to one or more wafer pads.
[0097] The term "oxidation" means losing electron to oxidize. The
term "reduction" means gaining electrons to reduce. The term "redox
reaction" refers to any chemical reaction which involves oxidation
and reduction.
[0098] The term "wafer" means a semiconductor substrate. A wafer
could be fashioned into various sizes and shapes. It could be used
as a substrate for a microchip. The substrate could be overlaid or
embedded with circuitry, for example, a pad, via, an interconnect
or a scribe line. The circuitry of the wafer could also serve
several purpose, for example, as microprocessors, memory storage,
and/or communication capabilities. The circuitry can be controlled
by the microprocessor on the wafer itself or controlled by a device
external to the wafer.
[0099] The term "molecular binding event" means the occurrence of
contact between a probe molecule and a target molecule. The devices
for detecting a molecular binding event according to the
embodiments of the present invention are intended for use in a
molecular recognition-based assay for the analysis of a sample
suspected of containing one or more target molecules or moieties
such as specific nucleic acid sequences. The probe molecules of the
array are provided for the purpose of binding and detecting
specific target molecules, e.g., nucleic acid sequences. The
hybridization between the probe and target nucleic acid sequences
may occur through the standard Watson-Crick hydrogen-bonding
interactions or other known specific binding interactions known in
the art.
[0100] The term "polarization change" means a change in the amount
of charge on an electrode produced by the deposition of a target
molecule.
[0101] The term "differential amplifier" means a device that
amplifies the difference between two input signals (-) and (+).
This amplifier is also referred to as a differential-input
single-ended output amplifier. It is a precision voltage difference
amplifier, and could form the central basis of more sophisticated
instrumentation amplifier circuits.
[0102] The term "field effect transistor" (FET) is a family of
transistors that rely on an electric field to control the
conductivity of a "channel" in a semiconductor material. FETs, like
all transistors, can be thought of as voltage-controlled resistors.
Most FETs are made using conventional bulk semiconductor processing
techniques, using the single-crystal semiconductor wafer as the
active region, or channel.
[0103] The term "CMOS" means complementary metal oxide
semiconductor.
[0104] An embodiment for detecting the concentration of an analyte
includes exposing a surface to an analyte, detecting a change in
capacitance on a surface of the substrate as a function of time,
and correlating the change in capacitance as a function of time
with a concentration of the analyte.
[0105] The capacitance change may be measured utilizing an
integrating charge amplifier. The capacitance change may be caused
by DNA hybridization, peptide/protein binding, peptide
phosphorylation, or aptamer/protein binding.
[0106] The analyte may be in a conductive solution, for example an
aqueous solution or conductive gel. Preferably, the surface is an
electrode surface. Preferably, the electrode is part of an array of
electrodes fabricated on a single substrate.
[0107] An embodiment of a device for detecting the concentration of
an analyte includes a surface, a detector configured to detect
changes in capacitance on the surface, a clock configured to keep
track of the time as changes in capacitance on the surface occur,
and a processor configured to correlate the change in capacitance
on the surface with the concentration of the analyte.
[0108] An embodiment of a method of detecting a binding
characteristic of an analyte to a surface includes exposing a
functionalized surface to an analyte, detecting a change in
capacitance on the surface as the analyte binds to the surface,
heating the surface and detecting the change in capacitance on the
heated surface, and correlating the capacitance change on the
heated surface with a binding characteristic of the analyte.
[0109] Preferably, the binding characteristic is the match quality
of the analyte and a probe molecule attached to the surface. The
probe may be a DNA molecule.
[0110] An embodiment of a device configured to detect an analyte
binding to a surface may include a substrate; a functionalized
surface configured to bind to selected analytes; a heater
configured to heat the surface after one or more selected analytes
have bound to the surface; and a detector configured to detect
capacitance changes on the surface.
[0111] Described are methods for real-time detection of the binding
of analytes. The devices do not require tagging, such as
fluorescent tagging, in order to detect analytes. The methods are
also potentially more sensitive than many methods of detection,
which may reduce the need for amplification if DNA is being
detected. For example, experiments show charge detection with
.about.5 fF resolution. The devices and method also potentially
offer a much broader dynamic range of operation, potentially as
much as 7 orders of magnitude by precise control of manufacturing
and layout parameters (e.g. effective electrode area, amplifier
gain, affinity probe uniformity, etc).
[0112] The same devices can also be used to synthesis polymers,
particularly bio-polymers. The devices and methods offer
unprecedented capabilities for highly flexible polymer microarray
synthesis at micron and sub-micron scale with reproducibility
driven by CMOS manufacturing.
[0113] One embodiment is a method and apparatus for real-time
detection of the binding of analytes. More specifically, the
methods and apparatuses detect binding on an electrode surface or
to an affinity probe attached to an electrode surface on a CMOS
device. The device may be made in a standard or modified CMOS
process flow by one skilled in the art.
[0114] The device can be used to detect a wide variety of analyte
bindings to the electrode surface in many cases by attachment of an
appropriate affinity probe. Preferred bindings include, but are not
limited to, DNA hybridization, peptide/protein binding, peptide
phosphorylation, aptamer/protein binding and chemical bindings and
adsorption.
[0115] Preferred detection devices include those that can be
monolithically integrated with the synthesis devices, for example
field effect devices (direct and floating gate), impedance
spectroscopy devices, integrating charge amplifiers, and optical
devices capable of being integrated with electro-chemical synthesis
devices. More preferred devices include integrating charge
amplifiers.
[0116] One preferred embodiment of the integrating charge amplifier
design includes several components that can be implemented by one
skilled in the art in a traditional or modified CMOS
process/fabrication process. The first element is a drive circuit
that provides voltage pulses (can be a variety of waveforms:
square, sine, saw tooth, etc) to an exposed drive electrode (i.e.
accessible to the introduction of analyte, fluid, or gas). The
second is an integrating charge amplifier that has one input as an
exposed sensing electrode and the other as an exposed or unexposed
reference electrode.
[0117] The exposed reference electrode allows for common mode noise
rejection by inputting to one input of the amplifier a signal
representing the same environmental conditions (pH, temperature,
ion concentration, non-binding analytes, etc). Alternatively, the
reference capacitor can be exposed to air or covered to establish
an absolute reference. An example, of such an embodiment is
described below with respect to FIG. 5.
[0118] To the sense electrodes, affinity probes can be attached
through chemical methods. The reference electrode may or may not
have a similar or different affinity probe attached and each
sensing electrode can have a different affinity probe attached to
detect a variety of analytes (e.g. multiple genes in a sample). The
integrated charge value can be converted to a voltage through a two
stage amplifier. An internal (not exposed, monolithic NMOS or
Metal-Insulator-Metal) capacitor may be connected to the amplifier
via an internal switch to be used as a reference capacitor. These
elements provide the driving, sensing, and referencing capability
of the device. FIG. 1 shows these elements in each reference
configuration. In FIG. 1 shows an exposed electrode array including
large area drive electrodes and micron or sub-micron scale sense
and reference electrodes. The array can be of any density
manufacturable by standard semiconductor fabrication
techniques.
[0119] FIG. 2 shows a representation of sense and reference
electrodes coated with chemistries of attachment and attached DNA
probes (scales are not relative, .about.100,000 single strand DNA
oligonucleotides fit in a 1 um2 area. Also, probe length may vary,
with lengths between 24-mer and 60-mer preferred).
[0120] FIG. 3 shows a representation of attached single strand DNA
probe unhybridized and a double strand DNA representing a probe
that has found a complementary match from the sample solution and
hybridized.
[0121] A device including one or more integrating charge amplifiers
is preferably configured to measure the integrated charge and
effective capacitance at the analyte-electrode interface. A change
in integrated charge or effective capacitance can then be used to
ascertain whether the analytes have bound at the electrode surface
or to the affinity probe attached to the electrode surface. This
configuration need not be specific to any analyte but preferably
can be applied to all analytes.
[0122] When measuring the effective capacitance, preferably the
analyte is provided in a conductive solution that provides a
conductive path between the driving and integrating electrodes of
the amplifier, for example a conductive solution, such as liquid
aqueous solution, or a conductive gel. A preferred method of using
the device including one or more integrating charge amplifiers
includes providing a voltage pulse through the drive electrode to
the conductive matrix including the analyte. This pulse can be
applied to the matrix with respect to an integrating electrode and
the charge can be accumulated on the integrating electrode over a
fixed time.
[0123] The measured capacitance is established by the fixed sensing
electrode, the dielectric formed by the attachment chemistry,
attached probe, and bound analyte (if a match is found), and a
virtual parallel plate formed above the sense electrodes by the
charge/ion distribution in the matrix. The measured capacitance is
a function of the electrode area, the dielectric constant, and the
distance of the virtual plate from the sensing electrode. Analytes
binding to the electrode or attached affinity probe will change the
dielectric constant and/or distance between the virtual plate and
sense electrode, thereby changing the effective capacitance and
accumulated charge on the sense electrode when a voltage is
applied. The area and distance to the drive electrode are not
material since the conductive matrix carries the voltage to the
virtual plate. Any capacitance contributed by the drive electrode
is in series with the measured capacitance and is small owing to
the large electrode area.
[0124] To compensate for any noise at the time of the test (due to
1/f noise, thermal noise, etc.) a calibrating reference pulse is
preferably applied to an internal test capacitor to normalize the
response of the amplifier during each measurement cycle (this is
different from the reference electrode). The output of this
amplifier can then be digitized and post-processed. Post-processing
is an algorithm that is applied through software to remove random
noise, slopes, etc. The parameters can be determined experimentally
by characterizing the various contributing parameters: e.g
electrode size, drive voltage, environmental conditions such as
temperature, analyte binding concentration, etc.
[0125] Preferably, individually addressable sensing electrode
arrays of various effective areas are created to increase the
detection range of the amplifier to various concentrations of
target in the solution. A large array of driving electrodes can be
created to allow close coupling of driving voltage to the solution.
Since the drive electrode capacitance is in series with the sense
electrode interface+probe/target through the solution, preferably
the driving electrode area is larger than sensing electrode area to
reduce parasitic effects. A system comprised of a large capacitor
in series with a small capacitor is dominated by the small
capacitor. In this case: 1/C
series=1/Cintegrated+1/Cdrive->1/Cintegrated as Cdrive gets
large.
[0126] An array of integrating amplifiers and respective electrode
arrays are preferably fabricated on the same substrate. (also
synthesis and detection drive circuits, may also include logic for
switching, latches, memory, IO devices, and other device able to be
integrated in silicon)
[0127] For improved sensitivity, preferably a device that includes
one or more reference electrodes is used for differential
measurements. Reference and sensing electrode routing paths can be
matched in a layout pattern to reduce parasitic coupling.
[0128] Preferably, the measurement of the change in capacitance at
the sensing electrode is accomplished in one of two manners. First,
the change can be detected with respect to the exposed reference
capacitor. In this embodiment, the reference electrode is exposed
to the same solution as the sensing electrode. Preferably, a probe
that is designed to have similar electrical characteristics as the
affinity probed but not to bind to a target in the solution in
attached to the reference electrode. A change in integrated charge
is measured as binding occurs on the sensing electrode (or affinity
probe attached thereon) whose electrical characteristics change,
but not on the reference electrode whose electrical characteristic
remain the same. Second, two measurements of the same electrode,
before and after the analyte binds, can be compared to establish
the change in integrated charge resulting from binding. In this
case, the same electrode at a previous time provides the reference.
FIG. 4 shows an example of a device configured to operate in this
fashion. In FIG. 4 the dotted lines show resistance and capacitive
paths established by the conductive matrix and insulating affinity
probe/analyte layer on the electrode. This schematic shows the
device operation in differential detection mode, in which both
reference and sense electrode have attached affinity probes (of
different affinity) to reject common mode noise contributed by the
matrix and other parasitics and noise sources.
[0129] In an alternative configuration, the reference electrode can
be configured so that the sensing electrode takes direct
capacitance measurements (non-differential). In this configuration,
the reference electrode can be covered with a small dielectric
substance such as epoxy or the device passivation or left exposed
to air. The signal from the electrode can then be compared to an
open circuit which establishes an absolute reference for
measurement but may be more susceptible to noise. FIG. 5 shows an
example of a device in an absolute detection mode, in which the
reference is an unexposed (or exposed to a fix environment such as
air) fixed capacitor.
[0130] This device preferably provides real-time detection
capability. In more traditional approaches, all of the sample
analytes are tagged with an optical label (Cy dye, FITC, etc.). To
determine what has bound to the surface, the sample must be washed
off after a time to remove unbound analytes and their associated
labels. This wash stops all kinetics of the analytes and
electrode/probes. In this invention, analytes are not tagged and
detection is electrical, so washing is not needed to remove
unwanted signal. Therefore real-time monitoring of binding kinetics
can be accomplished by providing dynamic measurement at the
solid-solution interface by applying a pulse and integrating the
response at various times during the development of hybridization.
In other words, since no wash is required to remove the unbound but
labeled analytes, the invention can operate without the experiment
being halted with the wash.
[0131] Preferably, the device has a digital mode capability. For
example, a 1 bit latch can be provided on the chip device. The
response of the amplifier to a drive or reference pulse can then be
stored in this latch. For instance, the response can be above or
below the response of the reference electrode. By varying the value
of the drive or reference pulses and capturing the responses to
these pulses more than 1 bit resolution can be obtained. Parallel
operation of a large number of sensing nodes and amplifiers can be
done this way. Alternatively, an analog signal can be read out
directly or digitized through an internal or external analog to
digital converter.
[0132] FIG. 6 is a circuit schematic of a detection device showing
connection of the sense and reference electrode capacitors,
internal switches, etc.
[0133] FIG. 7 is a circuit schematic of the device showing
connection of the addressing circuits and attached amplifiers.
[0134] FIG. 8 is an image of a completed device prototype according
to the invention.
[0135] FIG. 9 is a graph showing how the device operates to detect
analyte binding. In FIG. 9 device measurement of integrated charge
on two electrode: the first (red) with attached affinity probe only
and the second (green) with analyte bound to attached affinity
probe. In this experiment, the affinity probe and analyte are
single strand oligonucleotides.
[0136] Another embodiment is a method and device for
electrochemically synthesize polymers. The electrodes may be the
same electrodes used to detect analyte bindings with circuitry to
connect them to either drive circuitry or the integrating charge
amplifiers.
[0137] Preferred polymers that are manufactured include, but are
not limited to, DNA oligonucleotides, peptides, and aptamers.
[0138] The electrodes may be made from a variety of materials
utilized in standard CMOS fabrication. Preferred electrode
materials include Ti, TiN, and Ta. Alternatively, materials that
are compatible with a CMOS fabrication process but not
traditionally used, such as Au and Pt, can be employed in this
invention.
[0139] During polymer synthesis, the electrodes are used to control
the acidic or basic region directly above them. For example, micron
and/or sub-micron exposed surface area, confinement electrodes of
opposite polarity or floating separate attachment electrodes that
may be grounded or floating. Having these drive voltage options
allows the user to optimize the chemistry for the synthesis
preferred. For example, the drive electrode can source the voltage
that creates the acid field, the floating electrode can be placed
so that the chemistry is optimal for synthesis, and the electrode
of opposite polarity can quench the acid or base to confine the
reaction to the desired area. One skilled in the art will
understand how to appropriately drive these electrodes to maximize
the electrochemical synthesis process. Preferably, the electrode on
which the polymer is synthesized is also the electrode connected
via circuitry to the integrating charge amplifier.
[0140] Preferably, large arrays of electrodes are arranged on a
substrate. The electrodes are preferably, in various arrangements
and sizes on the same substrate to enable a diversity of polymers
and multiplexing of individual electrodes to create polymers of
desired sizes and shapes.
[0141] Preferably, one or more distinct voltage pulses can be
applied to the each of the electrodes. This allows creation of an
active or group of active electrodes surrounded by an array of
confinement electrodes without addition of any other special
function electrodes. In other words, multiple electrodes can be
similarly driven to create larger regions of acid or base field.
Likewise, multiple electrodes can be used to form a common
attachment or quenching region.
[0142] FIG. 10 is an example of a device in electrochemical
synthesis of polymer affinity probe operation. The acid/base field
generated by the activated electrode deprotects an existing
attachment chemistry or polymer base allowing subsequent base
attachment. Note the acid/base field is free to diffuse across the
surface of the device when other electrodes are inactive. Also note
that the exposed electrodes can be the same as those used in the
detection operation.
[0143] FIG. 11 is an alternative configuration of a device in
electrochemical synthesis of polymer affinity probe operation. The
acid field generated by the activated electrode deprotects an
existing attachment chemistry or polymer base allowing subsequent
base attachment. Note the acid field confined in this mode of
operation when surrounding electrodes are activated to the opposite
polarity (or otherwise driven appropriately to quench the acid or
base field). Again note that the exposed electrodes can be the same
as those used in the detection operation.
[0144] In another embodiment, electrode can be used that have
arbitrary size and shape to define the chemistry. For example, a
confinement electrode can be a ring of metal around the drive
and/or floating electrode. FIG. 12 is an image of a synthesis
electrode pattern in which concentric rings are used to more
effectively confine the acid/base field. Again note that the
exposed electrodes can be the same as those used in the detection
operation. The electrode size and shape are immaterial.
[0145] Preferably, a set of two latches are provided at each active
electrode site to allow the electrode to exist in three states
driven by voltage 1, driven by voltage 2, or floated during the
synthesis cycle.
[0146] The voltage sources for the electrodes on the device can be
internally multiplexed from external sources through digital
control, and preferably can be applied in parallel to a large array
of electrodes.
[0147] In application, voltages are applied to a programmed
selection of electrodes as a solution of polymer base is flowed
over the electrodes. The applied voltage creates an acidic or basic
field that deprotects the polymer base so that it attaches to the
electrode surface, surface chemistry, or previous base. By flowing
different bases over the electrodes with the desired programmed
electrode activation, the polymer sequence is generated at each
electrode.
[0148] Yet another configuration is a method and device to
synthesize polymers and detect binding to the polymer on a common
integrated device surface. The device may be the same device used
to detect analyte bindings and synthesize polymers previously
described. The device is capable of carrying out on-chip
electrochemical polymerization reactions (functionalization) and
also on-chip label-free analyte detection.
[0149] Polymers that can be synthesized and detected utilizing the
devices and methods include, but are not limited to, DNA
oligonucleotides, peptides, and aptamers. Bindings include, but are
not limited to, DNA hybridization, peptide/protein binding, peptide
phosphorylation, and aptamer/protein binding. Detection devices
include those that can be integrated with the synthesis devices,
for example field effect devices (direct and floating gate),
impedance spectroscopy devices, integrating charge amplifiers, and
optical devices capable of being integrated with electro-chemical
synthesis devices. Preferred devices include devices that utilize
integrated charge amplifiers.
[0150] In one preferred configuration, the same CMOS circuitry that
enables the voltage outputs of the electrochemical synthesis
reactions above are designed to be easily re-programmed for
electrical detection. In particular, the sensing AND synthesis
electrodes can be individually addressed, and any electrode can
behave as detection, driving, active synthesis or shielding
electrode.
[0151] Preferably, the device includes one or more integrating
charge amplifiers and one or more electrodes capable of being
driven to a given voltage in a pulsed manner, or in any arbitrary
shape. Preferably, large arrays of electrodes of various sizes are
arranged on the same substrate.
[0152] Preferably, one or more voltage patterns can be applied to
the each of the electrodes. This allows creation of an active or
group of active electrodes surrounded by an array of shielding
electrodes without addition of any other special function
electrodes.
[0153] Preferably, a set of two latches are provided at each site
to allow the electrode to exist in the three states: driven by
voltage 1, driven by voltage 2, or floated during the synthesis
cycle.
[0154] Preferably, the voltage sources are internally multiplexed
from external sources through digital control, and can be applied
in parallel to a large array of electrodes. By modulating voltages
at electrodes on a case-by-case basis, synthesis chemistries can by
tailored to the particular requirements of each electrode.
[0155] The same CMOS circuitry and electrodes used for voltage
outputs of the electrochemical synthesis reactions can also be used
to detect bindings. Integrating charge amplifiers are preferably
utilized to measure the changes in charge and effective capacitance
at the analyte-electrode interface.
[0156] Preferably, a pulse of voltage is applied to the solution
with respect to an integrating electrode and the charge is
accumulated over a fixed time. A calibrating reference pulse can be
applied to the solution through an internal test capacitor to
normalize the response of the amplifier during each measurement
cycle.
[0157] Preferably, a two stage integrating charge amplifier to
convert the charge to a voltage.
[0158] Logic circuits can be used to digitize and post-process the
output of the two stage integrating amplifier. Post-processing
removes random noise, slopes, etc. These circuits can be on the
same chip or off chip.
[0159] Individually addressable sensing electrode arrays of various
effective areas can be used to increase detection range.
Preferably, a large array of driving electrodes is created to allow
close coupling of driving voltage to the solution. In addition,
preferably the driving electrode area is larger than sensing
electrode area to reduce parasitic effects.
[0160] In application, voltages are applied to a programmed
selection of electrodes as a solution of polymer base is flowed
over the electrodes. The applied voltage creates an acidic or basic
field that deprotects the polymer base so that it attaches to the
electrode surface, surface chemistry, or previous base. By flowing
different bases over the electrodes with the desired programmed
electrode activation, the polymer sequence is generated at each
electrode.
[0161] A sample solution can be applied to the electrode array with
polymers sequences attached. Where the analytes in the sample have
affinity with the attached polymer, they bind.
[0162] The detection circuits can used with the same electrodes as
described above to detect the change in capacitance of the
electrode interface. In this manner, an integrated
synthesis/detection device can use a common set of electrodes to
synthesize polymers and detect binding. This method offers
unprecedented capabilities for merging highly flexible polymer.
[0163] Real Time Polymerase Chain Reaction (PCR) Monitoring
[0164] Progress of DNA amplification during a Polymerase Chain
Reaction (PCR) can be monitored in "real time" by measuring
capacitance change at each feature location. Reaction rates can be
measured continuously, or determined at a fixed time point during
the exponential amplification phase. A computer can be used to
measure the rate of capacitance change of all simultaneous
experimental PCR reactions occurring on the detection chip. Unlike
ordinary preparative PCR, RT-PCR allows the success of multiple PCR
reaction to be determined automatically after only a few cycles,
without separate analysis of each reaction, and avoids the problem
of "false negatives".
[0165] PCR Assay Protocol
[0166] Typical PCR protocols can be followed. The number of copies
of total RNA used in the reaction are preferably enough to give a
signal by 25-30 cycles. The optimal concentrations of the reagents
are as follows: i. Magnesium chloride concentration should be
between 4 and 7 mM. ii. Concentrations of dNTPs should be balanced
with the exception of dUTP (if used). iv. The optimal probe
concentration is 50-200 nM, and the primer concentration is 100-900
nM. AmpErase uracil-N-glycosylase (UNG) is added in the reaction to
prevent the re-amplification of carry-over PCR products by removing
any uracil incorporated into amplicons. It is necessary to include
at least three No Amplification Controls (NAC, a minus-reverse
transcriptase control) as well as three No Template Controls (NTC,
a minus sample control) in each reaction plate (to achieve a 99.7%
confidence level in the definition of +/- thresholds for the target
amplification, six replicates of NTCs must be run). NAC is a mock
reverse transcription containing all the RT-PCR reagents, except
the reverse transcriptase; NTC includes all of the RT-PCR reagents
except the RNA template.
[0167] Electrochemical Biochip Design
[0168] To configure the chip for RT-PCR a set probes,
oligonucleotides or cDNA fragments, are selected and optimized from
target sequences based on the criteria of specificity of the
hybridization with the target sequence, uniform melting temperature
of the probes, and secondary structure stability. The following
strategies for efficient selection of probe sequences satisfying
these criteria are considered: 1) Removal of exactly repetitive
sequences: to efficiently find sequences appearing in more than one
open reading frame (ORF), and remove them from candidates for probe
sequences. 2) Minimization of frequency of occurrence: to estimate
the frequency of occurrence of a probe sequence based on the
frequency of occurrence of all k-tuples consisting of a probe
sequence. Only rarely occurring sequences are selected for probe
candidates. 3) Unifying melting temperature: to calculate the
melting temperature of matching probe. The filter classifies probe
sequences into fewest groups with a uniform melting temperature.
All DNA probes on a chip surface are subjected to the same
hybridization and wash conditions. Therefore, the uniform melting
temperature minimizes false-positive and/or false-negative signals,
making accurate target identification possible. 4) Filtering
secondary structure stability: to calculate the free energy of
optimal secondary structure of probe. Stable intra-strand secondary
structure of probe hinders rapid hybridization to a target
sequence, resulting in extensive decrease of the signal intensity.
This filter removes those unfavorable probe sequences. 5)
Minimization of Hamming distance: to calculate the minimum Hamming
distance between a probe sequence and a target sequence. It
examines the specificity of probe.
[0169] On-Chip PCR
[0170] As shown in FIG. 13, in contrast to conventional PCR, the
reaction is performed directly on chip and reaction products are
measured by capacitance change. The underlying principle of
sequence detection is based on the well-known process of
semi-nested PCR. On-chip PCR includes liquid phase PCR with two
sequence-specific primers, which is performed on the chip with
covalently bound nested, allele-specific PCR primers. PCR products
generated in the liquid phase are then re-amplified in a
semi-nested PCR directly on the chip surface. Thus in on-chip PCR
amplification and sequence detection are combined within a single
step. The oligonucleotide microarray is designed such that positive
signals reveal the presence and nature of the target DNA of
interest. On-chip PCR can be employed to identify single nucleotide
polymorphisms (SNPs) in human genomic DNA. On-chip PCR can be used
for detection and identification of pathogens. This has the
benefits of combining conventional PCR amplification with
microarray technology for the development of simple and rapid DNA
diagnostic systems.
Method and Apparatus for Match Quality Analysis of Analyte
Binding
[0171] The match quality of the binding between an analyte and a
probe attached to an electrode on the electrochemical synthesis
and/or detection chip can also be determined. Specifically, beyond
simply detecting the presence of a binding match, the
concentration, and percent specific vs nonspecific binding can be
determined.
[0172] The match quality can be determined utilizing the synthesis
and/or detection chips previously described in combination with one
or more of the following: 1) a clock--for precisely measuring time
intervals; 2) a thermometer--for precisely measuring the chip's
temperature; 3) a temperature regulator--for precisely heating
and/or cooling the chip to a desired temperature.
[0173] These technologies are preferably incorporated into the chip
itself, although they also may be incorporated into the chip's
package and/or instruments associated with the chip to provide the
functionality. These technologies can be utilized to provide users
with the ability to more closely evaluate the qualities of
molecular interactions between analytes and probe molecules that
are attached to a chip's electrochemical detection (or
electrochemical synthesis/detection) electrode.
[0174] FIG. 14 shows an example of how match quality can be
determined. In FIG. 14 capacitance change as a function of DNA
binding to DNA that had been attached to an electrode on a chip
were recorded. In this experiment, polymers of DNA were manually
attached to the surface of the chip (probe DNA), and then either
fully complementary or one base-mismatched DNA was allowed to
specifically hybridize (bind) to the probe DNA. Changes in
capacitance at the electrode surface were measured once the binding
reaction was completed. Mismatched DNA exhibited less capacitance
change when binding to probe DNA than when binding to DNA that was
perfectly matched. Accordingly, the extent of the capacitance
change depended on the degree of match between the bound and probe
DNA.
[0175] The timing and extent of capacitance changes will also vary
with the concentration of the DNA molecule that is binding to probe
DNA. FIG. 15 depicts an example of how the timing and/or extent of
capacitance changes can vary depending on these factors. FIG. 15
shows a graph of timing and extent of capacitance change as a
function of the concentration of added DNA that is binding to probe
DNA attached to an electrode. In this example, "saturation
concentration" refers to the addition of sufficient DNA to the
system such that probe DNA is covers the electrode as much as can
be permitted. "Sub-saturating concentration" refers to the addition
of enough DNA that capacitance changes are measured, but are not as
great in magnitude as is observed with saturation. As shown in FIG.
15, the use of the precision clock can thus be utilized to
calibrate the rate of capacitance change observed with DNA binding
in order to infer the concentration of that DNA in a given
sample.
[0176] It is, however, possible for conditions to exist in which
the same capacitance changes are found for the binding of two
dissimilar types of DNA to probe DNA. FIG. 16 depicts an example of
one such set of conditions. In FIG. 16 capacitance change as a
function of the concentration and type of added DNA binding to
probe DNA are shown. As shown in FIG. 16, hybridization of
complimentary pairs at sub-saturating conditions and hybridization
of mismatched pairs at saturating concentrations may be produce the
same or similar capacitance changes.
[0177] The use of a thermostat and temperature controller can be
utilized to differentiate the binding of large amounts of weakly
binding DNA from the binding of sub-saturating amounts of strongly
binding DNA. Chip scale devices for controlling the temperature of
a chip are known. An example of one type of known chip-scale
thermoelectric temperature controller is shown in FIG. 17. FIG. 17
is an image of a known Peltier thermoelectric controller for
precisely controlling the temperature of a chip over time.
Information on this type of controller can be found at
www.peltier-info.com/info.html.
[0178] DNA-to-DNA binding (hybridization) result from hydrogen
bonding between the base components on two DNA strands. The
hydrogen bonding rules governing such base pairing are depicted in
FIG. 18 (abbreviations: [A], adenine; [T], thymine; [G], guanine;
[C], cytosine).
[0179] The strength of DNA hybridization is proportional to the
number and type of base pairing between the strands. Perfectly
matched base pairings (complementary hybridization) will be
stronger than mismatched DNA hybridization. The strength of this
binding can be tested by its resistance to breaking apart when
heated. Mismatched hybridized DNA pairs will break apart at a lower
temperature than perfectly complementary DNA pairs. Thus, the
temperature and/or rate of capacitance change as the chip is heated
can be calibrated to infer the presence and/or type of mismatched
DNA that is bound to probe DNA.
[0180] This heating method can also be used to determine if
mixtures of two or more different types of DNAs have hybridized to
probe DNA. FIG. 19 shows capacitance changes as a function of
heating of electrodes bearing different types of DNA hybridized to
probe DNA. Circled A and B refer to the lower and higher
temperatures at which mismatched and fully complementary DNAs,
respectively, "melt" free from their attachment to probe DNA. As
shown in FIG. 19, the capacitance changes detected on the electrode
will "step" as DNAs with different hydrogen bonding strengths
"melt" free from the probe DNA. In addition, the relative heights
of these steps can be calibrated to infer the proportion of the
relative amounts of the different DNAs that are bound to the probe
DNA.
[0181] The use of the invention to evaluate the molecular
interactions between DNA pairs is provided only as an example. The
same principles apply to the interactions between other types of
molecule, for example, but not limited to, the interactions of
proteins and nucleic acids, DNA and RNA, proteins and other
proteins, small molecules and proteins, oligosaccharides and
proteins, etc. Similarly, the sign (positive or negative), the
magnitude, and the timing of capacitance changes described here for
DNA/DNA interactions are provided only as examples. The actual
changes observed with interactions between other molecules are
anticipated to be different, but nonetheless will be measurable as
described.
[0182] This application discloses several numerical range
limitations that support any range within the disclosed numerical
ranges even though a precise range limitation is not stated
verbatim in the specification because the embodiments of the
invention could be practiced throughout the disclosed numerical
ranges. Finally, the entire disclosure of the patents and
publications referred in this application, if any, are hereby
incorporated herein in entirety by reference.
* * * * *
References