U.S. patent application number 14/256804 was filed with the patent office on 2014-10-09 for magnetic-nanoparticle conjugates and methods of use.
This patent application is currently assigned to The General Hospital Corporation. The applicant listed for this patent is The General Hospital Corporation. Invention is credited to Lee Josephson, J. Manuel Perez, Ralph Weissleder.
Application Number | 20140303022 14/256804 |
Document ID | / |
Family ID | 23141754 |
Filed Date | 2014-10-09 |
United States Patent
Application |
20140303022 |
Kind Code |
A1 |
Josephson; Lee ; et
al. |
October 9, 2014 |
Magnetic-nanoparticle conjugates and methods of use
Abstract
The present invention provides novel compositions of binding
moiety-nanoparticle conjugates, aggregates of these conjugates, and
novel methods of using these conjugates, and aggregates. The
nanoparticles in these conjugates can be magnetic metal oxides,
either monodisperse or polydisperse. Binding moieties can be, e.g.,
oligonucleotides, polypeptides, or polysaccharides. Oligonucleotide
sequences are linked to either non-polymer surface functionalized
metal oxides or with functionalized polymers associated with the
metal oxides. The novel compositions can be used in assays for
detecting target molecules, such as nucleic acids and proteins, in
vitro or as magnetic resonance (MR) contrast agents to detect
target molecules in living organisms.
Inventors: |
Josephson; Lee; (Reading,
MA) ; Weissleder; Ralph; (Peabody, MA) ;
Perez; J. Manuel; (Boston, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The General Hospital Corporation |
Boston |
MA |
US |
|
|
Assignee: |
The General Hospital
Corporation
Boston
MA
|
Family ID: |
23141754 |
Appl. No.: |
14/256804 |
Filed: |
April 18, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12772782 |
May 3, 2010 |
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14256804 |
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12194475 |
Aug 19, 2008 |
7829350 |
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12772782 |
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10165258 |
Jun 6, 2002 |
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12194475 |
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60296378 |
Jun 6, 2001 |
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Current U.S.
Class: |
506/9 ; 435/19;
435/23; 436/501; 436/94 |
Current CPC
Class: |
C07H 21/02 20130101;
C12Q 1/37 20130101; B82Y 5/00 20130101; C07F 15/02 20130101; Y10S
435/969 20130101; G01N 33/54326 20130101; Y10S 977/918 20130101;
C12Q 1/44 20130101; C12Q 1/6816 20130101; G01N 33/577 20130101;
Y10S 977/92 20130101; Y10T 436/143333 20150115; C07K 1/22 20130101;
Y10S 977/773 20130101; G01N 33/5434 20130101; G01N 33/54346
20130101; A61K 49/1851 20130101 |
Class at
Publication: |
506/9 ; 436/94;
435/23; 436/501; 435/19 |
International
Class: |
G01N 33/543 20060101
G01N033/543; C12Q 1/37 20060101 C12Q001/37; C12Q 1/44 20060101
C12Q001/44; C12Q 1/68 20060101 C12Q001/68 |
Claims
1.-10. (canceled)
11. A method for determining the presence of a target molecule in a
sample, the method comprising: (i) providing one or more aggregates
in a fluid, wherein the aggregates comprise (a) nanoparticles
comprising a magnetic metal oxide linked to a binding moiety, and
(b) an aggregation inducing molecule, wherein the binding moiety
comprises a cleavage site for the target molecule and specifically
binds to the aggregation inducing molecule, or wherein the
aggregation inducing molecule comprises a cleavage site for the
target molecule and specifically binds to the binding moiety; (ii)
following step (i), combining the fluid and the sample under
conditions that enable a target molecule in the sample to cleave
the cleavage site; and (iii) following step (ii), determining
whether a target molecule in the sample cleaved the cleavage site
by measuring the spin-spin (T2) relaxation time of the fluid,
wherein an increase in T2 relaxation times indicates the presence
of the target molecule in the sample.
12. The method of claim 11, wherein the target molecule is an
enzyme, and the binding moiety comprises a polypeptide that
contains the cleavage site.
13. The method of claim 12, wherein the binding moiety comprises a
polypeptide that contains the cleavage site and biotin, and the
aggregation inducing molecule comprises avidin.
14. The method of claim 11, wherein the target molecule is an
endonuclease, and the binding moiety and aggregation inducing
molecule are complementary single-stranded oligonucleotides that
hybridize to form a double-stranded nucleic acid comprising the
cleavage site selectively cleaved by the endonuclease.
15. The method of claim 11, wherein the binding moiety comprises
avidin and the aggregation inducing molecule comprises biotin and
the cleavage site.
16. The method of claim 15, wherein the aggregation inducing
molecule comprises an oligonucleotide with a biotin molecule at
each end, and the cleavage site is an internal site.
17. The method of claim 15, wherein the aggregation inducing
molecule comprises a polypeptide with a biotin molecule at each
end, and the cleavage site is an internal site.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation of U.S. patent
application Ser. No. 12/772,782, filed May 3, 2010, which is a
divisional of U.S. patent application Ser. No. 12/194,475, filed on
Aug. 19, 2008, which is a continuation of U.S. patent application
Ser. No. 10/165,258, filed on Jun. 6, 2002, which claims priority
to U.S. Provisional Patent Application Ser. No. 60/296,378, filed
on Jun. 6, 2001, the contents of each of which are incorporated
herein by reference in their entirety.
TECHNICAL FIELD
[0002] This invention relates to magnetic nanoparticle conjugates
and methods of use.
BACKGROUND
[0003] Magnetic particles are widely used reagents for the
purification and extraction of nucleic acids. For example, U.S.
Pat. Nos. 4,554,488 and 4,672,040 attach a nucleic acid to
silanized magnetic particles that are about one micron in diameter.
U.S. Pat. No. 5,898,071 utilizes one-micron silanized particles in
the presence of polyethylene glycol (PEG) to extract DNA. Similar
magnetic particles have been used to capture and release target
nucleic acid for the detection of specific sequences of DNA (see,
e.g., U.S. Pat. No. 5,750,338). Streptavidin has been attached to
magnetic particles and can be used to recover biotinylated nucleic
acids after sequence specific hybridization.
[0004] U.S. Pat. No. 5,512,439 describes attaching oligonucleotides
to 1-10 micron microspheres impregnated with iron oxide and using
the microspheres to bind to target nucleic acids, which can then be
separated from their surrounding media.
[0005] U.S. Pat. No. 6,027,945 describes the use of magnetic silica
particles having a diameter of 4-7 microns to extract and purify
nucleic acids including DNA fragments, plasmid DNA, and RNA.
[0006] U.S. Pat. No. 5,508,164 describes linking chromosomes to
silanized glass supports with disulfide crosslinking agents to link
to cell organelles. Cell organelles are then labeled and
biotinylated magnetic particles are used to magnetically recover
the particles after separation from the solid support using
reducing agents.
[0007] Preparations of magnetic particles designed for separation
and extraction use particles that are amenable to easy manipulation
by weak applied magnetic fields. These materials are typically
micron sized and have a high magnetic moment per particle; their
effects on water relaxation rate are unspecified and not relevant
to their application. Nanoparticles do not respond to the weak,
magnetic fields of hand held magnets.
[0008] Magnetic particles have also been used to assay for analytes
based on their ability to bind analytes and change magnetic
resonance (MR) relaxation rates. In U.S. Pat. No. 5,164,297, bovine
serum albumin (BSA) coated magnetic particles were used to react
with an antibody. Addition of BSA favors dissociation of the
complex between the antibody and the BSA-coated iron oxide
particles. As a result of this dissociation of aggregates, the
solvent T2 relaxation time decreased (1/T2 increased) and the BSA
concentration can be determined from T2.
[0009] In another example, WO 01/19405 describes the preparation
and uses of magnetic nanoparticles with various biomacromolecules
attached.
SUMMARY
[0010] The present invention provides new magnetic conjugates and
methods for their synthesis and use. Each conjugate comprises a
magnetic nanoparticle linked to a binding moiety that specifically
binds to a target in a sample, such as a nucleic acid or protein,
to another binding moiety on another conjugate, or to an
aggregation inducing molecule, such as avidin. The novel
compositions can be used in assays for detecting specific target
molecules, such as biological molecules in sample solutions, e.g.,
by altering the magnetic resonance (MR) relaxation rate of the
solution. Thus, the new conjugates can be considered to be magnetic
relaxation switches (MRS).
[0011] The biological target molecules can be nucleic acid
sequences (e.g., a sequence complementary to the binding moiety for
hybridization), protein sequences (e.g., an antibody binding site),
or polysaccharide sequences. Biological molecules are molecules of
biological origin or synthetically made molecules that mimic the
performance of biological molecules. Examples include, but are not
limited to, peptides with non-natural amino acids, peptide nucleic
acids (PNA's), or natural or man-made organic molecules that react
with specific sites on target biological molecules.
[0012] The assay method is accomplished by synthesizing a
population and, in some aspects of the invention, at least two
populations of the binding moiety-nanoparticle conjugates. Each
conjugate in a population has a plurality, e.g., two, three, four,
or more, of a single type of binding moiety attached to a
nanoparticle. The nanoparticle is composed of a magnetic metal
oxide and one or more functional groups, e.g., a polymer comprising
one or more functional groups. When polymers are included, they
contain functional groups that enable the binding moiety to be
attached to the nanoparticle to form the conjugate. The polymer can
be a natural polymer, a synthetic polymer, a combination of natural
and synthetic polymers, or derivatives of each type. The functional
groups can be carboxy, amino, or sulfhydryl groups. In some
embodiments, the binding moiety is attached to the nanoparticle
through disulfide groups. The metal oxides can also be associated
with non-polymer functional groups to form the nanoparticles.
[0013] In one aspect of the invention, a population of conjugates
(or a mixture of two or more populations of conjugates with
differing binding moieties directed to the same target molecule or
type of target molecule) is placed into a sample solution. If the
sample solution contains a target molecule to which the binding
moieties specifically bind, the binding moieties interact with and
bind to the target resulting in the formation (self-assembly) of
aggregates, which are groups of 2 to about 20 conjugates bound
together via a target molecule, an aggregation inducing molecule,
or by their binding moieties. Thus, the dispersed state of the
conjugates switches to an aggregate state, which decreases T2
relaxation times. FIG. 1 depicts one embodiment of such an
interaction in which two conjugates, P1 and P2, combine to form an
aggregate of six conjugates.
[0014] In another aspect of the invention, small aggregates of
conjugates are prepared and then placed into a sample solution. In
this assay system, the binding moieties when bound together to form
the aggregates form a substrate that is cleaved by a specific
target molecule, such as an enzyme that cleaves a specific site
within a double-stranded nucleic acid formed by the hybridization
of two single-strand oligonucleotide binding moieties.
Alternatively, the binding moieties can be bound to an aggregation
inducing molecule to form the aggregate. If the sample solution
contains a target molecule, the substrate formed by the binding
moieties is cleaved, resulting in the dissolution of the
aggregates. Thus, the aggregate state switches to a dispersed
state, which increases T2 relaxation times.
[0015] In various specific embodiments, the magnetic metal oxide
contains superparamagnetic iron oxide crystals. The
superparamagnetic character of the iron oxide of the nanoparticle
makes it a potent enhancer of water relaxation rates, an
enhancement that is altered when a target molecule binds
specifically with a binding moiety of a conjugate to create an
aggregate. Aggregates exert sensitive and reversible effects on the
spin-spin relaxation of adjacent water protons upon hybridization
in fluid phase. As a consequence, the presence of the target
molecule interacting with the conjugate, in one embodiment,
decreases T2.
[0016] The assays can be run in a single tube or in an array
format, i.e., T2 can be determined for a single sample or for a
number of samples simultaneously. The assays can be performed in
fluid media that are optically transparent, optically translucent,
optically opaque, or in turbid solutions. The fluid can be water,
saline, buffered saline, or biological fluids, such as, but not
limited to, blood, cell and/or tissue homogenates, extracts,
suspensions, saliva, semen, milk, spinal fluid, and urine. Target
molecules include sequences of nucleic acids unique to specific
microorganisms such as viruses or bacteria or mRNA of specific
genes expressed in specific cells (see below). The methods can also
be used for genotyping DNA from humans or mammals.
[0017] In one embodiment, the invention features an aggregate
including a plurality of conjugates, wherein each conjugate
includes a magnetic nanoparticle linked to a binding moiety that
specifically binds to a target molecule, to another binding moiety,
or to an aggregation inducing molecule, and wherein each conjugate
within the aggregate is bound to at least one other conjugate in
the aggregate through their respective binding moieties. The
aggregates can include 2 to about 20 conjugates, and can have a
size of about 100 to 500 nm, e.g., 200, 300, or 400 nm.
[0018] The aggregates can also include a target molecule to which
at least two different binding moieties specifically bind. In
certain embodiments, the target molecule is a nucleic acid, and
each binding moiety includes one of two or more different
oligonucleotides, wherein each oligonucleotide is complementary to
a region on the target nucleic acid that is different than the
regions to which the other oligonucleotides are complementary. In
other embodiments, the target molecule can be a polypeptide, and
each binding moiety includes one of two or more different
antibodies, wherein each antibody specifically binds to a binding
site on the polypeptide that is different than the binding sites to
which the other antibodies bind.
[0019] The aggregates can further include an aggregation inducing
molecule, such as avidin or an antibody, wherein the binding
moieties each selectively bind to the aggregation inducing
molecule. For example, the binding moieties can include biotin.
[0020] In some embodiments, the binding moieties bind to each other
to form the aggregate. For example, each binding moiety can include
a cleavage site that is selectively cleaved by a target molecule,
and cleavage of the binding moiety results in separation of the
conjugates and dispersal of the aggregate. Alternatively, the
binding moieties can be polypeptides and the target molecule can be
an enzyme. In other examples, each binding moiety can bind to
another binding moiety to form a cleavage site that is selectively
cleaved by a target molecule, and cleavage of the binding moiety
results in dispersal of the aggregate. For example, each binding
moiety can include one of two complementary single-stranded
oligonucleotides that hybridize to form a double-stranded nucleic
acid comprising a cleavage site, and wherein the target molecule is
an endonuclease.
[0021] "Linked" means attached or bound by covalent bonds, or
non-covalent bonds, or other bonds, such as van der Waals
forces.
[0022] "Specifically binds" means that one molecule, such as a
binding moiety, e.g., an oligonucleotide or antibody, binds
preferentially to another molecule, such as a target molecule,
e.g., a nucleic acid or a protein, in the presence of other
molecules in a sample.
[0023] In another aspect, the invention features a composition
including a mixture of at least two populations of conjugates that
specifically bind to a target molecule, wherein each conjugate in
the first population comprises a nanoparticle including a magnetic
metal oxide (e.g., a superparamagnetic metal oxide) linked to a
plurality (e.g., two or three) of first binding moieties (e.g.,
oligonucleotides, polypeptides such as antibodies, and
polysaccharides) that bind to a first binding site on the target
molecule, and wherein each conjugate in the second population
comprises a nanoparticle comprising a magnetic metal oxide linked
to a plurality of second binding moieties that bind to a second
binding site on the target molecule.
[0024] These compositions can include conjugates that further
include functional groups that link the nanoparticles to the
binding moieties. The functional groups can be amino, carboxy, or
sulfhydryl groups. Alternatively, the conjugates can further
include a polymer associated with the nanoparticles, and wherein
the functional groups are bound to the polymer and to the binding
moieties. The polymers can be hydrophilic, a natural or synthetic
polymer, or a derivative of a natural or synthetic polymer.
Examples of polymers include dextran, carboxymethyl dextran,
reduced carboxymethyl dextran, crosslinked aminated dextran,
pullanan, polyethylene glycol, and silane. In some embodiments, the
binding moieties are attached to the functional groups through a
covalent bond or by a disulfide bond. For example, oligonucleotides
can be attached to the nanoparticles by a single covalent bond at
the 3' or 5' end of each oligonucleotide.
[0025] In these compositions, the magnetic metal oxide can have a
diameter between about 1 nm and about 25 nm, and the conjugate can
have a diameter between about 15 nm and 100 nm, e.g., between about
40 nm and about 60 nm. In addition, each conjugate in the
composition can have an R1 relaxivity between about 5 and 30
mM.sup.-1 sec.sup.-1 and an R2 relaxivity between about 15 and 100
mM.sup.-1 sec.sup.-1. In particular embodiments, the nanoparticle
is an amino-derivatized cross-linked iron oxide nanoparticle.
[0026] In another aspect, the invention features a conjugate
including a magnetic nanoparticle linked to a first binding moiety,
wherein the first binding moiety includes a cleavage site for a
target molecule and specifically binds to an aggregation inducing
molecule, forms a cleavage site for the target molecule when the
first binding moiety binds to a second binding moiety, or
specifically binds to an aggregation inducing molecule that
comprises a cleavage site. For example, the first binding moiety
can include a polypeptide that has the cleavage site, and the
target molecule can be an enzyme. Alternatively, the first binding
moiety can bind to the second binding moiety to form the cleavage
site that is selectively cleaved by a target molecule, wherein the
target molecule is an enzyme. For example, the first and second
binding moieties can be complementary single-stranded
oligonucleotides that hybridize to form a double-stranded nucleic
acid comprising the cleavage site, wherein the target molecule is
an endonuclease.
[0027] In another example, the first binding moiety includes a
polypeptide that contains the cleavage site and biotin, and the
aggregation inducing molecule is avidin, or the first binding
moiety includes avidin and the aggregation inducing molecule
includes biotin and the cleavage site. The aggregation inducing
molecule can also be an oligonucleotide with a biotin molecule at
each end, wherein the cleavage site is an internal site, e.g., a
site that is not at either end of the oligonucleotide. The
aggregation inducing molecule can also include a polypeptide with a
biotin molecule at each end, where the cleavage site is an internal
site.
[0028] In another aspect, the invention features a method for
determining the presence of a target molecule in a sample, by
obtaining a mixture of at least two populations of conjugates that
specifically bind to the target molecule to form an aggregate,
wherein each conjugate in the first population includes a
nanoparticle that includes a magnetic metal oxide linked to a
plurality of first binding moieties that bind to a first binding
site on the target molecule, and wherein each conjugate in the
second population includes a nanoparticle including a magnetic
metal oxide linked to a plurality of second binding moieties that
bind to a second binding site on the target molecule; contacting
the mixture with a fluid sample under conditions that enable the
first and second binding moieties to specifically bind to any
target molecules in the sample and form an aggregate of conjugates;
and determining the presence of an aggregate in the sample, wherein
the presence of the aggregate indicates the presence of the target
molecule.
[0029] In this method, the presence of an aggregate can be
determined by obtaining the relaxation properties of the fluid in
the sample, wherein a change in the relaxation properties of the
fluid indicates the presence of the target molecule. For example, a
decrease in spin-spin relaxation time (T2) indicates the presence
of the target molecule.
[0030] In certain embodiments, the target molecule is a nucleic
acid, the first binding moieties are first oligonucleotides that
are complementary to a first region of the target nucleic acid, and
the second binding moieties are second oligonucleotides that are
complementary to a second region of the target nucleic acid. In
other embodiments, the target molecule is a polypeptide, the first
binding moieties are first antibodies that specifically bind to a
first binding site of the target polypeptide, and the second
binding moieties are second antibodies that specifically bind to a
second binding site of the target polypeptide. For example, the
first and second antibodies can be monoclonal antibodies.
[0031] In another aspect, the invention features a method for
determining the presence of a target molecule in a sample, by
obtaining one or more populations of conjugates that are capable of
forming an aggregate, wherein each conjugate in a first population
includes a nanoparticle including a magnetic metal oxide linked to
a first binding moiety, wherein the first binding moiety includes a
cleavage site for the target molecule and specifically binds to an
aggregation inducing molecule, forms a cleavage site for the target
molecule when the first binding moiety binds to a second binding
moiety in a second population of conjugates, or specifically binds
to an aggregation inducing molecule that includes a cleavage site;
mixing the conjugates of the one or more populations in a fluid
under conditions that enable the binding moieties to specifically
bind to each other or to an aggregation inducing molecule to form
aggregates in the fluid; mixing the fluid containing the aggregates
with a fluid sample under conditions that enable any target
molecules in the sample to cleave the cleavage sites in the
aggregates; and determining the presence of aggregates in the
sample, wherein the absence of aggregates indicates the presence of
the target molecule.
[0032] In this method, the absence of aggregates can be determined
by obtaining the relaxation properties of the fluid in the sample,
wherein a change in the relaxation properties of the fluid
indicates the presence of the target molecule. For example, an
increase in spin-spin relaxation time (T2) indicates the presence
of the target molecule. In this method, the target molecule can be
an enzyme, and the first binding moiety can include a polypeptide
that contains the cleavage site. In addition, the binding moieties
can be a polypeptide that contains the cleavage site and biotin,
and the aggregation inducing molecule can be avidin. In some
embodiments, the target molecule is an endonuclease, and the first
and second binding moieties are complementary single-stranded
oligonucleotides that hybridize to form a double-stranded nucleic
acid comprising the cleavage site selectively cleaved by the
endonuclease. In other embodiments, the first binding moiety
includes avidin and the aggregation inducing molecule includes
biotin and the cleavage site. For example, the aggregation inducing
molecule can include an oligonucleotide or polypeptide with a
biotin molecule at each end, and the cleavage site is an internal
site.
[0033] In another aspect, the invention features a method for
determining the presence of a target molecule in a sample, by
obtaining first and second populations of
oligonucleotide-nanoparticle conjugates, wherein each conjugate in
the first population includes a nanoparticle having a magnetic
metal oxide associated with a polymer having functional groups; and
a plurality of first oligonucleotides attached to the functional
groups on the nanoparticle; and wherein each conjugate in the
second population includes a nanoparticle having a metal oxide
associated with a polymer having functional groups; and a plurality
of second oligonucleotides attached to the functional groups on the
nanoparticle; wherein the first and second oligonucleotides are
each complementary to first and second portions of the target
nucleic acid, and wherein the oligonucleotides in each population
are the same on each conjugate in the population and different than
the oligonucleotides on the conjugates in the other populations;
preparing a mixture of the first and second populations of
oligonucleotide-nanoparticle conjugates; obtaining a fluid sample;
contacting the mixture with the sample under conditions that enable
any target nucleic acid in the sample to hybridize to the first and
second oligonucleotides of both populations of conjugates; and
obtaining the relaxation properties of the fluid in the sample,
wherein a change in the relaxation properties of the fluid
indicates the presence of the target nucleic acid.
[0034] In other aspects, the invention includes assays for
determining aggregate formation in a fluid sample by adding a new
composition of the invention to the fluid sample under conditions
that enable aggregate formation; and measuring the relaxation
properties of the sample over time after addition of the
composition, wherein a decrease in spin-spin relaxation (T2)
indicates aggregate formation. In another version, the invention
includes assays for determining aggregate dispersal in a fluid
sample by adding an aggregate formed from the new conjugates to the
fluid sample under conditions that enable cleavage of the
aggregate; measuring the relaxation properties of the sample over
time after addition of the conjugate, wherein an increase in
spin-spin relaxation (T2) indicates aggregate dispersal.
[0035] In the new methods, the sample fluid can be optically
transparent, optically translucent, optically turbid, or optically
opaque. The fluid can be water, saline, buffered saline, or a
biological fluid. The biological fluid can be blood, a cell
homogenate, a tissue homogenate, a cell extract, a tissue extract,
a cell suspension, a tissue suspension, milk, urine, saliva, semen,
or spinal fluid.
[0036] In these methods, the amount of change in the relaxation
properties can indicate a concentration of target molecules in the
sample.
[0037] In another aspect, the invention features a method for
purifying a target molecule (such as a nucleic acid or polypeptide)
from a sample by obtaining a conjugate including a nanoparticle
having a magnetic metal oxide linked by a cleavable bond (e.g., a
reducible disulfide bond) to a binding moiety that specifically
binds to a binding site on the target molecule; obtaining a sample
containing the target molecule in a fluid; mixing the conjugates
with the sample under conditions sufficient to enable target
molecules in the sample to bind to the binding moiety on the
conjugate to form target molecule-binding moiety complexes;
separating the conjugates from the sample; and cleaving the
cleavable bond to separate the target molecule-binding moiety
complexes from the conjugates, thereby purifying the target
molecules.
[0038] In the methods for the extraction and purification of
nucleic acids or materials hybridizing to nucleic acids. The
conjugates can be oligonucleotide-nanoparticle conjugates having a
reducible disulfide bond to couple the oligonucleotides to the
nanoparticles, and as a result reducing agents can separate the
oligonucleotides from the nanoparticles at a desired time.
Materials bound to the oligonucleotide portion of these
oligonucleotide nanoparticle conjugates, such as double-stranded
nucleic acids, can be obtained by the use of reducing agents rather
than by use of the high ionic strength, chaotropic agents, or
extremes of pH, that are required in previously known methods.
[0039] The invention also includes an assay for simultaneously
determining the presence of a target nucleic acid in a plurality of
samples, by obtaining first and second populations of
oligonucleotide-nanoparticle conjugates, wherein each conjugate in
the first population includes a nanoparticle having a magnetic
metal oxide associated with a polymer having functional groups; and
a plurality of first oligonucleotides attached to the functional
groups on the nanoparticle, and wherein each conjugate in the
second population includes a nanoparticle having a metal oxide
associated with a polymer having functional groups; and a plurality
of second oligonucleotides attached to the functional groups on the
nanoparticle; wherein the first and second oligonucleotides are
each complementary to first and second portions of the target
nucleic acid, and wherein the oligonucleotides in each population
are the same on each conjugate in the population and different than
the oligonucleotides on the conjugates in the other populations;
preparing a mixture of the first and second populations of
oligonucleotide-nanoparticle conjugates; obtaining a plurality of
fluid samples; contacting a portion of the mixture with each of the
plurality of samples under conditions that enable any target
nucleic acid in the samples to hybridize to the first and second
oligonucleotides of both populations of
oligonucleotide-nanoparticle conjugates; and simultaneously
obtaining the relaxation properties of the fluid in each of the
plurality of samples, wherein a change in the relaxation properties
of a sample indicates the presence of the target nucleic acid in
that sample.
[0040] In this method, the amount of change in the relaxation
properties of a sample can indicate a concentration of target
nucleic acid in that sample.
[0041] The invention also features a method for determining the
presence of a target molecule in a subject by administering to the
subject at least one population of conjugates, wherein each
conjugate includes a nanoparticle having a magnetic metal oxide
linked to a binding moiety that specifically binds to the target
molecule; providing sufficient time for the binding moieties to
bind to target molecules in the subject; and generating a magnetic
resonance (MR) image of the subject, wherein a signal in the image
indicates the presence of a target molecule. For example, the
target molecule can be a nucleic acid or protein, and the binding
moiety can be an oligonucleotide that is complementary or an
antibody that specifically binds to a portion of the target nucleic
acid. In one embodiment, at least two populations of conjugates are
administered to the subject, wherein the binding moieties on the
conjugates in each population are identical within the population
and different from the binding moieties on the conjugates in other
populations; and wherein the binding moieties in different
populations of conjugates specifically bind to different portions
of the target molecule.
[0042] In another aspect, the invention features a method for
determining the levels of mRNA in cells using a mixture of
populations of superparamagnetic oligonucleotide-iron oxide
nanoparticle conjugates and MR imaging. When the conjugates react
with a target, e.g., mRNA, the relaxation rate of the solvent
changes. Hence, the level of an mRNA in a sample can be determined
from measurements of spin-spin or spin-lattice relaxation times of
water. In another embodiment, a detector is used that can
simultaneously measure the relaxation properties of many spatially
separated samples simultaneously, e.g., in an array format. In yet
another embodiment, the invention features a method in which the
oligonucleotide-nanoparticle conjugates and an MR detector are used
to determine the pattern of gene expression in an organism.
[0043] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, suitable methods and materials are described below. All
publications, patent applications, patents, and other references
mentioned herein are incorporated by reference in their entirety.
In case of conflict, the present specification, including
definitions, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting.
[0044] Other features and advantages of the invention will be
apparent from the following detailed description, and from the
claims.
DESCRIPTION OF DRAWINGS
[0045] FIG. 1 is a schematic diagram showing a reaction scheme in
which alkanethiooligonucleotides were reacted with N-succinimidyl
3-(2-pyridyldithio) propionate (SPDP) activated nanoparticles to
form nanoparticle conjugates P1 and P2. P1 and P2 hybridize with
complementary oligonucleotides followed by aggregation and magnetic
relaxivity changes. Dithiothreitol (DTT) treatment breaks the bond
between nanoparticle and alkanethiooligonucleotide.
[0046] FIGS. 2A to 2D are images of test tubes illustrating the
effect of incubating oligonucleotide-nanoparticle conjugates with
oligonucleotides. From left to right, 2A: P1 and P2; 2B: P1, P2
plus complementary oligonucleotide; 2C: P1, P2 plus
half-complementary oligonucleotide; 2D: P1, P2 and
non-complementary oligonucleotide. The precipitate in the tube in
FIG. 2B was moved to the side with a hand held magnet as indicated
by two arrows.
[0047] FIGS. 3A and 3B are images of gel electrophoresis of a
P1/P2/oligonucleotide nanoparticle precipitate. FIG. 3A shows a gel
run in non-denaturing conditions. Lane 1: No DTT. Oligonucleotide
remains with P1/P2 at the top of the gel (arrow). Lane 2: With DTT.
A single band of double stranded oligonucleotide is seen. FIG. 3B
shows a gel run with denaturing conditions and with DTT. Two bands
are evident, the complementary oligonucleotide (slower band) and a
band of 5' and 3' alkanethioligonucleotides (faster band).
[0048] FIG. 4 is a graph illustrating the temporal change of water
T2 relaxation times with (square) and without complementary
oligonucleotide (diamond). The insert shows the effect of
increasing concentrations of complementary oligonucleotide on T2.
All data points shown represent the average of three measurements
with standard deviations ranging between 0.4-0.6 msec for T2 values
(too small to graph).
[0049] FIG. 5 is a graph illustrating the T2 changes of an aqueous
solution of P1/P2/complementary oligonucleotide as a function of
temperature cycling. T2 is different between two solutions of
P1/P2, one with complementary and without complementary
oligonucleotide. At 80.degree. C. there is no hybridization and a
very small difference in T2 values.
[0050] FIG. 6 is a graph showing T2 values of a turbid medium
(INTRALIPID.RTM.) after a complementary oligonucleotide is added to
an oligonucleotide nanoparticle conjugate mixture, P1 and P2. DTT
was added after 180 minutes.
[0051] FIG. 7 is an MR image showing the signal intensity of 24
wells of a 384 well microtiter plate. Wells had 3 or 6 Tg Fe/mL as
mixture of P1 and P2. Wells had the indicated amounts of either
complementary or noncomplementary oligonucleotide.
[0052] FIG. 8A is a graph depicting the specificity of magnetic
nanosensors. Temporal change of T2 relaxation times of P1-GFP and
P2-GFP with the addition of various target oligonucleotides
containing single nucleotide mismatches G, T, C. The perfect target
sequence is clearly distinguished from single nucleotide
mismatches. FIG. 8B is an MR image corresponding to the graph in
FIG. 8A acquired 2 hours after hybridization indicating that T2
relaxation time measurements correlate with the fluorescence
measurements
[0053] FIG. 9A is an image of a section of a 384 well plate
containing GFP-P1 and GFP-P2 with total RNA extracted from various
cell lines. FIG. 9B is an image of the nanoparticle conjugates with
lysed cells from WT or GFP+ human glioma lysate two hours following
hybridization. FIG. 9C is a graph illustrating GFP fluorescence and
T2 relaxation time measurements of GFP mRNA indicating that the two
measurements correlate well in whole cell lysate experiments
indicating that mRNA is readily detectable by MR imaging.
[0054] FIG. 10A is a graph illustrating the incubation of
anti-GFP-P1 nanoparticle conjugates with GFP or BSA protein
resulting in a significant decrease in T2. FIG. 10B is a graph
illustrating the incubation of an aggregate of conjugates, each
containing a DEVD peptide, with the enzyme caspase, which cleaves
the DVED peptide sequence resulting in a dissolution of the
conjugates, and an increase of T2 relaxation time.
[0055] FIG. 11 is a schematic image of a small aggregate held
together by double stranded oligonucleotide (P1/P2). Sequence
specific cleavage by BamHI results in separation of the particles
in the aggregate with a corresponding increase in T2 relaxation
times.
[0056] FIGS. 12A and 12B are atomic force micrographs, of the
conjugates of FIG. 11 before (aggregates of FIG. 12A) and after
(dispersed conjugates of FIG. 12B) addition of BamHI treatment.
DETAILED DESCRIPTION
[0057] The present invention provides compositions of conjugates
and aggregates of conjugates, and methods of making and using these
conjugates and aggregates. Each conjugate comprises one or more
binding moieties (e.g., an oligonucleotide, nucleic acid,
polypeptide, or polysaccharide) linked, e.g., covalently or
non-covalently, to a magnetic, e.g., superparamagnetic,
nanoparticle. The binding moiety causes a specific interaction with
a target molecule (or, in some embodiments, an aggregation inducing
molecule, such as avidin). Either, the binding moiety specifically
binds to a selected target molecule, which can be, for example, a
nucleic acid, polypeptide, or polysaccharide, or the binding moiety
can be designed to bind to another binding moiety to form a
substrate that is cleaved by the target molecule. Binding causes
aggregation of the conjugates, resulting in a decrease of the
spin-spin relaxation time (T2) of adjacent water protons in an
aqueous solution. Cleavage causes dispersal of the aggregate into
separate conjugates, resulting in an increase of the spin-spin
relaxation time (T2) of adjacent water protons in an aqueous
solution.
Nanoparticles
[0058] Nanoparticles can be monodisperse (a single crystal of a
magnetic material, e.g., metal oxide, such as superparamagnetic
iron oxide, per nanoparticle) or polydisperse (a plurality of
crystals, e.g., 2, 3, or 4, per nanoparticle). The magnetic metal
oxide can also comprise cobalt, magnesium, zinc, or mixtures of
these metals with iron. The term "magnetic" as used in this
specification and the accompanying claims means materials of high
positive magnetic susceptibility such as superparamagnetic
compounds and magnetite, gamma ferric oxide, or metallic iron.
Important features and elements of nanoparticles that are useful to
produce the new conjugates include: (i) a high relaxivity, i.e.,
strong effect on water relaxation, (ii) a functional group to which
the binding moiety can be covalently attached, (iii) a low
non-specific binding of interactive moieties to the nanoparticle,
and (iv) stability in solution, i.e., the nanoparticles do not
precipitate.
[0059] In all embodiments, the nanoparticles are attached (linked)
to the binding moieties via functional groups. In some embodiments,
the nanoparticles are associated with a polymer that includes the
functional groups, and also serves to keep the metal oxides
dispersed from each other. The polymer can be a synthetic polymer,
such as, but not limited to, polyethylene glycol or silane, natural
polymers, or derivatives of either synthetic or natural polymers or
a combination of these. Useful polymers are hydrophilic. In some
embodiments, the polymer "coating" is not a continuous film around
the magnetic metal oxide, but is a "mesh" or "cloud" of extended
polymer chains attached to and surrounding the metal oxide. The
polymer can comprise polysaccharides and derivatives, including
dextran, pullanan, carboxydextran, carboxmethyl dextran, and/or
reduced carboxymethyl dextran. The metal oxide can be a collection
of one or more crystals that contact each other, or that are
individually entrapped or surrounded by the polymer.
[0060] In other embodiments, the nanoparticles are associated with
non-polymeric functional group compositions. Methods are known to
synthesize stabilized, functionalized nanoparticles without
associated polymers, which are also within the scope of this
invention. Such methods are described, for example, in Halbreich et
al., Biochimie, 80 (5-6):379-90, 1998.
[0061] The nanoparticles have an overall size of less than about
1-100 nm. The metal oxides are crystals of about 1-25 nm, e.g.,
about 3-10 nm, or about 5 nm in diameter. The polymer component in
some embodiments can be in the form of a coating, e.g., about 5 to
20 nm thick or more. The overall size of the nanoparticles is about
15 to 200 nm, e.g., about 20 to 100 nm, about 40 to 60 nm; or about
50 nm.
[0062] The conjugates have high relaxivity owing to the
superparamagnetism of their iron or metal oxide. They have an R1
relaxivity between about 5 and 30 mM.sup.-1 sec.sup.-1, e.g., 10,
15, 20, or 25 mM.sup.-1 sec.sup.-1. They have an R2 relaxivity
between about 15 and 100 mM.sup.-1 sec.sup.-1, e.g., 25, 50, 75, or
90 mM.sup.-1 sec.sup.-1. They typically have a ratio of R2 to R1 of
between 1.5 and 4, e.g., 2, 2.5, or 3. They typically have an iron
oxide content that is greater than about 10% of the total mass of
the particle, e.g., greater than 15, 20, 25 or 30 percent.
[0063] Synthesis of Nanoparticles
[0064] There are varieties of ways that the nanoparticles can be
prepared, but in all methods, the result must be a nanoparticle
with functional groups that can be used to link the nanoparticle to
the binding moiety.
[0065] For example, oligonucleotide binding moieties can be linked
to the metal oxide through covalent attachment to a functionalized
polymer or to non-polymeric surface-functionalized metal oxides. In
the latter method, the nanoparticles can be synthesized according
to the method of Albrecht et al., Biochimie, 80 (5-6): 379-90,
1998. Dimercapto-succinic acid is coupled to the iron oxide and
provides a carboxyl functional group. By functionalized is meant
the presence of amino or carboxyl or other reactive groups (see,
Table 1, which is described in further detail below).
[0066] In another embodiment, oligonucleotides are attached to
magnetic nanoparticles via a functionalized polymer associated with
the metal oxide. In some embodiments, the polymer is hydrophilic.
In a specific embodiment, the conjugates are made using
oligonucleotides that have terminal amino, sulfhydryl, or phosphate
groups, and superparamagnetic iron oxide nanoparticles bearing
amino or carboxy groups on a hydrophilic polymer. There are several
methods for synthesizing carboxy and amino
derivatized-nanoparticles. Methods for synthesizing functionalized,
coated nanoparticles are discussed in further detail below.
[0067] Carboxy functionalized nanoparticles can be made, for
example, according to the method of Gorman (see WO 00/61191). In
this method, reduced carboxymethyl (CM) dextran is synthesized from
commercial dextran. The CM-dextran and iron salts are mixed
together and are then neutralized with ammonium hydroxide. The
resulting carboxy functionalized nanoparticles can be used for
coupling amino functionalized oligonucleotides, see Table 1.
[0068] Carboxy-functionalized nanoparticles can also be made from
polysaccharide coated nanoparticles by reaction with bromo or
chloroacetic acid in strong base to attach carboxyl groups. In
addition, carboxy-functionalized particles can be made from
amino-functionalized nanoparticles by converting amino to carboxy
groups by the use of reagents such as succinic anhydride or maleic
anhydride.
[0069] Nanoparticle size can be controlled by adjusting reaction
conditions, for example, by using low temperature during the
neutralization of iron salts with a base as described in U.S. Pat.
No. 5,262,176. Uniform particle size materials can also be made by
fractionating the particles using centrifugation, ultrafiltration,
or gel filtration, as described, for example in U.S. Pat. No.
5,492,814.
[0070] Nanoparticles can also be synthesized according to the
method of Molday (Molday, R. S. and D. MacKenzie, "Immunospecific
ferromagnetic iron-dextran reagents for the labeling and magnetic
separation of cells," J. Immunol. Methods, 1982, 52(3):353-67, and
treated with periodate to form aldehyde groups. The
aldehyde-containing nanoparticles can then be reacted with a
diamine (e.g., ethylene diamine or hexanediamine), which will form
a Schiff base, followed by reduction with sodium borohydride or
sodium cyanoborohydride.
[0071] Dextran-coated nanoparticles can be made and cross-linked
with epichlorohydrin. The addition of ammonia will react with epoxy
groups to generate amine groups, see Hogemann, D., et al.,
Improvement of MRI probes to allow efficient detection of gene
expression Bioconjug. Chem. 2000. 11(6):941-6, and Josephson et
al., "High-efficiency intracellular magnetic labeling with novel
superparamagnetic-Tat peptide conjugates," Bioconjug. Chem., 1999,
10(2):186-91. This material is known as cross-linked iron oxide or
"CLIO" and when functionalized with amine is referred to as
amine-CLIO or NH.sub.2-CLIO.
[0072] Carboxy-functionalized nanoparticles can be converted to
amino-functionalized magnetic particles by the use of water-soluble
carbodiimides and diamines such as ethylene diamine or hexane
diamine.
[0073] Avidin or streptavidin can be attached to nanoparticles for
use with a biotinylated binding moiety, such as an oligonucleotide
or polypeptide. See e.g., Shen et al., "Magnetically labeled
secretin retains receptor affinity to pancreas acinar cells,"
Bioconjug. Chem., 1996, 7(3):311-6. Similarly, biotin can be
attached to a nanoparticle for use with an avidin-labeled binding
moiety.
[0074] In all of these methods, low molecular weight compounds can
be separated from the nanoparticles by ultra-filtration, dialysis,
magnetic separation, or other means. The unreacted oligonucleotides
can be separated from the oligonucleotide-nanoparticle conjugates,
e.g., by magnetic separation or size exclusion chromatography.
Binding Moieties
[0075] The binding moiety is a molecule, synthetic or natural, that
specifically binds to, e.g., covalently or non-covalently binds to
or hybridizes with, a target molecule, or with another binding
moiety (or, in certain embodiments, with an aggregation inducing
molecule). For example, the binding moiety can be a synthetic
oligonucleotide that hybridizes to a specific complementary nucleic
acid target. The binding moiety can also be an antibody directed
toward an antigen or any protein-protein interaction. Also, the
binding moiety can be a polysaccharide that binds to a
corresponding target. In certain embodiments, the binding moieties
can be designed or selected to serve, when bound to another binding
moiety, as substrates for a target molecule such as enzyme in
solution.
[0076] Oligonucleotide Binding Moieties
[0077] In certain embodiments, the binding moieties are
oligonucleotides, attached to the nanoparticles using any one of a
variety of chemistries, by a single, e.g., covalent, bond, e.g., at
the 3' or 5' end to a functional group on the nanoparticle.
[0078] The new conjugates are useful in various types of MR
applications, including but not limited to, in vitro methods for
assaying the presence or concentration of nucleic acids, and in
vivo methods as MR imaging agents.
[0079] An oligonucleotide binding moiety of the invention can be
constructed using chemical synthesis. A double-stranded DNA binding
moiety can be constructed by enzymatic ligation reactions using
procedures known in the art. For example, a nucleic acid (e.g., an
oligonucleotide) can be chemically synthesized using naturally
occurring nucleotides or variously modified nucleotides designed to
increase the biological stability of the molecules or to increase
the physical stability of the duplex formed between the
complementary strands, e.g., phosphorothioate derivatives and
acridine substituted nucleotides can be used. The nucleic acid also
can be produced biologically using an expression vector into which
a nucleic acid has been subcloned.
[0080] One of the new in vitro assay methods uses at least two
populations of oligonucleotide magnetic nanoparticles, each with
strong effects on water relaxation (see Table 2). As the
oligonucleotide-nanoparticle conjugates react with a target
oligonucleotide, they form aggregates (100-500 nm; aggregates were
215 nm in size in Table 2). Upon prolonged standing, e.g.,
overnight at room temperature, the aggregates form large clusters
(micron-sized particles), which settle out of solution, see FIG.
2B. The invention uses magnetic resonance to determine the
relaxation properties of the solvent, which are altered when the
mixture of magnetic oligonucleotide nanoparticles reacts with a
target nucleic acid to form aggregates.
[0081] A feature of the analytical method when using
oligonucleotide binding moieties is the need for a mixture of at
least two types of magnetic metal oxide nanoparticles, each with a
specific sequence of oligonucleotide, and each with more than one
copy of the oligonucleotide attached, e.g., covalently, per
nanoparticle. The assay protocol involves preparing a mixture of
populations of oligonucleotide-nanoparticle conjugates and reacting
the mixture with a target nucleic acid. Alternatively,
oligonucleotide-nanoparticle conjugates can be reacted with the
target in a sequential fashion. A second feature of the new
analytical method is the use of magnetic resonance to detect the
reaction of the oligonucleotide-nanoparticle conjugates with the
target nucleic acid. When a target is present, the dispersed
conjugates self-assemble to form small aggregates.
[0082] Synthesis of Oligonucleotides
[0083] The oligonucleotides used to make the conjugates are
preferably deoxyribonucleotides. Ribose-based oligonucleotides can
also be use used, provided care is taken to eliminate RNA digesting
enzymes. The oligonucleotide can be synthesized with a single
reactive group at the 3' or 5' end, as indicated in Table 1, by
methods known in the art. The reactive group at the 3' or 5' end
insures covalent attachment on one end of the oligonucleotide.
These can have 3' or 5' amino, phosphate, or sulfhydryl groups. One
useful method, as described in Example 2, includes the use of
5'-alkanethiol-oligonucleotide and 3'-alkanethiol-oligonucleotides.
Oligonucleotides can be obtained from numerous commercial sources.
Alternatively, oligonucleotides with biotin attached at the 3' or
5' end can be synthesized by methods known in the art, and used in
conjunction with an avidin-bound nanoparticle.
[0084] Polypeptide Binding Moieties
[0085] In certain embodiments, the binding moiety is a polypeptide
(i.e., a protein, polypeptide, or peptide), attached, using any of
a variety of chemistries, by a single covalent bond in such a
manner so as to not affect the biological activity of the
polypeptide. In one embodiment, attachment is done through the
thiol group of single reactive cysteine residue so placed that its
modification does not affect the biological activity of the
polypeptide. In this regard the use of linear polypeptides, with
cysteine at the C-terminal or N-terminal end, provides a single
thiol in a manner similar to which alkanethiol supplies a thiol
group at the 3' or 5' end of an oligonucleotide. Similar
bifunctional conjugation reagents, such as SPDP and reacting with
the amino group of the nanoparticle and thiol group of the
polypeptide, can be used with any thiol bearing binding moiety. The
types of polypeptides used as binding moieties can be antibodies,
antibody fragments, and natural and synthetic polypeptide
sequences. In all embodiments, these peptide binding moieties must
have a binding partner, a molecule to which they selectively
bind.
[0086] Use of peptides as binding moieties offers several
advantages: First, the mass per binding site is low. For example,
up to twenty 2 kDa peptides can be attached to a nanoparticle,
calculated assuming 2064 iron atoms per nanoparticle. With larger
binding moieties like proteins (generally greater than about 30
kDa) the same mass of attached polypeptide results in only
approximately 1-4 binding moieties per nanoparticle. Second,
polypeptides can be engineered to have uniquely reactive residues,
distal from the residues required for biological activity, for
attachment to the nanoparticle. The reactive residue can be a
cysteine thiol, an N-terminal amino group, a C-terminal carboxyl
group or a carboxyl group of aspartate or glutamate, etc. A single
reactive residue on the peptide is used to insure a unique site of
attachment. These design principles can be followed with chemically
synthesized peptides or biologically produced polypeptides.
[0087] The binding moieties can also contain amino acid sequences
from naturally occurring (wild-type) polypeptides or proteins. For
example, the natural polypeptide may be a hormone, (e.g., a
cytokine, a growth factor), a serum protein, a viral protein (e.g.,
hemagglutinin), an extracellular matrix protein, a lectin, or an
ectodomain of a cell surface protein. In each case, the resulting
binding moiety-nanoparticle is used to measure the presence of
analytes in a test media reacting with the binding moiety.
[0088] Examples of protein hormones include: platelet-derived
growth factor (PDGF) which binds the PDGF receptor; insulin-like
growth factor-I and -II (Igf) which binds the Igf receptor; nerve
growth factor (NGF) which binds the NGF receptor; fibroblast growth
factor (FGF) which binds the FGF receptor (e.g., aFGF and bFGF);
epidermal growth factor (EGF) which binds the EGF receptor;
transforming growth factor (TGF, e.g., TGF-.alpha. and TGF-.beta.)
which bind the TGF receptor; erythropoietin, which binds the
erythropoitin receptor; growth hormone (e.g., human growth hormone)
which binds the growth hormone receptor; and proinsulin, insulin,
A-chain insulin, and B-chain insulin, which all bind to the insulin
receptor.
[0089] Receptor binding moieties are useful for detecting and
imaging receptor clustering on the surface of a cell.
[0090] Useful ectodomains include those of the Notch protein, Delta
protein, integrins, cadherins, and other cell adhesion
molecules.
[0091] Polypeptide Synthesis
[0092] Methods for synthesizing polypeptides in solution are well
established in the field. Solid-phase peptide synthesis (SPPS) can
be used effectively to produce peptides and small proteins of
specific sequences for use in the present invention.
[0093] The concept of the solid-phase approach involves covalent
attachment (anchoring) of the growing peptide chain to an insoluble
polymeric support (resin carrier), so that unreacted soluble
reagents can be removed by simple filtration and washing without
manipulative losses. Subsequently, the insoluble peptide-resin is
extended by a series of additional cycles, which are required to
proceed with high yields and fidelities. Excess soluble reagents
are used to drive reactions to completion. Because of the speed and
simplicity of the repeated steps, the major portion of the
solid-phase procedure is amenable to automation. Once chain
elaboration has been accomplished, it is necessary to release
(cleave) the crude peptide from the support under conditions that
are minimally destructive towards sensitive residues in the
sequence.
[0094] Antibody Binding Moieties
[0095] Other polypeptide binding moieties include immunoglobulin
binding moieties that include at least one immunoglobulin domain,
and typically at least two such domains. An "immunoglobulin domain"
refers to a domain of a antibody molecule, e.g., a variable or
constant domain. An "immunoglobulin superfamily domain" refers to a
domain that has a three-dimensional structure related to an
immunoglobulin domain, but is from a non-immunoglobulin molecule.
Immunoglobulin domains and immunoglobulin superfamily domains
typically include two .beta.-sheets formed of about seven
.beta.-strands, and a conserved disulphide bond (see, e.g.,
Williams and Barclay 1988 Ann. Rev Immunol. 6:381-405). Proteins
that include domains of the Ig superfamily domains include T cell
receptors, CD4, platelet derived growth factor receptor (PDGFR),
and intercellular adhesion molecule (ICAM).
[0096] One type of immunoglobulin binding moiety is an antibody.
The term "antibody," as used herein, refers to a full-length,
two-chain immunoglobulin molecule and an antigen-binding portion
and fragments thereof, including synthetic variants. A typical
antibody includes two heavy (H) chain variable regions (abbreviated
herein as VH), and two light (L) chain variable regions
(abbreviated herein as VL). The VH and VL regions can be further
subdivided into regions of hypervariability, termed
"complementarity determining regions" (CDR), interspersed with
regions that are more conserved, termed "framework regions" (FR).
The extent of the framework region and CDR's has been precisely
defined (see, Kabat, E. A., et al. (1991) Sequences of Proteins of
Immunological Interest, Fifth Edition, U.S. Department of Health
and Human Services, NIH Publication No. 91-3242, and Chothia, C. et
al. (1987) J. Mol. Biol. 196:901-917). Each VH and VL is composed
of three CDR's and four FRs, arranged from amino-terminus to
carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3,
CDR3, FR4.
[0097] An antibody can also include a constant region as part of a
light or heavy chain. Light chains can include a kappa or lambda
constant region gene at the COOH--terminus (termed CL). Heavy
chains can include, for example, a gamma constant region (IgG1,
IgG2, IgG3, IgG4; encoding about 330 amino acids). A gamma constant
region can include, e.g., CH1, CH2, and CH3. The term "full-length
antibody" refers to a protein that includes one polypeptide that
includes VL and CL, and a second polypeptide that includes VH, CH1,
CH2, and CH3.
[0098] The term "antigen-binding fragment" of an antibody, as used
herein, refers to one or more fragments of a full-length antibody
that retain the ability to specifically bind to a target.
[0099] Examples of antigen-binding fragments include, but are not
limited to: (i) a Fab fragment, a monovalent fragment consisting of
the VL, VH, CL and CH1 domains; (ii) a F(ab').sub.2 fragment, a
bivalent fragment comprising two Fab fragments linked by a
disulfide bridge at the hinge region; (iii) a Fd fragment
consisting of the VH and CH1 domains; (iv) a Fv fragment consisting
of the VL and VH domains of a single arm of an antibody, (v) a dAb
fragment (Ward et al., (1989) Nature 341:544-546), which consists
of a VH domain; and (vi) an isolated complementarity determining
region (CDR). Furthermore, although the two domains of the Fv
fragment, VL and VH, are coded for by separate genes, they can be
joined, using recombinant methods, by a synthetic linker that
enables them to be made as a single protein chain in which the VL
and VH regions pair to form monovalent molecules (known as single
chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426;
and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883).
Such single chain antibodies are also encompassed within the term
"antigen-binding fragment."
[0100] Antibody Production and Isolation
[0101] Typically, an immunoglobulin binding moiety is monospecific.
Monospecific antibodies can be obtained by cloning and expressing
antibody genes, e.g., from a monoclonal antibody cDNA. Also,
polyclonal antibodies can be generated by immunization of, e.g., a
horse, goat, rabbit, sheep, with an antigen. Production of
antibodies and antibody fragments is well documented in the field.
See, e.g., Harlow and Lane, 1988. Antibodies, A Laboratory Manual.
Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory. For
example, Jones et al., Nature 321: 522-525 (1986), which discloses
replacing the CDRs of a human antibody with those from a mouse
antibody. Marx, Science 229: 455-456 (1985), discusses chimeric
antibodies having mouse variable regions and human constant
regions. Rodwell, Nature 342: 99-100 (1989), discusses lower
molecular weight recognition elements derived from antibody CDR
information. Clackson, Br. J. Rheumatol. 3052: 36-39 (1991),
discusses genetically engineered monoclonal antibodies, including
Fv fragment derivatives, single chain antibodies, fusion proteins
chimeric antibodies and humanized rodent antibodies. Reichman et
al., Nature 332: 323-327 (1988) discloses a human antibody on which
rat hypervariable regions have been grafted. Verhoeyen, et al.,
Science 239: 1534-1536 (1988), teaches grafting of a mouse antigen
binding site onto a human antibody.
[0102] Polysaccharide Binding Moieties
[0103] In certain embodiments, the binding moiety is a
polysaccharide, linked, using any of a variety of chemistries, by a
single bond, e.g., a covalent bond, at one of the two ends, to a
functional group on the nanoparticle. The polysaccharides can be
synthetic or natural. Mono-, di-, tri- and polysaccharides can be
used as the binding moiety. These include, e.g., glycosides,
N-glycosylamines, O-acyl derivatives, O-methyl derivatives,
osazones, sugar alcohols, sugar acids, sugar phosphates when used
with appropriate attachment chemistry to the nanoparticle.
[0104] A generally useful method of accomplishing linking is to
couple avidin to a magnetic nanoparticle and react the
avidin-nanoparticle with commercially available biotinylated
polysaccharides, to yield polysaccharide-nanoparticle conjugates.
For example, sialyl Lewis based polysaccharides are commercially
available as biotinylated reagents and will react with avidin-CLIO
(see Syntesome, Gesellschaft fur medizinische Biochemie mbH.). The
sialyl Lewis.times.tetrasaccharide (Sle.sup.X) is recognized by
proteins known as selectins, which are present on the surfaces of
leukocytes and function as part of the inflammatory cascade for the
recruitment of leukocytes.
[0105] Still other targeting moieties include a non-proteinaceous
element, e.g., a glycosyl modification (such as a Lewis antigen) or
another non-proteinaceous organic molecule.
[0106] Polysaccharide Isolation
[0107] Bacterial membrane-attached polysaccharide can be purified,
for example, from the SKU 1100 strain by cell disruptions using
either ultrasonic treatment or lysozyme treatment, followed by
ultracentrifugation, enzyme treatments, dialysis against SDS,
DEAE-cellulose column chromatography, alcohol precipitation, and
gel filtration chromatography.
[0108] Polysaccharides can also be synthesized and are commercially
available.
Coupling of Binding Moieties to Nanoparticles to Prepare
Conjugates
[0109] The conjugates are prepared by linking two or more binding
moieties to each magnetic nanoparticle. A general procedure for
synthesizing amino-cross linked iron oxide nanoparticle begins with
the synthesis of a dextran coated superparamagnetic iron oxide.
There are a variety of satisfactory procedures which can employed
such as those in Weissleder "Monocrystalline iron oxide particles
for studying biological tissues" U.S. Pat. No. 5,492,814; Molday,
R. S. and D. MacKenzie, "Immunospecific ferromagnetic iron-dextran
reagents for the labeling and magnetic separation of cells," J.
Immunol. Methods, 1982, 52(3):353-67, Palmacci "Synthesis of
Polysaccharide Coated Superparamagnetic Oxide Colloids," U.S. Pat.
No. 5,262,176.
[0110] For example, a pure dextran coated superparamagnetic iron
oxide can be reacted with a crosslinking agent such as 5-50%
epichlorohydrin or epibromohydrin in strong base (final
concentration 1-3 M NaOH). After a sufficient time at room
temperature, liquid ammonia in excess is added to aminate the
polysaccharide. Low molecular weight impurities are removed, e.g.,
by centrifugation or exhaustive ultrafiltration using a membrane
with a 10 kDa cutoff.
[0111] Coupling of Oligonucleotides to Nanoparticles
[0112] The invention provides for preparing oligonucleotides with
reactive 3', 5', or both termini. One terminus is attached to the
surface of the nanoparticle, leaving the other terminus free for
attachment to another molecule, e.g., a biotin group or another
tag.
[0113] Table 1 provides a partial list of techniques and reagents
that can be used to couple oligonucleotides to amino- or
carboxy-functionalized nanoparticles. The general strategy is to
provide an oligonucleotide with a unique reactive group on the 3'
or 5' end. Exemplary groups include sulfhydryl, amino, and
phosphate groups. Oligonucleotides with sulfhydryl groups at the 3'
or 5' end are of particular value, and are commercially available.
They can be coupled to amino-nanoparticles through the use of
reagents such as N-succinimidyl 3-(2-pyridyldithio)propionate
(SPDP) and long chain SPDP (lc-SPDP) that produce a cleavable
disulfide bond between the nanoparticle and the oligonucleotide.
Amino-nanoparticles can also be reacted with reagents such as
succinimidyl-iodoacetate to produce non-cleavable bonds between the
nanoparticle and oligonucleotide.
TABLE-US-00001 TABLE 1 Functional Groups and Strategies for
coupling oligonucleotides to nanoparticles Oligonucleotide
Nanoparticle Coupling Terminal Group Functional Group Chemistry
Cleavable Sulfhydryl Amino SPDP, lc-SPDP Yes (lc, long chain)
Sulfhydryl Amino Succinimidyl- No iodoacetate Amino Carboxyl CDI No
(carbodiimide) Phosphate Amino CDI No Biotin Avidin Not applicable
Not applicable
[0114] Thus, nanoparticles can be conjugated to oligonucleotides
through a variety of conjugation chemistries. See U.S. Pat. No.
5,512,439; Greg Hermanson "Bioconjugate Techniques," Academic
Press, 1996; Gordon Bickerstaff "Immobilization of Enzymes and
Cells," Humana Press, 1997. If a colloid containing a variety of
sizes results, particles can be fractionated according to size,
e.g., by ultrafiltration.
[0115] Non-polymeric surface functionalized metal oxides are
coupled to oligonucleotides using coupling chemistries as shown,
for example, in Table 1.
[0116] In other embodiments, populations of nanoparticle conjugates
can be synthesized by allowing biotinylated oligonucleotides,
polypeptides, or polysaccharides, to react with avidin (or
streptavidin)-bound nanoparticles. Here a non-covalent, but tight,
bond between the biotinylated binding moiety, e.g.,
oligonucleotide, and avidin of the nanoparticle attaches the
oligonucleotide to the nanoparticle. Oligonucleotide-nanoparticle
conjugate populations prepared in this fashion are analogous to
those prepared with covalent chemistries (Table 1), and can be
reacted with target oligonucleotides. Specific binding ligand pairs
other than avidin-biotin are well known, and can also be used,
e.g., fluorescein and antibodies specific for fluorescein, peptide
hormones and their receptors, and steroids and their receptors, as
long as they do not interfere with the function of the binding
moieties.
[0117] An alternative protocol involves allowing two biotinylated
oligonucleotides to react with (e.g., hybridize to) a target
oligonucleotide. Following this reaction, a cross-linked iron oxide
(CLIO) particle linked to avidin or streptavidin is added. The
presence of the target nucleotide again results in the formation of
aggregates and changes in T2. In this case, two populations of
oligonucleotide-nanoparticle conjugates are formed when the
avidin-nanoparticle is reacted with two biotinylated
oligonucleotides. An advantage of this indirect capture method is
that the biotinylated oligonucleotides that react with a target
oligonucleotide are far smaller, and hence react faster, than
oligonucleotide-nanoparticle conjugates.
Biotinylated-oligonucleotides have molecular weights less than 50
kDa, while oligonucleotide-nanoparticle conjugates have molecular
weights greater than about 1000 kDa (e.g., 1000, 2000, 3500, 5000,
or more up to about 10,000 kD).
[0118] An alternative to the avidin-biotin system is the use of
two-dye labeled oligonucleotides, which hybridize to a target
oligonucleotide. An antibody to the dye coupled to a CLIO is then
added.
[0119] Coupling of Polypeptides and Antibodies to Nanoparticles
[0120] The invention provides for preparing polypeptides with
reactive 3', 5', or both termini. One end is linked to the surface
of the nanoparticle, leaving the other end free for attachment to
another molecule, e.g., a biotin group or another tag.
[0121] The conjugation of polypeptides to nanoparticles can be
accomplished by a large number of conjugation chemistries and
reagents some of which are also used for attaching oligonucleotides
to nanoparticles, see Table 1. A preferred general strategy is to
use one of the large number of bifunctional agents that can be
reacted first with the amino group of the nanoparticle, and
secondly with the thiol group of the polypeptide (or biomolecule).
Examples of such bifunctional reagents are SPDP, MBS, lc-SPDP and
SMCC and are available from companies, e.g., Pierce Chemical,
Molecular Probes or Molecular Biosciences. The bifunctional agent
is dissolved in DMSO and reacted in excess with the amino
functionalized nanoparticle at pH 8 using a non-amine containing
buffer (e.g., borate, phosphate). Unreacted bifunctional agent is
removed by dialysis, ultrafiltration, gel permeation chromatography
or by using magnetic filters. The sulfhydryl bearing polypeptide
(biomolecule) is then added and allowed to react. Unreacted
polypeptide can be removed by the separation methods above. For
details see Josephson et al, (1999) High-efficiency intracellular
magnetic labeling with novel superparamagnetic-Tat peptide
conjugates, Bioconjugate Chemistry, 10, 186-91; Perez et al. (2002)
DNA-based magnetic nanoparticle assembly acts as a magnetic
relaxation nanoswitch allowing screening of DNA-cleaving agents,
Journal of the American Chemical Society, 124, 2856-2857; Kang et
al. (2002) Magnetic Resonance Imaging of Inducible E-Selectin
Expression in Human Endothelial Cell Culture, Bioconjugate
Chemistry, 13, 122-127; Hoegemann et al, (2000) Improvement of MRI
Probes To Allow Efficient Detection of Gene Expression,
Bioconjugate Chemistry, 11, 941-946. Detailed protocols are also
available from the manufacturers.
[0122] In one embodiment, the conjugate can be synthesized by
allowing a biotinylated antibody or antibody fragment to react with
avidin (or streptavidin) nanoparticles. Here a non-covalent, but
tight, bond between the biotinylated antibody and avidin of the
nanoparticle attaches the antibody to the nanoparticle.
[0123] In another embodiment, a natural or synthetic polypeptide is
covalently or non-covalently attached to the nanoparticle while the
other terminal is biotinylated.
[0124] In one aspect of the invention, both ends of the polypeptide
are biotinylated and avidin is directly attached to the
nanoparticle.
[0125] In another embodiment, both termini of the peptide are
covalently or non-covalently attached to two nanoparticles.
[0126] Coupling of Polysaccharides to Nanoparticles
[0127] The invention provides for preparing polysaccharides with
reactive ends. One end is attached to the surface of the
nanoparticle, leaving the other end free for attachment to another
molecule. For example, as described above, the free end of the
polysaccharide can be biotinylated and aggregation can be induced
by exposure to avidin. Also, the polysaccharide can be biotinylated
on both termini and exposed to avidin linked to a nanoparticle.
Characterizing Conjugates
[0128] The conjugates can form several conformations, or "states,"
in solution. The first is the monodispersed conformation,
represented when a binding moiety of a conjugate has not reacted
with a target molecule. This conformation is approximately 4-100 nm
(e.g., 5, 10, 25, 40, 50, 75, or 90 nm) in size.
[0129] The second conformation is a small aggregate, which contains
2 to about 20 (e.g., 3, 5, 7, 10, 15, or 20) individual
nanoparticle conjugates held together by the interaction (e.g.,
binding) of the binding moiety with a target, or with another
binding moiety. The association of the nanoparticles is mediated by
the attached biomolecules and not by nanoparticle non-specific
attractions. This aggregate is approximately 100-500 nm (e.g., 200,
250, 300, or 400 nm) in size, is stable, and remains in solution.
The metal oxide, e.g., iron oxide, concentration used to form the
small aggregate is about 1-25, e.g., 5-20 .mu.g/ml. The small
aggregates do not settle out of solution and are "porous" in that
they do not sterically block large molecules (e.g., enzymes) from
entering the aggregate. The "pores" are really spaces or openings
between the binding moieties that combine to form the aggregates,
which can be envisioned as a three-dimensional lattice or mesh. The
size of the openings can be controlled by adjusting the size of the
nanoparticles and the size of the binding moieties on each
conjugate. The small aggregates are stable under a variety of
conditions, e.g., stable from 4.degree. C. to 80.degree. C., stable
in denaturants, stable in high salts, and is stable at a pH varying
from about 5.5 to 14.
[0130] The third conformation is the large aggregate cluster, which
is, in effect, an aggregate of aggregates. The cluster contains
greater than 20 nanoparticles and is greater than 500 nm in size.
The cluster is not useful since it typically clumps and falls out
of solution.
[0131] The nanoparticle conjugates can be used as magnetic
nanosensors or magnetic relaxation switches (MRS) in various
detection systems. For example, the new methods can utilize
detectors that measure the magnetic properties of the conjugates
and aggregates (e.g., magnetometers, oscillating magnetic field
readers, and superconducting quantum interference device (SQUID)
detectors). Other detection methods include magnetic force
microscopy or atomic force microscopy, flow cytometry,
centrifugation, light scattering, and size separation.
[0132] In magnetic resonance (MR) imaging applications, the novel
conjugates provide methods for the detection and a spatial
localization of specific sequences of target molecules, such as
nucleic acids, in living systems. This is based on the remarkable
ability of the magnetic conjugates to effect water relaxation in a
sequence specific manner even in media that will not permit assays
using light-based methods of gene detection (see Example 5). Hence,
the new conjugates can function as MR contrast agents for the
detection of target molecules, such as nucleic acids and
polypeptides in vivo.
[0133] The new conjugates are essentially nontoxic to mammalian
cells. In one embodiment, non-degradable oligonucleotide analogs
(e.g., peptide nucleic acid or PNA) may be coupled to nanoparticles
and used to image sequences of nucleic acids in vivo. Nontoxicity
is evident from the use of magnetic nanoparticles as the active
ingredient of COMBIDEX.RTM., a nanoparticle-based MR contrast
agent, which has been judged approvable by the FDA (January 1999).
COMBIDEX.RTM. is similar to MION (monodisperse iron oxide
nanospheres). MION is a starting material for aminated CLIO used in
one embodiment herein (see FIG. 1.). Thus, the new conjugates and
aggregates can be administered to a subject, e.g., a human or
animal, such as a mammal (e.g., dogs, cats, cows, pigs, and
horses). Various routes of administration can be used to achieve
systemic or local delivery. Because of the specific binding
characteristics
[0134] Oligonucleotide Conjugates
[0135] The starting material used in some of the examples described
herein consists of monodisperse or polydisperse, fluid-phase
nanoparticles containing superparamagnetic
Fe.sub.2O.sub.3/Fe.sub.3O.sub.4 (3-5 nm), caged by epichlorohydrin
cross-linked dextran, and functionalized with amine groups
(NH.sub.2-CLIO). Thiolated oligonucleotides were coupled to
NH.sub.2-CLIO using N-succinimidyl 3-(2-pyridyldithio)propionate
(SPDP) as a linker (FIG. 1). The physical properties of the
conjugates P1 (CLIO-SS-((CH.sub.2).sub.6-CGC-ATT-CAG-GAT) (SEQ ID
NO:1)) and P2 ((TCT-CAA-CTC-GTA-(SEQ ID
NO:2)(CH.sub.2).sub.3)-SS-CLIO) are summarized in Table 2. P1 and
P2 each had an average of 3 oligonucleotides per particle based on
a single crystal per particle and 2064 iron atoms per crystal (see
Shen reference above). They could be stored at room temperature or
4.degree. C. for several months without precipitation.
[0136] To effect maximum detection of target oligonucleotide
sequence, hybridization conditions are established by methods well
known in the art. Hybridization of the oligonucleotide-nanoparticle
conjugates to the target nucleic acids is typically performed under
moderate to high stringency conditions. The parameters of salt
concentration and temperature, which affect stringency of
hybridization, can be varied to achieve the optimal level of
identity between the base sequences of the
oligonucleotide-nanoparticle conjugates and those of the target
oligonucleotide or nucleic acid being detected. These techniques
and methods are well-known in the field. Additional guidance
regarding such conditions is available, for example, in Sambrook et
al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring
Harbor Press, N.Y.; and Ausubel et al. (eds.), 1995, Current
Protocols in Molecular Biology, (John Wiley & Sons, N.Y.) at
Unit 2.10.
[0137] For example, if stringent hybridization conditions are
desired, one can perform hybridization in 6.times. sodium
chloride/sodium citrate (SSC) at about 45.degree. C., followed by
one or more washes in 0.2.times.SSC, 0.1% SDS at 50.degree. C.
Another example of stringent hybridization conditions is
hybridization in 6.times.SSC at about 45.degree. C., followed by
one or more washes in 0.2.times.SSC, 0.1% SDS at 55.degree. C. A
further example of stringent hybridization conditions is
hybridization in 6.times.SSC at about 45.degree. C., followed by
one or more washes in 0.2.times.SSC, 0.1% SDS at 60.degree. C.
Other stringency conditions are 0.5M sodium phosphate, 7% SDS at
65.degree. C., followed by one or more washes at 0.2.times.SSC, 1%
SDS at 65.degree. C.
[0138] To demonstrate the ability of P1 and P2 to hybridize to a
target oligonucleotide, P1/P2 mixtures were incubated with a
complementary oligonucleotide. The samples became slightly turbid
within 3-4 hours at room temperature, with a brown precipitate
forming after 16 hours (FIG. 2B). The precipitate in the vial shown
in FIG. 2B was moved to the side with a hand held magnet. Tubes
containing the P1/P2 mixture alone, the P1 with complementary
oligonucleotide, or the P1/P2 mixture with half-complementary
oligonucleotide did not show turbidity or precipitate formation
even after weeks at room temperature (FIGS. 2A, 2C, and 2D).
[0139] To further elucidate the interaction of P1/P2 with
complementary oligonucleotide, gel electrophoresis was performed.
Under non-denaturing conditions, and without DTT, the precipitate
(as shown in the vial in FIG. 2B) remained at the top of the gel
(FIG. 3A, lane 1). Treatment with DTT (FIG. 3A, lane 2) resulted in
a single band of hybridized oligonucleotide. Under denaturing
conditions and with DTT added (FIG. 3B), two bands were observed,
the slower one consisting of complementary oligonucleotide and the
faster one of a mixture of 3' and 5' oligonucleotides.
[0140] The nanoparticles P1 and P2 are potent enhancers of the
spin-spin and spin-lattice relaxation processes (Table 2).
Interestingly, the spin-spin relaxation was furthermore
significantly enhanced by oligonucleotide hybridization, rendering
the particles as potential "magnetic nanosensors." FIG. 4 shows the
effect of oligonucleotide addition to an aqueous solution of P1/P2.
Within several minutes, T2 decreased from 63 ms to 45 ms and this
effect persisted for the period of observation (2 hours). The
insert in FIG. 4 plots the T2 decrease as a function of
oligonucleotide added. Table 2 summarizes the concentration
independent R1 and R2 relaxivities before and after hybridization.
Hybridization primarily affected R2 with a doubling of the R2/R1
ratio. Concomitant laser light scattering indicated a significant
size increase of hybridized conjugates, presumably causing effects
on spin-spin relaxation.
TABLE-US-00002 TABLE 2 Size and relaxivities before and after
hybridization with target oligonucleotides Size R1** R2** Compound
Hybridization (nm) (sec.sup.-1 mM.sup.-1) (sec.sup.-1 mM.sup.1)
R2/R1 P1 No 53 .+-. 11 27.7 .+-. 0.3 75 .+-. 2 2.7 .+-. 0.1 P2 No
53 .+-. 11 26.7 .+-. 0.3 71 .+-. 10 2.6 .+-. 0.4 P1 + P2 + oligo No
65 .+-. 25 25.8 .+-. 0.4 67 .+-. 1 2.6 .+-. 0.1 non-complement. P1
+ P2 + oligo Yes 215 .+-. 19 23.0 .+-. 1.0 128 .+-. 3 5.6 .+-. 0.2
complement. *Determined by gel electrophoresis **Relaxivities
(units of sec.sup.-1 mM.sup.-1) are the slopes of plots of
relaxation rate (1/T, sec.sup.-1) against nanosensor concentration
(Fe, mM); values are plotted as means .+-. SD, n = 3. Size refers
to the unimodal size distribution as determined by light
scattering, mean .+-. SD, n =6.
[0141] The effect of temperature cycling on the hybridization of
the oligonucleotide nanoparticle was investigated by measuring
changes in T2 values (FIG. 5). At 80.degree. C., hybridization was
minimal and T2 changes were small. During multiple cycles of
heating and cooling representative T2 changes were observed.
Furthermore, upon addition of DTT, oligonucleotides were cleaved
from the nanoparticles and T2 did not change during further
temperature cycling. These results indicate that oligonucleotide
hybridization efficiently changes the spin-spin relaxation time of
water, that these effects occur within minutes, that the magnetic
effects are fully reversible through the use of DTT.
[0142] Selectivity
[0143] A unique feature of the magnetic nanoparticles is that they
are highly stable to temperature fluctuations and to different
ionic media. This stability enabled the use of buffer conditions
(e.g. 25 mM KCl, 50 mM Tris, pH 7.5) in which small differences in
base pairing can be detected by T2 measurements (Table 3). Thus,
the new conjugates are highly selective in binding to target
molecules. For example, a single nucleotide insertion in the center
of a target sequence can abrogate magnetic switching nearly
completely. Similar effects are also seen with larger and other
kinds of single and double inserts (Table 3).
[0144] To determine the effect that nucleotide mismatches could
have on T2 measurements, additional target sequences containing
both single and multiple mismatches were tested. Again, single
nucleotide mismatches were detectable while double mismatches
completely abrogated magnetic switching (Table 3).
TABLE-US-00003 TABLE 3 Summary of tested oligonucleotide sequences
and magnetic measurements Deviation .differential.T2 from (msec)*
normal ** p-value Perfect match TAC-GAG-TTG-AGA-ATC- 30 .+-. 2 NA
NA CTG-AAT-GCG (match) SEQ ID NO: 3 Insertions
AC-GAG-TTG-AGA-G-ATC- 5 .+-. 1 83% 0.0001 CTG-AAT-GCG SEQ ID NO: 4
TAC-GAG-TTG-AGA-GAG- 2 .+-. 0.6 93% 0.0001 TGC-ATC-CTG-AAT-GCG SEQ
ID NO: 5 TAC-GAG-G-TTG-AGA-ATC- 4 .+-. 2.5 87% 0.0002 CTG-AAT-GCG
SEQ ID NO: 6 TAC-GAG-G-TTG-AGA-ATC- 2 .+-. 0.5 93% 0.0001
CTG-G-AAT-GCG SEQ ID NO: 7 Mismatches TAC-GAG-TTG-AGA-CTC- 21 .+-.
1.2 30% 0.0029 CTG-AAT-GCG SEQ ID NO: 8 GAC-GAG-TTG-AGA-ATC- 21
.+-. 0.6 30% 0.0020 CTG-AAT-GCG SEQ ID NO: 9 TAC-GAG-TTG-AGA-ATC-
15 .+-. 0.6 50% 0.0030 CTG-CAT-GCG SEQ ID NO: 10
TAC-GAG-TTG-AGA-CTC- 1 .+-. 0.6 97% 0.0001 CTC-AAT-GCG SEQ ID NO:
11 TAC-GAC-TTG-AGA-ATC- 9 .+-. 1.7 70% 0.0002 CTG-CAT-GCG SEQ ID
NO: 12 *.differential.T2 = T2.sub.(t = 0 min) - T2.sub.(t = 30
min); ** deviation = (.differential.T2.sub.(perfect match) -
.differential.T2.sub.(insertion or
mismatch)/.differential.T2.sub.(perfect match) .times. 100
[0145] The selectivity of the MRS was further studied by preparing
probes to target a GFP gene sequence and three variants with a
single mismatch (T, C, G instead of an A). FIG. 8A shows the time
course of T2 measurements with these four sequences. The perfect
match (containing A) decreased T2 within minutes of oligonucleotide
addition. The single mismatches behaved differently and these
differences could be readily detected by T2 measurements at
40.degree. C. As in the previous experiments, we also performed MR
imaging at room temperature and were able to show similar
differences (FIG. 8B). These data show that selective measurements
capable of distinguishing single nucleotide mismatches can be
carried out reliably and at various temperatures using either NMR
or MRI techniques without the need for melting curve analysis.
[0146] Polypeptide Conjugates
[0147] Polypeptide conjugates behave in the same manner as the
oligonucleotide conjugates, in that they are highly selective in
their binding to target molecules and form aggregates as described
further herein.
Uses of Binding Moiety-Nanoparticle Conjugates
[0148] The new conjugates can be used in two broad applications. In
one application, the aggregate formation assay, a population of
conjugates (or a mixture of two or more populations of conjugates
with differing binding moieties directed to the same target
molecule or type of target molecule) is placed into a sample
solution. In this assay system, if the sample solution contains a
target molecule to which the binding moieties specifically bind,
the binding moieties interact with and bind to the target molecule
resulting in the formation (self-assembly) of aggregates. As a
result, the dispersed state of the conjugates switches to an
aggregated state, which decreases T2 relaxation times. FIG. 1
depicts one embodiment of such an interaction in which two
conjugates, P1 and P2, combine to form an aggregate of six
conjugates.
[0149] In the other application, the aggregate dispersion assay,
conjugates are used to prepare small aggregates, and the aggregates
are placed into a sample solution. In this assay system, the
binding moieties are designed so that they can be bound to each
other (or to a specific aggregation inducing molecule, such as
avidin) to form the aggregates, and to be (or form upon binding to
each other or to the aggregation inducing molecule) a substrate
that is cleaved by a specific target molecule. If the sample
solution contains a target molecule, the substrate formed by the
binding moieties is cleaved, resulting in the dissolution of the
aggregates. Thus, the aggregated state switches to a dispersed
state, which increases T2 relaxation times.
[0150] These aggregates can be observed and detected in vitro,
e.g., in vials or arrays, e.g., 2-D or 3-D arrays, as well as in
vivo, e.g., using MR imaging of a subject after administration of
the conjugates or aggregates.
[0151] Aggregate Formation Assays
[0152] In this application, the conjugates must include binding
moieties that specifically bind to at least two different binding
sites or epitopes on the target molecule, and each conjugate must
have at least two binding moieties. In general, the conjugates are
added to a sample solution under conditions that enable the binding
moieties to interact with and bind to the target molecule. As more
of these interactions occur over time, several conjugates will
accumulate together to form one aggregate. The endpoint of the
assay is the detection of the presence of the aggregates, e.g.,
using MR imaging or other detection methods.
[0153] This application of the invention can be used in several
assay systems. For example, when the binding moieties are nucleic
acids, the new conjugates can be used for an analytic method
referred to herein as the Hybridization Relaxation Assay System or
HYRAS. Like the earlier SMRAS (Solvent Mediated Relaxation Assay
System) technology (U.S. Pat. No. 5,164,297), HYRAS can be used to
determine the concentration of an analyte in a sample by monitoring
changes in a solvent relaxation rate. HYRAS differs from SMRAS in a
number of important ways.
[0154] First, HYRAS involves the assay of nucleic acids using
superparamagnetic iron oxide nanoparticles, and is based on the
observation that nucleic acids do not non-specifically adsorb to
iron oxides. This is surprising because the affinity between the
iron on the surface of the iron oxide and phosphate or
phosphate-containing compounds, such as nucleic acids, is strong.
For example, iron oxides have been used to bind and extract DNA
(see, e.g., examples 10 and 11 in U.S. Pat. No. 5,512,332). Thus,
it is surprising that oligonucleotides, which contain a
multiplicity of phosphate groups, do not interact non-specifically
with the iron oxide nanoparticles.
[0155] Second, to produce the needed aggregation of nanoparticles
by a specific target nucleotide, two types of
oligonucleotide-nanoparticles are needed, each with a single type
of oligonucleotide attached, each reacting with a different
sequence present on a target complementary oligonucleotide (see
FIG. 1). If two different oligonucleotides were coupled to the
sample nanoparticle, the target nucleic acid would hybridize to the
oligonucleotides on the same particle and no effect on water
relaxation rates (T2) would result. SMRAS has no requirement for
the synthesis of two different types of magnetic particles. Instead
SMRAS uses multivalent proteins coupled to an iron oxide, which
then reacts with multivalent proteins such as antibodies to produce
changes in relaxation.
[0156] Third, in SMRAS and HYRAS particle aggregation alters T2 in
opposite manners. For example, in SMRAS, the complex between
BSA-coated magnetic particles and anti-BSA antibodies causes an
increase in T2 (decrease in 1/T2); addition of BSA blocks this
effect increasing 1/T2, see FIG. 4 of U.S. Pat. No. 5,164,297. In
contrast, in HYRAS, when oligonucleotide-nanoparticles react with a
target nucleotide to form aggregates there is a decrease in T2.
[0157] Fourth, the conjugation strategy used in HYRAS differs from
that used in SMRAS. In HYRAS, oligonucleotides are attached to iron
oxide colloid polymers with a single covalent bond at the 3' or 5'
end of the oligonucleotide. This is essential because the
oligonucleotides are sufficiently small (short), that if they were
attached in the middle, and not by their 3' or 5' ends, they would
not be able to hybridize to target nucleotides. In contrast,
particles used in SMRAS, such as the dextran-coated iron oxide or
BSA-coated iron oxide, are synthesized by the adsorption of
polymers to the surface of the iron oxide. This attachment is
maintained by a large number of non-covalent bonds.
[0158] The new methods can also be used to detect nucleic acids by
magnetic resonance. This assay measures the presence of target
oligonucleotides in turbid or tissue-like samples (see Example 5).
This method provides advantages over light-based analytical
methods, such as the non-magnetic, gold based colorimetric assays
described in WO 98/04740. In one method using the gold
nanoparticles, the color change is determined in solution, which
requires a non-turbid, non-opaque solution. In a second method,
oligonucleotide-gold conjugates are collected on an oligonucleotide
bearing substrate, such as membrane or filter. Excess media, which
interferes with the detection, is removed and amplification by a
silver stain is employed. In the present invention, neither
separation nor amplification steps are used. Instead, the presence
of nanoparticle aggregate is detected by MR. The invention can be
distinguished by the ability to "see" aggregate formation in highly
turbid or opaque tissues by the use of magnetic resonance. This
yields assays with reduced processing and handling steps.
[0159] The novel conjugates of the invention can be used to measure
the T2 values, and levels of oligonucleotides, in several samples
simultaneously. This can be accomplished by replacing an MR
spectrometer (FIGS. 4, 5 and 6 with an MR imager (FIG. 7). MR
signal intensity was determined with a T2 weighted pulse sequence
for a matrix of 24 wells of a 384 well microtiter plate. Further
reduction in sample size, for example by the use of 1534 well
microtiter plates, can be achieved. Microtiter plates can be
stacked, and the capability of MR to measure the signal intensity
of many slices, i.e., in three-dimensions, can be used to further
increase assay throughput.
[0160] The new conjugates can also be used as MR contrast agents.
In one embodiment, dextran coated superparamagnetic iron oxides
(MION or COMBIDEX.RTM.) are synthesized (see U.S. Pat. Nos.
5,492,814 or 5,262,176) and then cross-linked and amino
functionalized to yield NH.sub.2-CLIO, as described herein.
Alternatively, non-polymer coated iron oxide particles can be used.
The nanoparticles are then coupled to specific oligonucleotides as
shown, e.g., in FIG. 1. The resulting oligonucleotide-nanoparticle
conjugates are then formulated in a physiologically acceptable
media (e.g., saline or isotonic mannitol) and injected into an
animal or human, intravenously at a dose between 0.1 and 10 mg
Fe/kg. The contrast agent is permitted to accumulate in target
tissue and is detected at highest sensitivity with T2 weighted
spin-echo or gradient-echo pulse sequences.
[0161] In another example, detection of an mRNA in solution can be
accomplished by synthesizing two populations of conjugates. The
first contains an oligonucleotide sequence complementary to a
sequence in the mRNA of interest and is bound at the 3' or 5'
termini to the nanoparticle. A second conjugate is synthesized with
a oligonucleotide sequence complementary to a different but
proximate sequence of the mRNA. Addition of these conjugates to a
solution containing the mRNA will result in the binding of the
conjugates resulting in aggregation of the conjugates. Aggregation
will produce a measurable decrease in the T2 by MR technology.
[0162] These novel conjugates can be used to determine the pattern
of gene expression in a specimen (expression analysis) by extension
of the methods shown in Example 6, below. Here a microtiter plate
is prepared where each well contains different combinations of
oligonucleotide-nanoparticles, i.e., combinations of
oligonucleotides with different sequences attached to the same
magnetic nanoparticle. The sequences of the oligonucleotides are
chosen to permit hybridization, followed by aggregation and T2
change, with a unique target sequence that may or may not be
present in the sample.
[0163] Another embodiment uses the same concept, but with proteins.
For example, the conjugate can be used to detect the presence of an
antigen in a sample. In this method, antibodies are linked
covalently or non-covalently to the nanoparticle. To ensure that
the antigen binding site is exposed, the C-terminus of the antibody
or antibody fragment is attached to the nanoparticle. Monoclonal
antibodies can be used for this method. A feature of this method is
the need for a mixture of at least two types of nanoparticles, each
with a specific binding moiety, e.g., monoclonal antibody attached.
The antibodies are directed toward the same antigen, but recognize
different determinants or epitopes. The populations are mixed in a
sample and binding of the conjugate to an antigen induces
aggregation, resulting in a measurable decrease in T2.
[0164] In another aspect of the invention, a polyclonal antibody
can be attached to the nanoparticle. Since by definition these
antibodies are multivalent, only a single population of conjugates
is required.
[0165] Antibody fragments can also be used as long as they are
bivalent. If single chain Fv fragments are used, there must be two
populations of conjugates prepared. Each population will contain a
single chain fragment directed to a distinct epitope of the same
antigen.
[0166] These conjugates can also be used, as described above for
the oligonucleotides, as magnetic nanosensors in other methods of
antigen detection systems. These methods can utilize detectors that
measure the magnetic properties of the particles (e.g.,
magnetometers, oscillating magnetic field readers, and
superconducting quantum interference device (SQUID) detectors).
Other detection methods include magnetic force microscopy or atomic
force microscopy.
[0167] In the MR imaging application, the novel conjugates provide
a method for the detection and a spatial localization of specific
antigens in living systems. Hence antibody conjugates can function
as MR contrast agents for the detection of polypeptides in
vivo.
[0168] In another embodiment, conjugates can be useful in detecting
a target molecule, e.g., an antibody, in solution. In this assay,
the antigen will be bound to the nanoparticle and placed into a
sample. If an antibody directed to the antigen is present, binding
of the antigen will cause aggregation of the conjugate resulting on
the decrease of T2. This assay method can be used for polyclonal
and monoclonal antibodies and antibodies of any subclass because of
the bivalent or polyvalent nature of the antibodies. This assay
method can be used in the detection of antibodies, for example, in
serum, acites fluid, cell culture medium, and cell lysates.
[0169] In another embodiment, the binding moiety can be a
receptor-binding protein bound to the nanoparticle. When applied to
a solution of cells, clustering of a cell surface receptor will
result in aggregation of the conjugate followed by the concomitant
decrease in T2. In another aspect of the invention, a kinase
activity can be assayed. A peptide sequence with a serine or
tyrosine kinase recognition site is attached to a nanoparticle at
one terminal end. Addition of a solution containing a kinase will
result in the phosphorylation of the binding moiety. Exposing the
conjugates to anti-phosphotyrosine or anti-phosphoserine antibody
will result in aggregation resulting the decrease of T2
[0170] Aggregate Dispersion Assays
[0171] In this application, a change in T2 is measured by preparing
an aggregate of several conjugates, and then placing the aggregate
into a solution (resulting in an immediate decrease in the T2),
which may contain a target molecule. The aggregate is prepared by
designing the binding moieties to form a substrate that is cleaved
by the target molecule, thus dispersing the aggregates into
conjugates, resulting in an increase of the T2 relaxation time. The
binding moieties can bind to each other to form the substrate, or
can contain the substrate, and form the aggregates by binding to an
aggregation inducing molecule, such as avidin. The endpoint of the
assay is the detection of the dissolution or dispersal of the
aggregates (or the lack of formation of an aggregate if the target
molecule and aggregate forming molecule are added to a solution of
the conjugates at the same time).
[0172] In one embodiment, the new methods can be used to detect
enzyme target molecules in a sample solution. The assay is based on
the attachment to the nanoparticle of a natural or synthetic
peptide that has an internal enzymatic site. Biotin is attached to
the free terminus of the peptide. These biotin-labeled conjugates
are mixed into a solution, and avidin (which binds four molecules
of biotin per molecule of avidin) is added as the aggregation
inducing molecule to form aggregates. These aggregates are then
added to a sample solution. If there is a measurable increase in
T2, then the enzyme is present. Alternatively, the conjugates can
be added to a sample solution along with the avidin. If binding
results in the aggregation of the conjugates, a measurable decrease
in T2 can be observed, indicating that the target proteolytic
enzyme is not present. However, if the enzyme is present and reacts
with the substrate peptide in a relatively slow manner, a decrease
in the T2 can be observed, followed by an increase of T2 when the
aggregates are dispersed. If the reaction is fast, no decrease in
T2 will be observed. This method can be used for any hydrolase that
has a known recognition sequence.
[0173] In another variation of the invention, a peptide binding
moiety containing an internal hydrolytic sequence can have biotin
attached to both termini. Avidin is attached to the nanoparticles
and mixed with the biotinylated peptide in a sample. Since one
avidin molecule binds four biotin molecules, aggregation will occur
if the biotinylated molecule is intact or if it has been cleaved.
However, the degree of aggregation will be greater if the molecule
is intact, therefore the sample will exhibit a greater degree of
decreased T2.
[0174] In another aspect of the invention, immediate aggregation is
induced by attaching a nanoparticle to both termini of the peptide.
The conjugate is placed in the sample and the relaxivity is
measured. If the enzyme of interest is present, then an increase in
T2 will be measured when the peptide is cleaved.
[0175] The assay for the presence of a particular polysaccharidase
can be accomplished in the same manner as described above for the
enzyme assays using a polysaccharide as the binding moiety.
[0176] In another aspect of the invention, the conjugate can be
used to detect a molecule that is transferred to the binding
moiety. For example, DNA methyltransferase activity can be assayed.
Hybridizing oligonucleotide conjugates can form a dam methylation
site (GATC). The hybridization results in aggregation of the
attached nanoparticle and a measurable decrease in T2. Upon contact
with a methylase, the adenine and cytosine are methylated.
Treatment with DpnI, a restriction endonuclease that specifically
cleaves the methylated sequence GATC, results in dispersion of the
aggregates followed by a measurable increase in T2.
[0177] In one aspect of the invention, oligonucleotide conjugates
are synthesized to be complementary to each other. Upon
hybridization of these conjugates in solution, the binding moieties
form a double-stranded nucleic acid with a unique endonuclease
restriction site (e.g., EcoRI, BamHI, PvuII). Hybridization of the
oligonucleotides also aggregates the nanoparticles attached to the
oligonucleotides resulting in a decreased T2. In this case, the
presence of a target endonuclease in a sample can be measured by an
increase in T2 when the restriction site is cleaved, resulting in
the dispersion of the aggregates.
EXAMPLES
[0178] The invention is further described in the following
examples, which do not limit the scope of the invention described
in the claims.
Example 1
Synthesis of Superparamagnetic Iron Oxide Nanoparticles
[0179] Biocompatible, fluid phase magnetic nanoparticles
(NH.sub.2--CLIO) were synthesized as described and reacted with
N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP) to yield
2Py-SS-CLIO (FIG. 1). See Josephson et al, (1999) Bioconjugate
Chemistry, 10, 186-91 and Perez et al., (2002) Journal of the
American Chemical Society, 124, 2856-2857.
[0180] The first step in the synthesis of amino-CLIO is the
synthesis of a dextran coated superparamagnetic iron oxide. A pure
dextran coated superparamagnetic iron oxide is reacted with a
crosslinking agent (5-50% epichlorohydrin) in strong base (final
concentration 1-3 M NaOH). After 24 hours at room temperature,
liquid ammonia in excess is then added to aminate the
polysaccharide. Low molecular weight impurities were removed by
exhaustive ultrafiltration using a membrane with a 10 kDa
cutoff
Example 2
Synthesis of Oligonucleotides and Alkanethiol-Oligonucleotides
[0181] The 5'-alkanethiol-oligonucleotide
(HS-(CH.sub.2).sub.6-CGC-ATT-CAG-GAT (SEQ ID NO:1)) and
3'-alkanethiol-oligonucleotide (TCT-CAA-CTC-GTA(SEQ ID
NO:2)-(CH.sub.2).sub.3-SH) were synthesized at a 1 .mu.mol-scale
using standard phosphoramidite chemistry. The sulfhydryl groups
were protected with a mercaptoalkyl linker. Immediately before
reaction with 2Py-SS-CLIO, oligonucleotides were deprotected with
dithiothreitol (DTT) (J. J. Storhoff, R. Elghanian, R. C. Mucic, C.
A. Mirkin, R. L. Letsinger, J Am Chem Soc 1998, 120, 1959).
[0182] Complementary
(.sup.5'TAC-GAG-TTG-AGA-ATC-CTG-AAT-GCG.sup.3')(SEQ ID NO:13),
half-complementary
(.sup.5'TAC-GAG-TTG-AGA-GAG-TGC-CCA-CAT.sup.3')(SEQ ID NO:14), and
non-complementary (.sup.5'ATG-CTA-AAT-GAC-GAC-TGC-CCA-CAT.sup.3')
(SEQ ID NO:15) oligonucleotides were synthesized using standard
phosphoramidite chemistry (underlined bases will hybridize).
Example 3
Conjugation of Nanoparticles to Alkanethiol Oligonucleotide
[0183] To 1.1 mL of 2Py-SS-CLIO (3 mg of Fe in 0.1 M phosphate
buffer, pH 8.0, see example 1), 550 .mu.g of either 5'- or
3'-alkanethiooligonucleotide was added and incubated overnight at
room temperature. The mixture was purified using an LS+ high
gradient magnetic separation column (Miltenyi Biotec, Auburn,
Calif.) equilibrated with 0.1 M phosphate buffer, pH 7.5. The
number of oligonucleotides attached per particle was determined by
treatment with DTT, followed by separation of iron and
oligonucleotide using a microconcentrator as above. Oligonucleotide
concentration was then determined from absorbance at 260 nm, using
an extinction coefficient of 1.2.times.10.sup.5 M.sup.-1cm.sup.-1.
The probes are denoted P1
(CLIO-SS-(CH.sub.2).sub.6-CGC-ATT-CAG-GAT(SEQ ID NO:1)) and P2
(TCT-CAA-CTC-GTA(SEQ ID NO:2)-(CH.sub.2).sub.3-SS-CLIO. To 1.1 mL
of 2Py-SS-CLIO (3 mg of Fe in 0.1 M phosphate buffer, pH 8.0), 550
.mu.g of either the 5-alkanethiol-oligonucleotide
(HS-(CH.sub.2).sub.6-CGC-ATT-CAG-GAT(SEQ ID NO:1)) or the
3-alkanethiol-oligonucleotide (TCT-CAA-CTC-GTA-(SEQ ID
NO:2)(CH.sub.2).sub.3--SH) were added and incubated overnight at
room temperature. The next day the mixture was applied to a
magnetic separations column (Miltenyi Biotec, Auburn, Calif.)
equilibrated with 0.1 M phosphate buffer, pH 7.5. The column was
washed with phosphate buffer to remove any non-bound
oligonucleotide.
Example 4
Assay for Target Oligonucleotide
[0184] Hybridization: To generate FIGS. 2A to 2D, equal volumes (25
.mu.L) of P1 and P2 (both at 550 .mu.g Fe/mL) were mixed with 14
.mu.L of 1 M NaCl, 0.1 M phosphate, pH 7.5. Two .mu.L (400 ng) of
various oligonucleotides were then added. The mixture was heated to
50.degree. C. for 5 minutes and allowed to react at room
temperature overnight. The precipitate shown in FIGS. 3A and 3B
were obtained after overnight incubation of P1/P2 with
complementary oligonucleotide; the precipitate was washed with 0.1
M NaCl, 0.1 M phosphate buffer and re-suspended in 300 .mu.L of the
same buffer. The sample was split into two 15 .mu.L portions and
electrophoresed without DTT (lane 1) or with 4 mM DTT (lane 2)
under non-denaturing conditions (FIG. 3A) or denaturing conditions
(FIG. 3B).
[0185] Gel electrophoresis: Non-denaturing gels (10%
polyacrylamide) and denaturing gels (20% polyacrylamide) were used
after optimization of the separation process. Gels were stained
with SYBR Gold dye (Molecular Probes, Eugene Oreg.).
[0186] Determination of Proton Relaxation Times: Relaxation time
measurements were performed at 0.47 Tesla, at 40.degree. C. (Bruker
NMR Minispec, Billerica, Mass.), except for the experiment used to
generate FIG. 5, where temperatures of 40.degree. C. and 80.degree.
C. were used. To determine the effect of hybridization on water T2,
equal amounts of P1 and P2 (5 .mu.L) were diluted in 1 mL 1 M NaCl,
0.1 M phosphate buffer, pH 7.5 to give a total iron of 10 .mu.g/mL.
T2 values were obtained before and after addition of 1 .mu.L (390
ng) of complementary, half-complementary or non-complementary
target nucleic acids and plotted as a function of time. Relaxivity
was determined by plotting water 1/T2 and 1/T1 as a function of
iron concentration, see Table 2. The size of conjugates was
determined by light scattering (Coulter N4, Hialeah, Fla.).
Example 5
Use of Nanoparticle Conjugates in Turbid Media
[0187] Equimolar amounts in iron of oligonucleotide-nanoparticle
conjugates denoted P1 and P2 were diluted in a 10% Fat Emulsion
(Intralipid.RTM. 10%, Baxter Healthcare Corporation) containing 1 M
NaCl. Changes in water T2 relaxation time were recorded after
addition of 1 .mu.L (53 femtomoles) of complementary
oligonucleotide. As was the case in non-turbid media (FIG. 4), a
rapid decrease in the T2 relaxation time is observed (FIG. 4).
Three hours after adding the complementary oligonucleotide, at the
arrow, 2 .mu.L of DTT (0.4 M) was added to the P1 and P2 solution.
A gradual increase in the T2 relaxation time is observed reaching
the original T2 value within two hours. These results indicate that
the new methods work even in turbid media.
Example 6
Array Based Assay
[0188] Equimolar amounts in iron of oligonucleotide-nanoparticles
denoted P1 and P2 were diluted with 1 M NaCl in 0.1 M sodium
phosphate, pH 7.4 to give iron concentrations of 6 .mu.g/mL or 3
.mu.g/mL. 100 .mu.L of the P1/P2 mixture and 1 .mu.L of
complementary or non-complementary target oligonucleotides were
added to 24 of the square wells of a 384-well microtiter plate.
Images were made on a clinical MR imager (GE Signal, 1.5 Tesla)
using a T2-weighted pulse sequence (TR=3000 ms/TE=300 ms). FIG. 7
shows 24 wells of the 384-well plate. The top two rows contain 3
.mu.g Fe/ml and the bottom two rows contain 6 .mu.g Fe/ml. Each
column has the indicated amounts of target nucleic acids added. The
wells get "darker," i.e., the signal intensity drops because T2
drops. This is due to a hybridization-induced formation of
aggregates between oligonucleotide-nanoparticle. No binding occurs
with non-complementary targets, and thus, there is no change in T2
and no change in signal intensity. These results illustrate the
utility of the new methods for use in in vitro arrays, which can be
two- or three-dimensional.
Example 7
Assay for Green Fluorescent Protein (GFP) mRNA by Imaging MRS
[0189] To test whether MRS could be used to identify a target
sequence in a higher throughput format, a panel of cell lines was
screened for GFP mRNA expression using an MR imager as a detector.
The panel consisted of primary human and rodent tumor cells lines,
one of which was transduced with a GFP encoding HSV amplicon
(Gli-36), while another one was transiently transfected with a GFP
encoding plasmid DNA (COS-1). In addition, the corresponding
parental cell lines were transfected with beta galactosidase as a
negative control and included in the panel. Total RNA from these
cell lines was isolated and imaged after sensing with GFP-P1/GFP-P2
(FIG. 9a). The sample in well C3 contained RNA from the Gli-36
cells line, whereas well D4 contained RNA from COS-1 cells. The
observed magnetic changes correlated well with fluorescence
measurements of the cell lines and RT-PCR (data not shown). Both
parental and beta galactosidase expressing Gli-36 and COS-1 cell
lines did not show a significant difference compared to wild type
cell lines.
[0190] While the above experiments were carried out with isolated
RNA, similar measurements were made in cell lysates. For these
experiments, a mild lysis buffer (20 mM Tris pH 8, 5 mM MgCl.sub.2,
0.5% NP-40, 200 .mu.g/mL tRNA) was added to adherent cells prior to
probing with P1/P2. This buffer has been previously used to extract
RNA from cell without the need of scrapping the cells off the dish.
As shown in FIG. 9b, differences in GFP mRNA expression between the
parental and GFP expressing Gli-36 cell lines were clearly
identified. In additional studies, this difference was quantified
using Gli-36 cell lines infected with different MOI of a GFP
bearing amplicon vector. FIG. 9c shows the correlation between cell
fluorescence measurements and mRNA measurements using MRS
technology in cell lysates. In these studies, a specific GFP mRNA
was detected in a pool of total RNA (1 .mu.g) and in whole cell
lysate with no prior amplification of the signal. This level of
detection with the MRS technology is comparable to traditional
fluorescent-based methods for oligonucleotide hybridization carried
out with purified total RNA.
Example 8
Assay for Caspase Activity Using a Monobiotinylated Peptide and
Avidin to Induce Formation of Small Aggregates
[0191] In this assay, a biotinylated peptide substrate for
caspase-3 was synthesized (Biotin-GDEVDGC caspase-3 recognition
site is underlined) and coupled to aminated CLIO using SPDP (see
example 1). Equimolar amounts of Avidin-CLIO and Biotinylated
peptide-CLIO conjugate were incubated in PBS (10 .mu.g Fe/ml) to
allow a small aggregate to form. The T2 was measured before and
after addition of 25 ng Caspase 3 (1.7 nM) in the presence or
absent of a caspase 3 inhibitor. See figure after example 10b.
[0192] The avidin-CLIO construct was made as follows: Amino-CLIO
(0.2 mmoles Fe) and fluorescein labeled hen egg white avidin
(7.5.times.10.sup.-5 mmoles) (Pierce, Rockford, Ill.) were dialyzed
against 0.01M sodium acetate buffer, pH 6.0 for 2 hours. Sodium
periodate (46 mmol) was added to the avidin, incubated for 30 min
at room temperature in the dark, and dialyzed against 150 mM sodium
chloride. The oxidized avidin was added to amino-CLIO, and the pH
adjusted by the addition of 100 .mu.l of 0.2 M sodium bicarbonate,
pH 9.5. The mixture was incubated for 2.5 hours with stirring.
Sodium cyanoborohydride was added (80 mmol) and the mixture was
incubated for 3.5 hours at room temperature. The avidin-CLIO
nanoparticle was separated from unreacted avidin using a magnetic
separation column (Miltenyi Biotec, Auburn, Calif.). Iron was
determined spectrophotometrically, and protein by the BCA method
(Pierce). The number of avidins attached per nanoparticle was
calculated using a molecular weight of 67 kDa for avidin and 2064
Fe atoms per crystal for CLIO.
[0193] FIG. 10b shows that in the absence of caspase or in the
presence of caspase inhibitor, the binding moiety is intact and
therefore, so is the aggregate. When the inhibitor is not added or
capase is added, the aggregate is dispersed resulting in an
increase of T2. These experiments indicate that the assay system
has the sensitivity to detect enzyme activity in solution.
Example 9
Assay for Protein (GFP) Using a Biotinylated Polyclonal
Anti-GFP
[0194] Avidin-CLIO nanoparticles made as described above were
reacted with biotinylated polyclonal anti-GFP (Research Diagnostics
Inc.) and were then attached to the particles. Unreacted molecules
were removed. To probe for protein-protein interactions, GFP (33
pmol, 200 nM) was incubated with anti-GFP-CLIO (10 .mu.g Fe/ml) and
T2 relaxation times were recorded (FIG. 10a).
[0195] The results show that the presence of the antibodies
resulted in a decrease of T2, indicating that the antibody
conjugates were bound to the antigen target resulting in aggregate
formation.
Example 10
Assay for Caspase Using a Dibiotinylated Peptide
[0196] In this assay, a dibiotinylated peptide is synthesized that
includes between the two biotins a "substrate" (cleavage site) that
can be cleaved by the protease caspase. An example of a
biotinylated peptide that is convenient to make has the general
structure biotin-G-X1-X2-X3-X4-G-K-biotin, wherein X1 to X4 are
residues providing protease specificity (the cleavage site was
between X1 and X4). FmocK(Dde) can be used in the synthesis of the
peptide. It can be deprotected with 2% hydrazine and biotin coupled
to the epsilon amino group of lysine. Alternatively, a biotinylated
form of lysine can be purchased. Biotin is added to the N terminus
of the peptide through the carboxyl group of biotin using HOBT/HBTU
as activating/coupling agents.
[0197] To perform the assay, the dibiotinylated peptide is
incubated with the protease and cleavage allowed to occur.
Avidin-CLIO, made as described herein, is then added. When mixed
with dibiotinylated peptide, small aggregates form (if no protease
is present). If the dibiotinylated peptide was cleaved, by a
protease such as caspase, the monobiotinylated products bind to the
avidin-CLIO, but do not induce the formation of small
aggregates.
Example 11
Assay for Endonuclease Using Aggregates of Double-Stranded
Oligonucleotides
[0198] Two self-complementary 3'-alkanethiololigonucleotides:
AAT-GCG-GGATCC-TAC-GAG-(CH.sub.2).sub.3-SH (SEQ ID NO:16) and
CTC-CTA-GGATC-CGC-ATT-(CH.sub.2).sub.3-SH (SEQ ID NO:17) were
conjugated to nanoparticles as described in Example 3. The
resulting conjugates (Magnetic Relaxation Switches, MRS), denoted
P1 (AAT-GCG-GGATCC-TAC-GAG-(CH.sub.2).sub.3-S-S-CLIO) and P2
(CTC-CTA-GGATC-CGC-ATT-(CH.sub.2).sub.3-S-S-CLIO) have on average 3
oligonucleotides per particle. The formation of MRS aggregates upon
mixing P1 and P2 was determined by atomic force microscopy (AFM)
(Dimension 3100, Digital Instruments). Images were recorded using
tapping mode and a surface area of 5.times.5 .mu.m.
[0199] The restriction endonuclease digestion was performed at
37.degree. C. with 0.4 U/.mu.l of BamHI, (New England BioLabs) in
500 .mu.l of 10 mM Tris HCl, 10 mM MgCl.sub.2, 50 mM NaCl pH 7.4
containing the MRS aggregate P1/P2 (10 .mu.g of Fe/mL). The water
relaxation of the solution was measured at either time intervals or
after a one-hour incubation and compared to control samples (with
no enzyme) using a 0.47 T NMR relaxometer (Bruker NMR Minispec,
Billerica, Mass.).
[0200] The oligonucleotide sequences were chosen so that P1 and P2
would self-hybridize with the formation of a MRS aggregate that
exhibits a more pronounce effect on T2. A pair of MRS(P1 and P2)
that self-assemble to form a BamHI recognition site (FIG. 1a) was
prepared. P1 (10 .mu.g Fe/mL) had a T2 of 61.6.+-.0.3 msec, while
P2 (10 .mu.g Fe/mL) had a T2 of 60.4.+-.0.5 msec. Meanwhile, the T2
of an equimolar mixture of P1 and P2 (total 10 .mu.g Fe/mL) had a
T2 of 32.3.+-.0.6 msec (p<0.0001), due to self-hybridization of
the particles and formation of aggregates. Incubation with BamHI,
resulted in an increase in T2 back to baseline levels (59.4.+-.0.4
msec). T2 changes were specifically inhibited by the addition of a
synthetic complementary oligonucleotide and other endonucleases did
not cause an increase in T2. Atomic force microscopy revealed that
P1/P2 consisted of stable aggregates with average sizes raging from
300 to 400 nm (FIG. 12a). After a one-hour incubation with BamHI,
the aggregates were no longer present and monodisperse nanoparticle
conjugates (50-60 nm) were observed instead (FIG. 12b).
Example 12
Protein Assay Using Monoclonal Antibody-Nanoparticle Conjugates
[0201] Monoclonal antibodies can be coupled to polymer coated
magnetic nanoparticles using a variety of chemistries (see, e.g.,
Weissleder et al., U.S. Pat. No. 5,492,814; and Kang et al. (2002)
Bioconjugate Chemistry, 13, 122-127). A useful method is that of
Kang because it uses the amino-CLIO chemistry described above and
avoids destroying the dextran with oxidative treatments with
periodate.
[0202] In this assay format a P1 (first monoclonal attached to a
nanoparticle) and P2 (second monoclonal attached to a nanoparticle)
are synthesized in separate reactions. The target protein must
contain epitopes for both monoclonals, so that small aggregates can
form in solution. If a target antigen is in solution, the
monoclonal antibodies will bind both epitopes on the antigen,
thereby aggregating the nanoparticles, resulting in a decrease of
T2.
Other Embodiments
[0203] It is to be understood that while the invention has been
described in conjunction with the detailed description thereof, the
foregoing description is intended to illustrate and not limit the
scope of the invention, which is defined by the scope of the
appended claims. Other aspects, advantages, and modifications are
within the scope of the following claims.
Sequence CWU 1
1
24112DNAArtificial SequenceSynthetically generated oligonucleotide
1cgcattcagg at 12212DNAArtificial SequenceSynthetically generated
oligonucleotide 2tctcaactcg ta 12324DNAArtificial
SequenceSynthetically generated oligonucleotide 3tacgagttga
gaatcctgaa tgcg 24424DNAArtificial SequenceSynthetically generated
oligonucleotide 4acgagttgag agatcctgaa tgcg 24530DNAArtificial
SequenceSynthetically generated oligonucleotide 5tacgagttga
gagagtgcat cctgaatgcg 30625DNAArtificial SequenceSynthetically
generated oligonucleotide 6tacgaggttg agaatcctga atgcg
25726DNAArtificial SequenceSynthetically generated oligonucleotide
7tacgaggttg agaatcctgg aatgcg 26824DNAArtificial
SequenceSynthetically generated oligonucleotide 8tacgagttga
gactcctgaa tgcg 24924DNAArtificial SequenceSynthetically generated
oligonucleotide 9gacgagttga gaatcctgaa tgcg 241024DNAArtificial
SequenceSynthetically generated oligonucleotide 10tacgagttga
gaatcctgca tgcg 241124DNAArtificial SequenceSynthetically generated
oligonucleotide 11tacgagttga gactcctcaa tgcg 241224DNAArtificial
SequenceSynthetically generated oligonucleotide 12tacgacttga
gaatcctgca tgcg 241324DNAArtificial SequenceSynthetically generated
oligonucleotide 13tacgagttga gaatcctgaa tgcg 241424DNAArtificial
SequenceSynthetically generated oligonucleotide 14tacgagttga
gagagtgccc acat 241524DNAArtificial SequenceSynthetically generated
oligonucleotide 15atgctaaatg acgactgccc acat 241618DNAArtificial
SequenceSynthetically generated oligonucleotide 16aatgcgggat
cctacgag 181718DNAArtificial SequenceSynthetically generated
oligonucleotide 17ctcctaggat cccgcatt 18187PRTArtificial
SequenceSynthetically generated peptide 18Gly Asp Glu Val Asp Gly
Cys1 5 1924DNAArtificial SequenceSynthetically generated
oligonucleotide 19taaacggcca caagttcggc gtgt 242024DNAArtificial
SequenceSynthetically generated oligonucleotide 20taaacggcca
caagttcagc gtgt 242124DNAArtificial SequenceSynthetically generated
oligonucleotide 21taaacggcca caagttctgc gtgt 242224DNAArtificial
SequenceSynthetically generated oligonucleotide 22taaacggcca
caagttccgc gtgt 242311DNAArtificial SequenceSynthetically generated
oligonucleotide 23gatcctacga g 112411DNAArtificial
SequenceSynthetically generated oligonucleotide 24gatcccgcat t
11
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