US20160161472A1 - Quantitative dna-based imaging and super-resolution imaging - Google Patents

Quantitative dna-based imaging and super-resolution imaging Download PDF

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US20160161472A1
US20160161472A1 US14/908,333 US201414908333A US2016161472A1 US 20160161472 A1 US20160161472 A1 US 20160161472A1 US 201414908333 A US201414908333 A US 201414908333A US 2016161472 A1 US2016161472 A1 US 2016161472A1
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strand
drift
protein
labeled imager
docking
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Ralf Jungmann
Peng Yin
Mingjie Dai
Maier S. Avendano Amado
Johannes B. Woehrstein
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Harvard College
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Harvard College
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    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
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    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • C—CHEMISTRY; METALLURGY
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
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    • C—CHEMISTRY; METALLURGY
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    • C07K2317/00—Immunoglobulins specific features
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    • G01N2333/195—Assays involving biological materials from specific organisms or of a specific nature from bacteria
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    • G01N2458/10—Oligonucleotides as tagging agents for labelling antibodies

Definitions

  • the present disclosure relates generally to the field of detection and quantification of targets.
  • the present disclosure provides, inter alia, methods, compositions (e.g., conjugates) and kits for imaging, at high or low spatial resolution, targets (e.g., biomolecules) of interest in, for example, a cellular environment.
  • targets e.g., biomolecules
  • the methods, compositions and kits of the present disclosure take advantage of repetitive, transient binding of short, labeled (e.g., fluorescently labeled) oligonucleotides (e.g., DNA oligonucleotides), or “imager” strands, to complementary “docking” strands, which are attached to targets of interest, in some embodiments, through an intermediate molecule such as an antibody such as a primary or a secondary antibody, to obtain stochastic switching between fluorescent ON- and OFF-states ( FIGS.
  • labeled e.g., fluorescently labeled
  • oligonucleotides e.g., DNA oligonucleotides
  • imager imager
  • a binding partner e.g., a protein-binding moiety or a nucleic acid-binding moiety, whether primary or secondary
  • a binding partner e.g., a protein-binding moiety or a nucleic acid-binding moiety, whether primary or secondary
  • targets e.g., biomolecules, optionally in a cellular environment
  • fluorescently-labeled imager strands that are complementary to and bind to the docking strands through transient Watson-Crick interactions.
  • the methods of the present disclosure are not limited by the number of spectrally distinct fluorophores available for detecting distinct targets (e.g., biomolecules).
  • nucleic acid e.g., DNA and/or RNA
  • sequential time-lapsed imaging are used herein to provide images of up to hundreds of distinct species of targets using, in some embodiments, only a single optimized fluorophore.
  • these different species of targets e.g., biomolecules
  • the methods can be used to generate super-resolution images, significantly even without the need for a super-resolution microscope. It should be understood that while the methods, compositions and kits as provided herein may be described for use in super-resolution imaging, they may also be used, in some embodiments, for imaging that does not require super-resolution. Thus, in some embodiments, the methods, compositions and kits of the present disclosure may be used for imaging, generally.
  • a protein-nucleic acid conjugate comprising a protein linked to a docking strand that is capable of transiently binding to a complementary labeled imager strand.
  • a protein-nucleic acid conjugate comprising a protein linked to a docking strand that is transiently bound to a complementary labeled imager strand.
  • Imager strands are labeled with a detectable label.
  • the detectable label may be, for example, a fluorescent label or other detectable label, e.g., gold nanoparticle.
  • a fluorescently-labeled imager strand (which may be detected by, for example, fluorescent microscopy) may be interchanged with an imager strand labeled with, for example, gold nanoparticles (which may be detected by, for example, dark field microscopy).
  • the docking strands may be capable of transiently binding a plurality of complementary labeled strands (e.g., the docking strand may comprise a plurality of binding sites for complementary labeled strands).
  • a method may be carried out involving a plurality of docking strand and imager strand pairs.
  • Such a method can be used to detect a plurality of targets (e.g., with each docking strand-imager strand pair corresponding to one target).
  • the docking strand-imager strand pairs in the plurality must share an approximately equal probability of hybridizing under a single environment or condition (as defined for example by temperature, salt concentration, strand molarity, etc.), such that if there is an observed difference between the level of binding (and thus the detection) of a population of imager strands, an end user can conclude that such difference is a function of the amount of docking strand and thus ultimately the amount of target.
  • the docking and imager strands are typically selected such that their bound states have a thermal stability in the range of about +/ ⁇ 0.5 kcal/mol. With this range of thermal stability, it is possible to select at least 200 orthogonal (e.g., different) sequences to be used in these multiplexing methods.
  • a protein is an antibody such as a primary antibody or a secondary antibody, an antigen-binding antibody fragment, or a peptide aptamer.
  • a protein is linked to the docking strand through an intermediate linker.
  • the intermediate linker comprises biotin and streptavidin.
  • an antibody is a monoclonal antibody.
  • a complementary fluorescently-labeled imager strand comprises at least one fluorophore.
  • a complementary labeled, optionally fluorescently labeled, imager strand is about 4 to about 30 nucleotides, or about 8 to about 10 nucleotides, in length. In some embodiments, a complementary labeled imager strand is longer than 30 nucleotides.
  • the docking strand may comprise a plurality of domains, each complementary to a labeled imager strand.
  • the domains may be identical in sequence (and thus will bind to the identical imager strands) or they may be of different sequence (and thus may bind to imager strands that are not identically labeled). Such domains may also be referred to herein as binding sites for imager strands.
  • a docking strand includes at least two or at least three domains, each respectively complementary to a labeled imager strand.
  • a target bound to at least one protein-nucleic acid conjugate is provided herein.
  • the target is a protein. In some embodiments, the target is a nucleic acid (e.g., DNA or RNA).
  • a plurality of protein-nucleic acid conjugates In some embodiments, the plurality comprises at least two subsets of the protein-nucleic acid conjugates, and the protein-nucleic acid conjugates of each subset bind to different targets.
  • composition or kit comprising a plurality of protein-nucleic acid conjugates, optionally wherein at least one of the protein-nucleic acid conjugates is bound to at least one target.
  • composition or kit comprising at least one protein-nucleic acid conjugate that comprises a protein linked to a docking strand, optionally wherein the at least one protein-nucleic acid conjugate is bound to a target, and at least one complementary labeled, optionally fluorescently labeled, imager strand that is transiently bound to (or is capable of transiently binding to) the at least one protein-nucleic acid conjugate.
  • a composition or kit comprises at least two complementary labeled, optionally fluorescently labeled, imager strands, wherein the at least two complementary labeled imager strands are identical. In some embodiments, the composition or kit comprises at least two complementary labeled imager strands, wherein the at least two complementary labeled imager strands are different.
  • the number of complementary labeled, optionally fluorescently labeled, imager strands is less than, greater than or equal to the number of protein-nucleic acid conjugates.
  • a composition or kit comprises at least 2, 3, 4, 5, 6, 7, 9 or 10 different complementary labeled, optionally fluorescently labeled, imager strands. In some embodiments, the composition or kit comprises at least 50 or at least 100 different complementary fluorescently-labeled imager strands.
  • a composition or a kit comprising a (e.g., one or more) docking strand and an (e.g., one or more) imager strand.
  • the docking strand may be modified to include an affinity label, thereby facilitating its subsequent attachment to one or more binding partners, such as an antibodies.
  • the docking strand may be biotinylated or it may be attached to avidin or streptavidin. Other affinity labels can be used instead.
  • the imager strands may be labeled, such as fluorescently labeled.
  • the imager strands may be a plurality of identical imager strands (e.g., with respect to sequence and label) or they may be a plurality of different imager strands (e.g., with respect to sequence and label).
  • the composition or kit may further comprise a target-specific binding partner, such as an antibody. It is to be understood that the components may be bound to each other or they may be unbound, including physically separated from each other, in such compositions and kits. These and other compositions and kits may further comprise one or more buffers including oxygen scavengers.
  • composition or kit comprising an antibody-nucleic acid conjugate, wherein the antibody is a “secondary antibody” having specificity for an antibody, typically specificity for a particular isotype or an Fc domain of an antibody from a particular species (e.g., a mouse antibody that is specific for a human IgG1 antibody).
  • the nucleic acid in the conjugate is a docking strand, as described herein.
  • the composition or kit may further comprise one or more imager strands (or one or more subsets or populations of imager strands), as described herein. These and other compositions and kits may further comprise one or more buffers including oxygen scavengers.
  • the present disclosure provides an antibody-DNA conjugate, comprising a monoclonal antibody linked to a docking strand that is bound to a complementary labeled, optionally fluorescently labeled, imager strand, wherein the antibody and the docking strand are each biotinylated and linked to each other through an avidin or streptavidin linker or a biotin-streptavidin linker.
  • an aptamer-nucleic acid conjugate comprising a nucleic acid aptamer linked to a docking strand that is transiently bound to a complementary labeled, optionally fluorescently labeled, imager strand.
  • a method of detecting a target in a sample comprising contacting a sample with (a) at least one protein-nucleic acid conjugate that comprises a protein linked to a docking strand and (b) at least one fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the at least one protein-nucleic acid conjugate, and determining whether the at least one protein-nucleic acid conjugate binds to the target in the sample.
  • the determining step comprises imaging transient binding of the at least one fluorescently-labeled imager strand to the docking strand of the at least one protein-nucleic acid conjugate.
  • a method of detecting a target in a sample comprising contacting a sample with (a) at least one protein-nucleic acid conjugate that comprises a protein linked to a docking strand and (b) at least one fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the at least one protein-nucleic acid conjugate, and imaging transient binding, optionally using time-lapsed imaging, of the at least one fluorescently-labeled imager strand to the docking strand of the at least one protein-nucleic acid conjugate.
  • a protein of the protein-nucleic acid conjugate is an antibody, an antigen-binding antibody fragment, or a peptide aptamer.
  • an antibody is a monoclonal antibody.
  • a protein of the protein-nucleic acid conjugate is linked to the docking strand through an intermediate linker.
  • an intermediate linker comprises biotin and/or streptavidin.
  • a complementary fluorescently-labeled imager strand comprises at least one fluorophore.
  • a complementary labeled, optionally fluorescently labeled, imager strand is about 4 to about 10 nucleotides, or about 8 to about 10 nucleotides in length.
  • a sample is a cell or cell lysate.
  • a target is a protein.
  • a target is a nucleic acid (e.g., DNA or RNA).
  • a target is obtained from a cell or cell lysate.
  • a method of detecting at least one or at least two targets in a sample comprising contacting a sample with (a) at least two protein-nucleic acid conjugates, each comprising a protein linked to a docking strand, and (b) at least two labeled (optionally spectrally distinct, or fluorescently labeled, or spectrally distinct and fluorescently labeled) imager strands that are complementary to and transiently bind to respective docking strands of the at least one, or at least, two different protein-nucleic acid conjugates and determining whether the at least two protein-nucleic acid conjugates bind to at least two targets in the sample.
  • the determining step comprises, in the following order, imaging transient binding of one of the at least two labeled imager strands to a docking strand of one of the at least two protein-nucleic acid conjugates to produce a first image (e.g., of a fluorescent signal), and imaging transient binding of another of the at least two labeled imager strands to a docking strand of another of the at least two protein-nucleic acid conjugates to produce at least one other image (e.g., of a fluorescent signal).
  • the method further comprises combining the first image and the at least one other image to produce a composite image of signal (e.g., fluorescent signal), wherein the signal of the composite image is representative of the at least two targets.
  • a protein of the protein-nucleic acid conjugate is an antibody, an antigen-binding antibody fragment, or a peptide aptamer.
  • an antibody is a monoclonal antibody.
  • a protein of the protein-nucleic acid conjugate is linked to the docking strand through an intermediate linker.
  • an intermediate linker comprises biotin and streptavidin.
  • each of the at least two spectrally distinct, fluorescently-labeled imager strands comprises at least one fluorophore.
  • each of the at least two labeled, optionally spectrally distinct, fluorescently labeled, imager strands is about 4 to about 10 nucleotides, or about 8 to about 10 nucleotides in length.
  • a sample is a cell or cell lysate.
  • At least two targets are proteins. In some embodiments, at least two targets are nucleic acids (e.g., DNA or RNA).
  • At least two targets are obtained from a cell or cell lysate.
  • a method of detecting at least one, or at least two, protein targets in a sample comprising (a) contacting a sample with at least two protein-nucleic acid conjugates, each comprising a protein linked to a docking strand and (b) sequentially contacting the sample with at least two labeled (e.g., optionally spectrally indistinct, or fluorescently labeled, or spectrally distinct and fluorescently labeled) imager strands that are complementary to and transiently bind to respective docking strands of the at least two protein-nucleic acid conjugates, and determining whether the at least one or at least two protein-nucleic acid conjugates bind to at least two targets in the sample.
  • at least two labeled e.g., optionally spectrally indistinct, or fluorescently labeled, or spectrally distinct and fluorescently labeled
  • a method comprises, in the following ordered steps, contacting the sample with a first protein-nucleic acid conjugate and at least one other protein-nucleic acid conjugate, contacting the sample with a first labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the first protein-nucleic acid conjugate, imaging the sample to obtain a first image, optionally using time-lapsed imaging, removing the first labeled imager strand, contacting the sample with at least one other labeled imager strand that is complementary to and transiently binds to the docking strand of the at least one other protein-nucleic acid conjugate, and imaging the sample to obtain at least one other image, optionally using time-lapsed imaging.
  • a method comprises, in the following ordered steps, contacting a sample with a first protein-nucleic acid conjugate, contacting the sample with a first labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the first protein-nucleic acid conjugate, imaging the sample to obtain a first image, optionally using time-lapsed imaging, removing the first labeled imager strand, contacting the sample with at least one other protein-nucleic acid conjugate, contacting the sample with at least one other labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the at least one other protein-nucleic acid conjugate, and imaging the sample to obtain at least one other image, optionally using time-lapsed imaging.
  • a method further comprises determining whether the first protein-DNA conjugate binds to a first target and/or whether the at least one other protein-DNA conjugate binds to at least one other target.
  • a method further comprises assigning a pseudo-color to the signal (e.g., fluorescent signal) in a first image, and assigning at least one other pseudo-color to the fluorescent signal in the at least one other image.
  • a pseudo-color to the signal (e.g., fluorescent signal) in a first image
  • assigning at least one other pseudo-color to the fluorescent signal in the at least one other image assigning a pseudo-color to the signal (e.g., fluorescent signal) in a first image, and assigning at least one other pseudo-color to the fluorescent signal in the at least one other image.
  • a method further comprises combining a first image and the at least one other image to produce a composite image of the pseudo-colored signals, wherein the pseudo-colored signals of the composite image are representative of the at least two targets.
  • the protein of the protein-nucleic acid conjugate(s) is an antibody, an antigen-binding antibody fragment, or a peptide aptamer.
  • the antibody is a monoclonal antibody.
  • the protein of the protein-nucleic acid conjugate(s) is linked to the docking strand through an intermediate linker.
  • the intermediate linker comprises biotin and/or streptavidin.
  • each of the fluorescently-labeled imager strands comprises at least one fluorophore.
  • each of the fluorescently-labeled imager strands is about 4 to about 30 nucleotides, or about 8 to about 10 nucleotides in length.
  • a sample is a cell or cell lysate.
  • a target(s) is a protein. In some embodiments, a target(s) is a nucleic acid (e.g., DNA or RNA).
  • a target(s) is obtained from a cell or cell lysate.
  • a method of detecting a target, optionally a naturally-occurring biomolecule comprising contacting a sample containing at least one target, optionally a naturally-occurring biomolecule, with (a) at least one BP-NA conjugate, optionally each BP-NA conjugate comprising a protein or nucleic acid linked to a docking strand, and (b) at least one labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds the docking strand of the at least one BP-NA conjugate, and determining whether the at least one BP-NA conjugate binds to at least one target, optionally a naturally-occurring biomolecule, in the sample.
  • the method may be carried out using a sample that is suspected of containing at least one target or a sample that an end-user desires to analyze for the presence of the at least one target without any prior knowledge of the sample respecting its likelihood of containing the target.
  • the determining step comprises imaging transient binding of the at least one labeled, optionally fluorescently labeled, imager strand to the docking strand of the at least one BP-NA conjugate.
  • a sample is a cell or cell lysate.
  • an at least one target is obtained from a cell or cell lysate.
  • a protein is an antibody, an antigen-binding antibody fragment, or a peptide aptamer. In some embodiments, an antibody is a monoclonal antibody.
  • a protein is linked to the docking strand through an intermediate linker.
  • an intermediate linker comprises biotin and/or streptavidin.
  • a nucleic acid is a nucleic acid aptamer.
  • a fluorescently-labeled imager strand comprises at least one fluorophore.
  • an imager strand optionally a fluorescently-labeled imager strand, is about 4 to about 30, or about 8 to about 10 nucleotides in length.
  • a method of detecting a target, optionally a naturally-occurring biomolecule comprising contacting a sample containing at least two targets, optionally naturally-occurring biomolecules, with (a) at least two different BP-NA conjugates, optionally each BP-NA conjugate comprising a protein or nucleic acid linked to a DNA docking strand, and (b) at least two labeled (optionally spectrally indistinct, or fluorescently labeled, or spectrally distinct and fluorescently labeled) imager strands that are complementary to and transiently bind to respective docking strands of the at least two BP-NA conjugates, and determining whether the at least two BP-NA conjugates bind to at least one or at least two naturally-occurring biomolecules in the sample.
  • a method comprises, in the following ordered steps, contacting the sample with a first BP-NA conjugate and at least one other BP-NA conjugate, contacting the sample with a first labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the first BP-NA conjugate, imaging the sample to obtain a first image, optionally using time-lapsed imaging, removing the first labeled imager strand, contacting the sample with at least one other labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the at least one other BP-NA conjugate, and imaging the sample to obtain at least one other image, optionally using time-lapsed imaging.
  • a method comprises, in the following ordered steps, contacting the sample with a first BP-NA conjugate, contacting the sample with a first labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the first BP-NA conjugate, imaging the sample to obtain a first image, optionally using time-lapsed imaging, removing the first labeled imager strand, contacting the sample with at least one other BP-NA conjugate, contacting the sample with at least one other labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the at least one other BP-NA conjugate, and imaging the sample to obtain a at least one other image, optionally using time-lapsed imaging.
  • a method further comprises determining whether the first protein DNA conjugate binds to a first target, optionally a naturally-occurring biomolecule, and/or whether the at least one other protein-DNA conjugate binds to at least one other target, optionally a naturally-occurring biomolecule.
  • a method further comprises assigning a pseudo-color to the signal (e.g., fluorescent signal) in a first image, and assigning at least one other pseudo-color to the signal (e.g., fluorescent signal) in at least one other image.
  • a pseudo-color to the signal (e.g., fluorescent signal) in a first image
  • at least one other pseudo-color to the signal (e.g., fluorescent signal) in at least one other image.
  • a method further comprises combining a first image and at least one other image to produce a composite image of pseudo-colored signals, wherein the pseudo-colored signals of the composite image are representative of at least one, or at least two, targets (e.g., naturally-occurring biomolecules).
  • a method of determining the number of targets in a test sample comprising obtaining a sample that comprises targets transiently bound directly or indirectly to labeled, optionally fluorescently labeled, imager strands, obtaining a time-lapsed image, optionally a time-lapsed diffraction-limited fluorescence image, of the sample, performing spot detection (e.g., fluorescence spot detection) and localization (e.g., through the use of Gaussian fitting) on the diffraction-limited image to obtain a high-resolution image of the sample, calibrating k on ⁇ c imager , optionally using a control sample with a known number of targets, wherein k on is a second order association constant, and c imager is concentration of labeled (e.g., fluorescently labeled) imager strands in the test sample, determining variable ⁇ d , optionally by fitting the fluorescence OFF-time distribution to a cumulative distribution function, and determining the number
  • a method of determining a relative amount of targets in a test sample comprising obtaining a sample that comprises targets transiently bound directly or indirectly to labeled imager strands, obtaining a time-lapsed image of the sample, performing spot detection and localization on the image to obtain a high-resolution image of the sample, determining variable ⁇ d , and determining the relative amount of two or more test targets in the sample based on ⁇ d .
  • test targets are protein targets.
  • protein targets are bound to protein-nucleic acid conjugates that comprise a protein linked to a docking strand, and the labeled (e.g., fluorescently labeled) imager strands are complementary to and transiently bind to respective docking strands of the protein-nucleic acid conjugates.
  • labeled e.g., fluorescently labeled
  • the protein of the protein-nucleic acid conjugate is an antibody, an antigen-binding antibody fragment, or a peptide aptamer.
  • test targets are single-stranded nucleic acids.
  • single-stranded nucleic acids are DNA or RNA.
  • each of the fluorescently-labeled imager strands comprises at least one fluorophore.
  • each of the labeled, optionally fluorescently labeled, imager strands is about 4 to about 30 nucleotides, or about 8 to about 10 nucleotides in length.
  • a time-lapsed fluorescence image is obtained over a period of about 25 minutes.
  • the number of test targets is determined with an accuracy of greater than 90%.
  • a single-stranded DNA probe comprising a target binding domain of about 20 nucleotides in length linked, optionally at its 3′ end, to a docking domain of at least one, at least two, or at least three subdomains, wherein the at at least one, least two, or at least three subdomains are respectively complementary to at least one, at least two, or at least three labeled, optionally fluorescently labeled, imager strands of about 4 to about 30, or about 8 to 10 nucleotides in length, and wherein the target binding domain is bound to a complementary domain of a single-stranded mRNA target strand.
  • At least one of the at least one, at least two, or at least three subdomains is transiently bound to at least one labeled, optionally fluorescently labeled, imager strand.
  • a method of performing drift correction for a plurality of images comprising determining a time trace for each of a plurality of drift markers identified in the plurality of images, wherein a time trace for each drift marker corresponds to movement of an object in the image over the time sequence of images, determining, with at least one computer processor, a first drift correction from at least one of the plurality of drift markers based, at least in part, on the time traces for the plurality of drift markers, determining a time trace for each of a plurality of geometrically-addressable marker sites from a plurality of drift templates identified from the plurality of images, wherein each drift template in the plurality of drift templates describes a geometrical relationship between the plurality of geometrically-addressable marker sites of transient events in the drift template, determining a second drift correction based, at
  • a method further comprises identifying a plurality of localizations in each of the plurality of images, creating a two-dimensional histogram of the plurality of localizations, and identifying locations of the plurality of drift markers based, at least in part, on the two-dimensional histogram, wherein determining the time traces for each of the plurality of drift markers comprises determining the time traces based, at least in part, on the locations of the plurality of drift markers.
  • identifying a plurality of localizations comprises identifying a plurality of spots on each of the plurality of images, and determining a fitted center position of each of the plurality of spots using a local Gaussian fitting algorithm, wherein each of the plurality of localizations comprises the spot identified on an image and its associated fitted center position.
  • each of the plurality of localizations further comprises a detected photon count corresponding to the localization.
  • creating the two-dimensional histogram of the plurality of localizations comprises binning all localizations into a two-dimensional grid and using a total number of localizations in each bin as a histogram count.
  • creating the two-dimensional histogram of the plurality of localizations comprises binning all localizations into a two-dimensional grid and using a total number of photon count of the plurality of localizations in each bin as a histogram count.
  • identifying locations of the plurality of drift markers based, at least in part, on the two-dimensional histogram comprises at least one of the following: binarizing the two-dimensional histogram using one or more selection criteria, wherein the one or more selection criteria include a lower-bound threshold of a histogram value or a upper-bound threshold of a histogram value; partitioning the binarized image into partitions and filtering the partitions based on one or more selection criteria, wherein the one or more selection criteria include one or more of a lower-bound threshold of an area of a partition area, an upper-bound threshold of the area, a lower-bound or an upper-bound of a longest or shortest linear dimension of a partition longest, and a lower-bound or an upper-bound of an eccentricity of a partition; and expanding and shrinking the binarized image using one or more binary image operations, wherein the one or more binary image operations include one or more of the following: dilate, erode, bridge, close, open, fill, clean, top-hat,
  • determining a first drift correction based, at least in part, on the time traces for the plurality of drift markers comprises: determining a relative time trace for each of the plurality of drift markers, wherein the relative time trace is determined by comparing the time trace for the drift marker with the average position of the same trace; and determining a combined time trace based on the relative time traces for each of the plurality of drift markers, wherein determining the first drift correction based, at least in part, on the time traces for the plurality of drift markers comprises determining the first drift correction based, at least in part, on the relative time traces for each of the plurality of drift markers.
  • determining the first drift correction based, at least in part, on the relative time traces for each of the plurality of drift markers comprises performing a weighted average of the relative time traces for each of the plurality of drift markers.
  • performing the weighted average comprises: determining a quality score for each of the relative time traces, wherein the quality score is determined based, at least in part, on a measure of variability over time associated with the time trace and/or a measure of localization uncertainty of individual localizations within the time trace.
  • the measure of variability over time comprises a standard deviation of the time trace over time.
  • the measure of localization uncertainty of individual localizations comprises, at least in part, an estimate of uncertainty from a Gaussian fitting or a comparison with other simultaneous localizations, wherein the other simultaneous localizations are from within a same image and from other time traces from the plurality of drift markers, wherein the comparison comprises a mean and standard deviation of all simultaneous localizations.
  • the method further comprises determining that a first drift marker of the plurality of drift markers is not present in at least one frame of the time sequence of images, and linearly interpolating the time trace for the first drift marker for the at least one frame to produce a smoothed time trace for the first drift marker.
  • determining a time trace for each of a plurality of geometrically-addressable marker sites from a plurality of drift templates identified from the plurality of images comprises: identifying a plurality of localizations in each of the plurality of images; creating a two-dimensional histogram of the plurality of localizations; and identifying the plurality of drift templates based, at least in part, on the two-dimensional histogram, wherein identifying the plurality of drift templates comprises evaluating the two-dimensional histogram using an lower-bound and/or an upper-bound threshold in a histogram count.
  • determining a time trace for each of a plurality of geometrically-addressable marker sites from a plurality of drift templates identified from the plurality of images comprises determining a time trace for each of a plurality of geometrically-addressable marker sites within each of the plurality of drift templates, and wherein determining the second drift correction comprises determining the second drift correction based, at least in part, on the time traces for each of the plurality of marker sites within each of the plurality of drift templates.
  • determining the second drift correction based, at least in part, on the time traces for each of the plurality of geometrically-addressable marker sites from each of the plurality of drift templates comprises: identifying a plurality of geometrically-addressable marker sites within each of the plurality of drift templates; and determining a relative time trace for each of a plurality of geometrically-addressable drift markers for each of the plurality of drift templates, wherein determining the second drift correction based, at least in part, on the time traces for the plurality of drift templates comprises determining the second drift correction based, at least in part, on the relative time traces for each of the plurality of drift markers within each of the plurality of drift templates.
  • identifying a plurality of geometrically addressable marker sites from each of the plurality of drift templates comprises determining a plurality of marker sites based on, at least in part, a two-dimensional histogram of the plurality of localizations in the corresponding drift template, and/or one or more selection criteria, wherein the one or more selection criteria include one or more of a total number of localizations, a surface density of localizations, and standard deviation of localizations.
  • determining the second drift correction based, at least in part, on the relative time traces for each of the plurality of drift markers within each of the plurality of drift templates comprises performing a weighted average of the relative time traces for each of the plurality of drift markers within each of the drift templates.
  • performing the weighted average comprises:
  • the quality score is determined based, at least in part, on a measure of variability over time associated with the time trace and/or a localization uncertainty within the time trace.
  • the measure of variability over time comprises a standard deviation of the time trace over time.
  • the measure of localization uncertainty of individual localizations comprises an estimate of uncertainty from a Gaussian fitting or a comparison with other simultaneous localizations, wherein the other simultaneous localizations are from within a same image and from the other time traces from the plurality of marker sites from the plurality of drift templates, wherein the comparison comprises a mean and standard deviation of all simultaneous localizations.
  • correcting the plurality of images based, at least in part, on the first drift correction and the second drift correction comprises correcting the plurality images using the first drift correction to produce a first corrected plurality of images, and wherein determining a time trace for each of a plurality of drift templates identified from the plurality of images comprises determining a time trace for each of the plurality of drift templates identified from the first corrected plurality of images.
  • a method further comprises smoothing the first drift correction prior to correcting the plurality of images using the first drift correction.
  • smoothing the first drift correction comprises processing the first drift correction using local regression with a window determined by a characteristic drift time scale of the first drift correction.
  • a method further comprises smoothing the second drift correction prior to correcting the plurality of images using the second drift correction.
  • smoothing the second drift correction comprises processing the second drift correction using local regression with a window determined by a characteristic drift time scale of the second drift correction.
  • a method further comprises selecting a single drift marker of the plurality of drift markers; and determining a third drift correction based, at least in part, on the selected single drift marker, wherein correcting the plurality of images comprises correcting the plurality of images based, at least in part, on the third drift correction.
  • correcting the plurality of images based, at least in part, on the third drift correction is performed prior to correcting the plurality of images based, at least in part on the first drift correction and the second drift correction.
  • a method further comprises identifying locations of a first plurality of points in a first image of the plurality of frames; identifying locations of a second plurality of points in a second image of the plurality of images, wherein the second image corresponds to a neighboring frame of the first image in the time sequence of images; and determining a fourth drift correction based, at least in part, on differences between the locations of the first plurality of points and the second plurality of points, wherein correcting the plurality of images comprises correcting the plurality of images based, at least in part, on the fourth drift correction.
  • the second image corresponds to a frame immediately following the frame corresponding to the first image in the time sequence of images.
  • determining the fourth drift correction based, at least in part, on differences between the locations of the first plurality of points and the second plurality of points comprises: creating a histogram of distances between the locations of the first plurality of points and the second plurality of points; determining based, at least in part, on the histogram, pairs of points between the first image and the second image that correspond to the same transient event; and determining a location offset between each of the determined pairs of points, wherein determining the fourth drift correction is based on a vector average of the location offsets for each of the determined pairs of points.
  • the plurality of images correspond to DNA-based images and wherein the plurality of transient events are binding events between an imaging strand and a DNA docking strand.
  • the imaging strand is a fluorescent imaging probe configured to fluoresce when associated with the DNA docking strand.
  • At least one of the drift markers is a DNA based nanostructure.
  • the DNA based nanostructure is a DNA origami nanostructure with docking strands.
  • At least one of the drift templates is a DNA based nanostructure.
  • the DNA based nanostructure is a DNA origami nanostructure with docking strands.
  • At least one of the drift templates is a three-dimensional drift template.
  • the three-dimensional drift template is a tetrahedron.
  • At least one of the drift templates includes multiple colors corresponding to different types of transient events.
  • the different types of transient events include a first binding event of a first imaging strand with a first type of DNA docking strand and a second binding event of a second imaging strand with a second type of DNA docking strand.
  • outputting the final image comprises displaying the final image on a display.
  • outputting the final image comprises sending the final image to a computer via at least one network.
  • outputting the final image comprises storing the final image on at least one storage device.
  • a non-transitory computer readable medium encoded with a plurality of instructions that, when executed by at least one computer processor, performs a method of performing drift correction for a plurality of images, wherein each of the plurality of images comprises a frame of a time sequence of images, wherein the time sequence of images captures a plurality of transient events, the method comprising: determining a time trace for each of a plurality of drift markers identified in the plurality of images, wherein a time trace for each drift marker corresponds to movement of an object in the image over the time sequence of images; determining a first drift correction from at least one of the plurality of drift markers based, at least in part, on the time traces for the plurality of drift markers; determining a time trace for each of a plurality of geometrically-addressable marker sites from a plurality of drift templates identified from the plurality of images, wherein each drift template in the plurality of drift templates describes a geometrical relationship between the plurality of geometrically-
  • a computer comprising: an input interface configured to receive a plurality of images, wherein each of the plurality of images comprises a frame of a time sequence of images, wherein the time sequence of images captures a plurality of transient events; at least one processor programmed to: determine a time trace for each of a plurality of drift markers identified in the plurality of images, wherein a time trace for each drift marker corresponds to movement of an object in the image over the time sequence of images; determine a first drift correction from at least one of the plurality of drift markers based, at least in part, on the time traces for the plurality of drift markers; determine a time trace for each of a plurality of geometrically-addressable marker sites from a plurality of drift templates identified from the plurality of images, wherein each drift template in the plurality of drift templates describes a geometrical relationship between the plurality of geometrically-addressable marker sites of transient events in the drift template; determine a second drift correction based, at least in part
  • FIG. 1A shows microtubule-like DNA origami polymers “labeled” with single-stranded DNA docking strands on a pair of opposite faces (colored in dark gray) spaced approximately 16 nanometers (nm) apart.
  • Complementary fluorescently-labeled imager strands transiently bind from solution to the docking strands.
  • Biotinylated DNA strands (present on the bottom two center helices) are used to bind the microtubule-like DNA structures to glass surfaces for fluorescence imaging.
  • FIG. 1B shows a graph demonstrating that transient binding of fluorescently-labeled imager strands to the docking strands produces fluorescence “blinking”(fluorescence intensity vs. time trace).
  • FIG. 1C shows a transmission electron microscope (TEM) image of DNA origami polymers with a measured width of 16 ⁇ 1 nm (mean ⁇ stdv) [scale bar: 40 nm].
  • FIG. 1D shows super-resolution fluorescence images obtained using Cy3b-labeled imager strands (15,000 frames, 5 Hz frame rate). Two distinct lines are visible [scale bars: 40 nm].
  • FIG. 1E shows a cross-sectional histogram of highlighted areas ⁇ i> and ⁇ ii> in FIG. 1D (arrows denote histogram direction), which show that the designed distance of approximately 16 nm is clearly resolved (full width at half maximum (FWHM) of each distribution is observed to be approximately 9 nm).
  • FWHM full width at half maximum
  • FIG. 2 shows an example of a biomolecule labeling scheme of the present disclosure where a protein (e.g., protein target) is labeled with antibody-DNA conjugates of the present disclosure and complementary fluorescently-labeled imager strands.
  • the antibodies are linked to the docking strands through a linker that contains biotin and streptavidin (e.g., biotin-streptavidin-biotin linker).
  • FIG. 3A shows a super-resolution image of a microtubule network inside a fixed HeLa cell using an antibody-DNA conjugate and Atto655-labeled imager strands (10,000 frames, 10 Hz frame rate) [scale bar: 5 ⁇ m].
  • FIG. 3B shows a high magnification image of the highlighted area in FIG. 3A [scale bar: 1 ⁇ m].
  • FIG. 3C shows a diffraction-limited representation of the same area in FIG. 3B . Arrows highlight positions where the increase in resolution of the image is clearly visible. Adjacent microtubules with an apparent width of approximately 46 nm at position ⁇ i> in FIG. 3B are separated by approximately 79 nm [scale bar: 1 ⁇ m].
  • FIG. 3A shows a super-resolution image of a microtubule network inside a fixed HeLa cell using an antibody-DNA conjugate and Atto655-labeled imager strands (10,000 frames, 10 Hz frame rate) [scale bar: 5
  • 3D shows a dual-color super-resolution image (15,000 frames, 10 Hz frame rate) of microtubules and mitochondria inside a fixed HeLa cell obtained using antibody-DNA conjugates, Cy3b-labeled imager strands for microtubules (linear-like structures) and Atto655-labeled imager strands for mitochondria (patch-like structures) [scale bar: 5 ⁇ m].
  • FIG. 3E shows a high magnification image of the highlighted area in FIG. 3D [scale bar: 1 ⁇ m].
  • FIG. 3F shows a diffraction-limited image of the same area shown in FIG. 3E [scale bar: 1 ⁇ m].
  • FIG. 4A shows one embodiment of the present disclosure using spectrally indistinct imager strands (e.g., each labeled with the same color fluorophore).
  • three different species of docking strands (a,b,c) label a surface. Such labeling may occur using the docking strand alone or linked to a protein-binding (e.g., antibody) or a nucleic acid-binding molecule that binds to the surface/biomolecule of interest.
  • step [2] multiple copies of the imager strand a* are introduced (where a* has a sequence complementary to a), and points labeled with docking strands a are imaged.
  • step [3] copies of the imager strand a* are flushed away, and imager strand b* is introduced to image the b labeled points. Images are obtained, and imager strands b* are washed away.
  • step [4] c labeled points are imaged in the same manner.
  • images from [2-4] are assigned pseudo-colors and combined to create the final image. Although pseudo-colors may be used in the final rendering of the image, all imager strands are actually labeled with the same color dye (e.g., fluorophore).
  • FIG. 4B ( 1 )- 4 B( 3 ) show that reducing the image density simultaneously increases the achievable resolution by up to a factor of 2 ⁇ square root over (2) ⁇ ln 2 ⁇ 2.35.
  • the resolution previously defined as the FWHM of the reconstructed localizations, can be understood as the standard deviation of the localization as in localization microscopy with sparse points.
  • FIG. 4B ( 1 ) shows seven points in a linear geometry spaced at 10 nm (top). Simulated super-resolution data with approximately 14 nm resolution (center). The points cannot be resolved.
  • Cross-sectional histogram data shows a broad peak (bottom).
  • FIGS. 4B ( 2 ) and 4 B( 3 ) show that imaging every other site allows the localization of individual spots. These localizations can then be combined to form the final image of the full pattern.
  • FIG. 4C shows an image of a DNA origami structure that displays docking strands spaced at 10 nm intervals.
  • FIG. 5A shows one embodiment of the present disclosure using DNA origami structures with different species of docking strands at designated positions resembling numbers 0-3 (0, 1, 2 and 3).
  • the respective imager strand sequence is added to an imaging chamber, image acquisition is carried out and the imager strands are washed out.
  • the designed number is imaged, showing a very sequence-specific interaction with no crosstalk between different rounds [Scale bar: 50 nm].
  • Note that all imager strands are labeled with the same color dye, though each structure (e.g., 0-3 (0, 1, 2 and 3)) is rendered a distinct color (e.g., purple, yellow, blue, or red; color rendering not shown).
  • FIG. 5B (i)-(v) show another embodiment of the present disclosure using DNA origami structures with different species of docking strands at designated positions resembling numbers 0-9 (0, 1, 2, 3, 4, 5, 6, 7, 8 and 9).
  • FIG. 5B (i) shows an exchange-PAINT schematic showing sequential imaging of multiple targets using imager strands labeled with the same fluorophore.
  • FIG. 5B (ii) shows a schematic of a DNA origami (70 100 nm) displaying docking strands that resemble digit 4.
  • FIG. 5B (iii) shows a combined overview image of all ten Exchange-PAINT cycles, demonstrating specific interaction with the respective target with no crosstalk between imaging cycles. Scale bar: 250 nm.
  • FIG. 5B (iv) shows a four-“color” image of digits 0 to 3 that are all present on the same DNA origami (10,000 frames each, 5 Hz frame rate; schematic at the bottom). Scale bar: 25 nm.
  • FIG. 5B (v) shows pseudocolor images of ten different origami structures, each rendered a distinct color (e.g., orange, green, blue, purple, pink, etc.; color rendering not shown), displaying digits 0 to 9 in one sample with high resolution (FWHM of bar-like features ⁇ 10 nm) and specificity. Image obtained using only one fluorophore (Cy3b) through ten imaging-washing cycles (imaging: 7,500 frames per cycle, 5 Hz frame rate; washing: 1-2 minutes per cycle). Scale bar: 25 nm.
  • FIG. 6A shows an experimental schematic for one embodiment of the present disclosure using fixed HeLa cells, where in one round, docking strands are bound to a target, labeled imager strands are then added, an image is acquired, and the imager strands are washed away. Each round is repeated with docking strands specific for different targets along with different labeled imager strands.
  • the docking strands may be used alone or linked to a protein-binding (e.g., antibody) or a nucleic acid-binding molecule that binds to the target of interest.
  • FIG. 6B shows two rounds of a method of the present disclosure using Cy3b-labeled imager strands in fixed HeLa cells.
  • FIG. 6C shows two rounds of a method of the present disclosure using ATTO655-labeled imager strands performed in fixed HeLa cells similar to FIG. 6B . [Scale bars: 5 ⁇ m]. Note that all imager strands are labeled with the same color dye.
  • FIG. 7A shows that fluorescently-labeled imager strands transiently bind from solution to complementary docking strands on a structure or molecule of interest.
  • the transient binding produces an apparent blinking as shown in the binding vs. time trace with characteristic fluorescence ON- and OFF-times ( ⁇ b and ⁇ d , respectively).
  • the detected binding frequency of imager strands from solution is linearly dependent on the number of available docking strands in a given image area (i.e., the more docking strands, the higher the binding frequency).
  • the time in-between binding events, i.e., the fluorescence OFF-time ( ⁇ d ) is inversely proportional to the number of docking strands.
  • FIG. 7C shows a super-resolution image of DNA origami structures designed to display 13 binding sites as a proof-of-concept platform. The incorporation efficiency for docking sites is not 100% leading to a distribution of actually incorporated sites ( FIG. 7D ( 1 )).
  • FIG. 7D ( 1 ) shows the binding site distribution for 377 origami structures obtained by direct visual counting.
  • FIG. 7D ( 2 ) shows the binding site distribution for the same structures obtained by binding kinetic analysis (kinetics) of the present disclosure.
  • FIG. 7D ( 3 ) shows the “offset” between direct and kinetic counting: the counting “error” or uncertainty for the method of the present disclosure is less than 7% (determined by the coefficient of variation of the Gaussian distribution).
  • FIG. 8A shows mRNA molecules of interest in fixed Escherichia coli cells tagged using docking strands in a FISH-like hybridization scheme.
  • FIG. 8B shows a readout scheme used to determine the binding frequency for each imaging color. The intensity vs. time profile of each single mRNA location yields a specific transient binding pattern (blinking) per color. The frequency of binding events depends on the number of binding sites allowing the use of the binding frequency to distinguish between different integer numbers of binding sites.
  • FIG. 8C shows an in vitro proof-of-principle experiment on DNA origami structures displaying 3, 9, 22 and 44 binding sites for each of the red, green, and blue imager strands, respectively (color rendering not shown).
  • the different binding levels are clearly distinguishable for each color, suggesting 4 possible “frequency levels” per color, yielding up to 124 different possible combinations for barcoding, e.g., mRNA molecules inside cells.
  • the barcoding space can be increased by using the fluorescence ON-time as an additional coding entity.
  • FIG. 9 shows a graph demonstrating that the fluorescence ON-time (related to the dissociation rate k off ) can be tuned independently of the fluorescence OFF-time (related to the association rate k on ). Extending the imaging/docking duplex from 9 to 10 nucleotides (nt) by adding a single CG base pair, the kinetic OFF-rate is reduced by almost one order of magnitude (8).
  • FIG. 10A shows a barcode probe that is roughly 50 nucleotide (nt) in length and can tag a biomolecule using a 21 nt target detection domain t* followed by an approximately 30 nt long “barcode” region with a combination of 8, 9, or 10 nt long binding domain for red, green, or blue imager strands.
  • 8, 9 or 10 nt long docking strands are displayed for three colors with a k off of 10, 1 and 0.1 per second, respectively (color rendering not shown).
  • FIG. 10B shows characteristic intensity vs. time traces with increased fluorescence ON-times ⁇ b for the 9 nt interaction domain compared to the 8 nt interaction domain.
  • FIG. 10C shows stochastic simulations demonstrating that k off values of 10, 1 and 0.1 per second can be distinguished.
  • FIG. 11A shows that in the traditional method of detection, where a single fluorophore is stably attached to the imaging surface (see FIG. 11B ( 1 )), a limited number of photons per “switching” event is emitted (top panel), that extraction of all photons from “replenishable” imager strands (see FIG. 11B ( 2 )) leads to higher localization accuracy per switching event (middle panel), and that a DNA metafluorophore (see FIG. 11B ( 3 ) and FIG. 11B ( 4 )) yields a significantly larger number of photons per switching event than the single fluorophore in FIG. 11B ( 2 ) (bottom).
  • FIG. 11B ( 1 )- 11 B( 3 ) show schematics of current imaging methods and methods of the present disclosure.
  • FIG. 11B ( 1 ) shows a traditional detection method (e.g., in STORM), which uses a fluorophore stably attached to the imaging surface.
  • FIG. 11B ( 2 ) shows one embodiment of a detection method of the present disclosure with fluorophores transiently binding to the imaging surface.
  • FIG. 11B ( 3 ) shows a bright metafluorophore with 8 fluorophores in a compact DNA nanostructure.
  • FIG. 11B ( 4 ) shows a conditional metafluorophore decorated with both quenchers (dark dots) and fluorophores (stars) that only fluoresces when transiently bound to the surface.
  • FIG. 11B ( 1 ) shows a traditional detection method (e.g., in STORM), which uses a fluorophore stably attached to the imaging surface.
  • FIG. 11B ( 2 )
  • FIG. 11C shows a DNA origami structure with docking sites arranged in a 4 ⁇ 3 grid, spacing 20 nm. Single sites are optically localized with an accuracy of approximately 3 nm, currently the highest demonstrated resolution [scale bar: 50 nm].
  • FIG. 11D shows a 280 nm ⁇ 240 nm DNA nano-rectangle (single-stranded tile structure ( 15 ), 10 ⁇ larger area than origami) displaying 2000 single-stranded docking strands (dots) with 7 or 5 nm spacing used as a test platform for ultra-resolution imaging [scale bar: 100 nm].
  • FIG. 12A (i) illustrates schematics showing the principle of each stage of drift correction.
  • black markers and lines indicate source data
  • gray values and curves indicate the calculated drift correction.
  • FIG. 12A (ii) shows a schematic drawing of the major type of drift markers (e.g., DNA drift markers) used in each stage.
  • FIG. 12B (i) illustrates an example structure showing the imaging quality after each stage or correction
  • FIG. 12B (ii) shows a zoomed image of the corresponding green rectangle in FIG. 12B (i) at each stage.
  • the scale bars shown in FIGS. 12B (i) and 12 B(ii) correspond to 50 nm.
  • FIG. 12C (i) illustrates an example drift trace after each stage of correction, and FIG.
  • FIG. 12C (ii) shows a zoomed image of the corresponding rectangle in FIG. 12C (i) at each stage.
  • the scale bars in FIG. 12C (i) correspond to x: 500 nm, t: 500 s, and the scale bars in FIG. 12C (ii) correspond to x: 10 nm, t: 10 s.
  • FIG. 13 illustrates a process for performing drift correction in accordance with some embodiments.
  • FIG. 14 illustrates a process for performing drift correction corresponding to stage 230 of FIG. 13 .
  • FIG. 15 illustrates a process for performing drift correction corresponding to stage 240 of FIG. 13 .
  • FIG. 16 illustrates 3D tetrahedrons used as templates for 3D drift correction.
  • the four corners are labeled with docking sites.
  • FIG. 16A shows that the four corners are clearly resolved.
  • FIG. 16B illustrates the X-Z projection of the structures with a height of ⁇ 85 nm.
  • FIG. 17 shows an illustrative implementation of computer system 600 that may be used in connection with any of the embodiments of the present disclosure described herein.
  • FIGS. 18A-18C illustrate an alternative representation of stages in a drift correction process in accordance with some embodiments of the present disclosure.
  • a super-resolved image of a 10 nm-spaced regular grid on a single-molecule DNA origami nanostructure is shown.
  • the DNA origami structure was designed to be a 5 ⁇ 8 square lattice of 10 nm spacing both vertically and horizontally.
  • FIG. 18A shows a scatter plot of collected and filtered localizations, represented by crosses.
  • FIG. 18B shows a binned 2-D histogram view of the above structure.
  • FIG. 18C shows a 1-D histogram by projecting all localizations in the rectangle in FIGS.
  • the fitted Gaussian peaks all have standard deviation in the range of 1.5-2.4 nm, allowing for 3.5-5.6 nm resolution in principle; and spacing between neighboring peaks in the range of 9.8-11.0 nm, consistent with the DNA origami design.
  • a few (5 in this case) spots are missing in the structure because of imperfect incorporation of staples in the assembly reaction, but not missed during the super-resolution imaging.
  • FIGS. 19A and 19B show that RNA aptamers modulate the fluorescence of GFP-like fluorophores.
  • FIG. 19A shows structures of HBI (green), in the context of GFP, and DMHBI.
  • FIG. 19B shows that the 13-2 RNA aptamer enhances the fluorescence of DMHBI by stabilizing a particular molecular arrangement favorable for fluorescence emission. Solutions containing DMHBI, 13-2 RNA, DMHBI with 13-2 RNA, or DMHBI with total HeLa cell RNA were photographed under illumination with 365 nm of light. The image is a montage obtained under identical image-acquisition conditions. (Image from Paige et al., ref. 19)
  • FIGS. 20A and 20B show single-molecule fluorescence characterization of the DFHBI binding kinetics.
  • FIG. 20A shows a 5′-extended Spinach (green) is immobilized on a
  • FIG. 20B shows a bulk fluorescence measurement of the Spinach-DFHBI before (bottom line) and after (top line) addition of the aptamer shows that the DFHBI binding activity is well maintained after the addition an extension to Spinach required for immobilizing to the glass surface in FIG. 20A .
  • FIGS. 21A and 21B show benchmarking Spinach-PAINT performance.
  • FIG. 20A shows a six-helix DNA origami structure used for placing two Spinach molecules in a defined distance.
  • FIG. 20B shows a simulated representation of a super-resolved reconstruction using DNA-PAINT to localize the DNA structure (P) and Spinach-PAINT to localize the Spinach molecules in three different distances.
  • FIG. 22 shows Spinach-based sensors.
  • the allosteric variant of the Spinach-based sensor (left) comprises the Spinach domain (black), the transducer module (medium gray), and the recognition module (light gray).
  • the transducer module In the absence of the target molecule, the transducer module is in a primarily unstructured state, which prevents the stabilization of the Spinach structure needed for activation of DFHBI.
  • the transducer module Upon binding of the target molecule, the transducer module forms a duplex, leading to structural rigidification of the Spinach module, and activation of DFHBI fluorescence (ref. 24).
  • FIGS. 23A and 23B show examples of in vitro and in situ Exchange-PAINT chambers.
  • the present disclosure provides, inter alia, methods, compositions and kits for multiplexed imaging, for example, in a cellular environment using nucleic acid-based imaging probes (e.g., DNA-based imaging probes).
  • the methods, compositions and kits for multiplexed fluorescence imaging are not limited by the degree of resolution attained. Thus, the methods, compositions and kits as provided herein may be used for imaging, generally.
  • the present disclosure further provides, inter alia, methods, compositions and kits for multiplexed super-resolution fluorescence imaging, for example, in a cellular environment using nucleic acid-based imaging probes (e.g., DNA-based imaging probes).
  • nucleic acid-based imaging probes e.g., DNA-based imaging probes.
  • “super-resolution” imaging refers to the process of combining a set of low resolution images of the same area to obtain a single image of higher resolution.
  • Many aspects of the present disclosure may be used to “switch” targets (e.g., biomolecules) of interest between fluorescent ON- and OFF-states to permit consecutive, or in some instances simultaneous, localization of individual targets.
  • a fluorescent “ON” state is a state in which fluorescence is emitted.
  • a fluorescent “OFF” state is a state in which fluorescence is not emitted. Switching between the two states is achieved, in some embodiments, with diffusing molecules that are labeled with a detectable label (e.g., fluorescent molecules) that interact transiently with the targets using an intermediate moiety that comprises the detectable label (e.g., fluorescent molecule(s)) and binds to the target.
  • a detectable label e.g., fluorescent molecules
  • an intermediate moiety that comprises the detectable label (e.g., fluorescent molecule(s)) and binds to the target.
  • Binding partner-nucleic acid conjugates (“BP-NA conjugates”) of the present disclosure transiently bind to complementary labeled, optionally fluorescently labeled, imager strands.
  • binding partner-nucleic acid conjugate or “BP-NA conjugate,” refers to a molecule linked (e.g., through an N-Hydroxysuccinimide (NHS) linker) to a single-stranded nucleic acid (e.g., DNA) docking strand.
  • NHS N-Hydroxysuccinimide
  • the binding partner of the conjugate may be any moiety (e.g., antibody or aptamer) that has an affinity for (e.g., binds to) a target, such as a biomolecule (e.g., protein or nucleic acid), of interest.
  • a target such as a biomolecule (e.g., protein or nucleic acid), of interest.
  • the binding partner is a protein.
  • BP-NA-conjugates that comprise a protein (or peptide) linked to a docking strand may be referred to herein as “protein-nucleic acid conjugates,” or “protein-NA conjugates.”
  • proteins for use in the conjugates of the present disclosure include, without limitation, antibodies (e.g., monoclonal monobodies), antigen-binding antibody fragments (e.g., Fab fragments), receptors, peptides and peptide aptamers.
  • Other binding partners may be used in accordance with the present disclosure. For example, binding partners that bind to targets through electrostatic (e.g., electrostatic particles), hydrophobic or magnetic (e.g., magnetic particles) interactions are contemplated herein.
  • antibody includes full-length antibodies and any antigen binding fragment (e.g., “antigen-binding portion”) or single chain thereof.
  • the term “antibody” includes, without limitation, a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding portion thereof.
  • Antibodies may be polyclonal or monoclonal; xenogeneic, allogeneic, or syngeneic; or modified forms thereof (e.g., humanized, chimeric).
  • antigen-binding portion of an antibody, refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen.
  • the antigen-binding function of an antibody can be performed by fragments of a full-length antibody.
  • binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the V H , V L , C L and C H1 domains; (ii) a F(ab′)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 V H and C H1 domains; (iv) a Fv fragment consisting of the V H and V L domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., Nature 341:544 546, 1989), which consists of a V H domain; and (vi) an isolated complementarity determining region (CDR) or (vii) a combination of two or more isolated CDRs, which may optionally be joined by a synthetic linker.
  • a Fab fragment a monovalent fragment consisting of the V H , V
  • the two domains of the Fv fragment, V H and V L 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 V H and V L regions pair to form monovalent molecules (known as single chain Fv (scFv); see, e.g., Bird et al. Science 242:423 426, 1988; and Huston et al. Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also encompassed within the term “antigen-binding portion” of an antibody.
  • receptors refer to cellular-derived molecules (e.g., proteins) that bind to ligands such as, for example, peptides or small molecules (e.g., low molecular weight ( ⁇ 900 Daltons) organic or inorganic compounds).
  • ligands such as, for example, peptides or small molecules (e.g., low molecular weight ( ⁇ 900 Daltons) organic or inorganic compounds).
  • peptide aptamer refers to a molecule with a variable peptide sequence inserted into a constant scaffold protein (see, e.g., Baines I C, et al. Drug Discov. Today 11:334-341, 2006).
  • the molecule of the BP-NA conjugate is a nucleic acid such as, for example, a nucleic acid aptamer.
  • nucleic acid aptamer refers to a small RNA or DNA molecules that can form secondary and tertiary structures capable of specifically binding proteins or other cellular targets (see, e.g., Ni X, et al. Curr Med Chem. 18(27): 4206-4214, 2011).
  • the BP-NA conjugate may be an aptamer-nucleic acid conjugate.
  • a “docking strand” refers to a single-stranded nucleic acid (e.g., DNA) that is about 5 nucleotides to about 50 nucleotides in length (or is 5 nucleotides to 50 nucleotides in length). In some embodiments, a docking strand is about 4 to about 60, about 6 nucleotides to about 40 nucleotides, about 7 nucleotides to about 30 nucleotides, about 8 to about 20 nucleotides, or about 9 nucleotides to about 15 nucleotides in length.
  • a docking strand is (or is about) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, or more nucleotides in length.
  • a docking strand may have one domain or more than one domain (i.e., a plurality of domains), each domain complementary to a respective imager strand.
  • a “docking strand domain” refers to a nucleotide sequence of the docking strand that is complementary to a nucleotide sequence of an imager strand.
  • a docking strand may contain one, two three, or more domains, each domain complementary to an imager strand.
  • Each complementary imager strand can contain a distinct label (e.g., a red fluorophore, a blue fluorophore, or a green fluorophore), or all complementary imager strands can contain the same label (e.g., red fluorophores).
  • the strand may contain a first domain complementary to an imager strand labeled with a red fluorophore, a second domain complementary to an imager strand labeled with a blue fluorophore, and a third domain complementary to an imager strand labeled with a green fluorophore.
  • each of three docking domains may be complementary to imager strands labeled with a red fluorophore.
  • a docking strand has at least 2, at least 3, at least 4, at least 5, or more domains, each respectively complementary to an imager strand.
  • a docking strand has 1 to 5, 1 to 10, 1 to 15, 1 to 20, 1 to 25, 1 to 50, or 1 to 100 domains, each respectively complementary to an imager strand.
  • an “imager strand” is a single-stranded nucleic acid (e.g., DNA) that is about 4 to about 30 nucleotides, about 5 to about 18 nucleotides, about 6 to about 15 nucleotides, about 7 to about 12 nucleotides, or about 8 to 10 nucleotides in length and is fluorescently-labeled.
  • the imager strand may be (or may be about) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides in length.
  • An imager strand of the present disclosure is complementary to and transiently binds to a docking strand.
  • nucleic acids or nucleic acid domains are “complementary” to one another if they base-pair, or bind, with each other to form a double-stranded nucleic acid molecule via Watson-Crick interactions.
  • binding refers to an association between at least two molecules due to, for example, electrostatic, hydrophobic, ionic and/or hydrogen-bond interactions under physiological conditions.
  • An imager strand is considered to “transiently bind” to a docking strand if it binds to a complementary region of a docking strand and then disassociates (unbinds) from the docking strand within a short period of time, for example, at room temperature.
  • an imager strand remains bound to a docking strand for about 0.1 to about 10, or about 0.1 to about 5 seconds.
  • an imager strand may remain bound to a docking strand for about 0.1, about 1, about 5 or about 10 seconds.
  • Imager strands of the present disclosure may be labeled with a detectable label (e.g., a fluorescent label, and thus are considered “fluorescently labeled”).
  • a detectable label e.g., a fluorescent label, and thus are considered “fluorescently labeled”.
  • an imager strand may comprise at least one (i.e., one or more) fluorophore.
  • spectrally distinct molecules of the present disclosure refer to molecules with labels (e.g., fluorophores) of different spectral signal or wavelength.
  • labels e.g., fluorophores
  • an imager strand labeled with a Cy2 fluorophore emits a signal at a wavelength of light of about 510 nm
  • an imager strand labeled with a Cy5 fluorophore emits a signal at a wavelength of light of about 670 nm.
  • the Cy2-labeled imager strand is considered herein to be spectrally distinct from the Cy5-labeled imager strand.
  • spectrally indistinct molecules of the present disclosure refer to molecules with labels having the same spectral signal or wavelength—that is, the emission wavelength of the labels cannot be used to distinguish between two spectrally indistinct fluorescently labeled molecules (e.g., because the wavelengths are the same or close together).
  • the BP-NA conjugates (e.g., protein-nucleic acid conjugates) of the present disclosure may, in some embodiments, comprise an intermediate linker that links (e.g., covalently or non-covalently) the molecule to a docking strand.
  • the intermediate linker may comprise biotin and/or streptavidin.
  • an antibody and a docking strand may each be biotinylated (i.e., linked to at least one biotin molecule) and linked to each other through biotin binding to an intermediate streptavidin molecule, as shown in FIG. 2 .
  • Other intermediate linkers may be used in accordance with the present disclosure.
  • an intermediate linker may not be required.
  • the docking strand of a BP-NA conjugate may be an extension (e.g., 5′ or 3′ extension) of a nucleic acid molecule such as, for example, a nucleic acid aptamer.
  • Pluralities of BP-NA conjugates e.g., protein-nucleic acid conjugates and imager strands are provided herein.
  • a plurality may be a population of the same species or distinct species.
  • a plurality of BP-NA conjugates of the same species may comprise conjugates that all bind to the same target (e.g., biomolecule) (e.g., the same epitope or region/domain).
  • a plurality of BP-NA conjugates of distinct species may comprise conjugates, or subsets of conjugates, each conjugate or subset of conjugates binding to a distinct epitope on the same target or to a distinct target.
  • a plurality of imager strands of the same species may comprise imager strands with the same nucleotide sequence and the same fluorescent label (e.g., Cy2, Cy3 or Cy4).
  • a plurality of imager strands of distinct species may comprise imager strands with distinct nucleotide sequences (e.g., DNA sequences) and distinct fluorescent labels (e.g., Cy2, Cy3 or Cy4) or with distinct nucleotide sequences and the same fluorescent (e.g., all Cy2).
  • the number of distinct species in a given plurality of BP-NA conjugates is limited by the number of binding partners (e.g., antibodies) and the number of docking strands of different nucleotide sequence (and thus complementary imager strands).
  • a plurality of BP-NA conjugates comprises at least 10, 50, 100, 500, 1000, 2000, 3000, 4000, 5000, 10 4 , 50000, 10 5 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 BP-NA conjugates.
  • a plurality of fluorescently-labeled imager strands comprises at least 10, 50, 100, 500, 1000, 2000, 3000, 4000, 5000, 10 4 , 50000, 10 5 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 fluorescently-labeled imager strands.
  • a plurality may contain 1 to about 200 or more distinct species of BP-NA conjugates and/or imager strands.
  • a plurality may contain at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200 or more distinct species.
  • a plurality may contain less than about 5 to about 200 distinct species of BP-NA conjugates and/or imager strands.
  • a plurality may contain less than 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175 or 200 distinct species.
  • a docking strand may contain, in additional to imager-binding domain(s) (e.g., one, two, three, or more, with the same or distinct fluorophores), a target domain that is complementary to and binds to a target, such as, for example, mRNA or other nucleic acid.
  • imager-binding domain(s) e.g., one, two, three, or more, with the same or distinct fluorophores
  • Methods provided herein are based, in part, on the programmability of nucleic acid docking strands and imager strands. That is, for example, docking strands and imager strands can be designed such that they bind to each other under certain conditions for a certain period of time. This programmability permits transient binding of imager strands to docking strands, as provided herein.
  • the methods provided herein are directed to identifying one or more target(s) (e.g., biomolecule(s) such as a protein or nucleic acid) in a particular sample (e.g., biological sample). In some instances, whether or not one or more target(s) is present in sample is unknown.
  • methods of the present disclosure may be used to determine the presence or absence of one or more target(s) in a sample suspected of containing the target(s).
  • a sample may contain or may be suspected of containing one or more target(s).
  • Methods provided herein can also be used to identify the absolute quantity of a single target (e.g., such as, for example, a particular protein), or the quantity of a single target relative to one or more other targets.
  • a single target e.g., such as, for example, a particular protein
  • methods provided herein may be used to identify the location of a target within a sample or relative to other targets in the sample.
  • Methods provided herein may comprise, in some embodiments, contacting a sample with (a) at least one BP-NA conjugate (e.g., protein-nucleic acid conjugate) that comprises a binding partner linked to a docking strand and (b) at least one labeled, optionally fluorescently labeled, imager strand that is complementary to and transiently binds to the docking strand of the at least one BP-NA conjugate, and then determining whether the at least one BP-NA conjugate binds to at least one target (such as a biomolecule target) in the sample.
  • BP-NA conjugate e.g., protein-nucleic acid conjugate
  • imager strand that is complementary to and transiently binds to the docking strand of the at least one BP-NA conjugate
  • the determining step comprises imaging (e.g., with time-lapsed fluorescent microscopy techniques) transient binding of the at least one labeled, optionally fluorescently labeled, imager strand to the docking strand of the at least one BP-NA conjugate.
  • Other methods provided herein may comprise, in some embodiments, contacting a sample with (a) at least two BP-NA conjugates, each comprising a binding partner linked to a docking strand, and (b) at least two labeled, optionally spectrally distinct, fluorescently labeled, imager strands that are complementary to and transiently bind to respective docking strands of the at least two different BP-NA conjugates, and then determining whether the at least two BP-NA conjugates bind to at least one, or at least two, targets (such as biomolecule targets) in the sample.
  • targets such as biomolecule targets
  • Binding of the BP-NA conjugates to respective targets can be determined by imaging transient binding of one of the at least two labeled, optionally spectrally distinct, fluorescently labeled, imager strands to a docking strand of one of the at least two BP-NA conjugates to produce a first image, and then imaging transient binding of another of the at least two labeled, optionally spectrally distinct, fluorescently labeled, imager strands to a docking strand of another of the at least two BP-NA conjugates to produce a second image.
  • the methods further comprise combining the first image and the second image to produce a composite image of signals (e.g., fluorescent signals), wherein the signals (e.g., fluorescent signals) of the composite image are representative of the at least two targets.
  • a “composite image” refers to a single image produced by combining (e.g., overlaying) multiple images of the same (or substantially similar) area.
  • a composite image may also be referred to as a super-resolution image, as described elsewhere herein.
  • FIG. 3 demonstrates one embodiment of the present disclosure in which two distinct species of BP-NA conjugates (e.g., antibody-nucleic acid conjugates) are used to label biomolecules in a fixed HeLa cell sample.
  • One species of antibody-nucleic acid conjugate comprises an antibody that recognizes and binds to an epitope on mitochondria.
  • the mitochondrial specific antibody is linked to a docking strand with a sequence complementary to a Cy3b-labled imager strand.
  • the other species of antibody-nucleic acid conjugate comprises an antibody that recognizes and binds to an epitope on microtubules.
  • the microtubule specific antibody is linked to a docking strand with a sequence complementary to an ATTO655-labeled imager strand.
  • Two spectrally distinct species of imager strands are then introduced at the same time: one species is labeled with Cy3b and is complementary to the docking strand that is linked to the mitochondrial specific antibody, and the other species is labeled with ATTO655 and is complementary to the docking strand that is linked to the microtubule specific antibody. While both the Cy3b-labled imager strand and the ATTO655-labled imager strand are present at the same time in solution with the sample, imaging is carried our sequentially in Cy3b and ATTO655 channels.
  • Yet other methods provided herein may comprise, in some embodiments, contacting a sample with (a) at least two BP-NA conjugates, each comprising a protein linked to a docking strand and (b) at least two spectrally indistinct (e.g., labeled with the same fluorophore) fluorescently-labeled imager strands that are complementary to and transiently bind to respective docking strands of the at least two BP-NA conjugates, and then determining whether the at last two BP-NA conjugates bind to at least two targets (e.g., biomolecule targets) in the sample.
  • targets e.g., biomolecule targets
  • the methods comprise, in the following ordered steps, contacting the sample with a first BP-NA conjugate and at least one other BP-NA conjugate, contacting the sample with a first fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the first BP-NA conjugate, determining whether the first BP-NA conjugate binds to a first target, removing the first fluorescently-labeled imager strand, contacting the sample with at least one other fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the at least one other BP-NA conjugate, and determining whether the at least one other BP-NA conjugate binds to at least one other target.
  • methods comprise, in the following ordered steps, contacting the sample with a first BP-NA conjugate, contacting the sample with a first fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the first BP-NA conjugate, determining whether the first BP-NA conjugate binds to a first target (e.g., biomolecule), removing the first fluorescently-labeled imager strand, contacting the sample with at least one other BP-NA conjugate, contacting the sample with at least one other fluorescently-labeled imager strand that is complementary to and transiently binds to the docking strand of the at least one other BP-NA conjugate, and determining whether the at least one other BP-NA conjugate binds to at least one other target.
  • a first target e.g., biomolecule
  • the first determining step comprises imaging transient binding of the first fluorescently-labeled imager strand to the docking strand of the first BP-NA conjugate to produce a first image
  • the second determining step comprises imaging transient binding of the at least one other fluorescently-labeled imager strand to the docking strand of the at least one other BP-NA conjugate to produce a second image.
  • the methods further comprise assigning a pseudo-color to the fluorescent signal in the first image, and assigning at least one other pseudo-color to the fluorescent signal in the second image.
  • the methods comprise combining the first image and the second image to produce a composite image of the pseudo-colored signals, wherein the pseudo-colored signals of the composite image are representative of the at least two targets (e.g., biomolecule targets).
  • the methods comprise combining the first image and the second image to produce a composite image of the pseudo-colored signals, wherein the pseudo-colored signals of the composite image are representative of the at least two targets (e.g., biomolecule targets).
  • three distinct species of docking strands (a,b,c) label the surface of a grid (chosen for illustrative purposes).
  • step [2] multiple copies of the imager strand a* are introduced, and points labeled with docking strands a are imaged.
  • copies of the imager strand a* are flushed away, and imager strand b* is introduced to image the b labeled points.
  • step [4] c labeled points are imaged in the same manner.
  • images from steps [2-4] are assigned artificial pseudo-colors (e.g., using a software program) and combined to create the final composite image. All imager strands may be labeled with the same fluorophore—that is, the imager strands are spectrally indistinct.
  • the docking strands are linked to binding partners (e.g., proteins such as antibodies, or nucleic acids such as DNA or nucleic acid aptamers).
  • An advantage of the methods of the present disclosure is that partitioning and sequential imaging can be used to obtain multiplexed super-resolved images of up to hundreds of different species using only a single optimized fluorescent dye.
  • the number of distinct nucleotide sequences e.g., DNA sequences
  • those that use an imager strand with a length of 9 nucleotides there are several hundred species within tight bounds for binding kinetics that may be used for a single sample, representing a tremendous increase in multiplexing compared to direct “traditional” imaging approaches.
  • FIG. 5A illustrates another embodiment of the present disclosure using spectrally indistinct imager strands.
  • a single DNA nanostructure displays four distinct species of docking strands (optionally linked to protein binding partners or nucleic acid binding partners) designed to resemble the digits from 0 to 3, respectively.
  • Imaging is performed sequentially using a simple flow chamber setup, first flushing in fluorescently-labeled imager strands complementary to the docking strands of the number 0, and then exchanging the solution for fluorescently-labeled imager strands with a sequence complementary to docking strands of the number 1, and so forth.
  • the resulting images have been pseudo-colored to represent the respective imaging cycles.
  • an “imaging cycle,” or “imaging round” refers to the process of introducing fluorescently-labeled imager strands complementary to docking strands under conditions that allow the imager strand to bind to the docking strand, even if such binding is transient, and obtaining an image (or imaging an area).
  • multi-domain docking strands e.g., docking strands with more than one domain
  • the following embodiments are described in terms of a docking strand binding to a target, e.g., without an intermediate binding partner. It should be understood, however, that multi-domain docking strands may be linked to a binding partner (e.g., of a BP-NA conjugate, as provided herein.
  • methods comprise contacting one or more target(s) with one or more docking strands, each containing two or more binding domains. In other embodiments, methods comprise contacting one or more target(s) with two or more docking strands, each containing one binding domain.
  • the docking strand domains may have orthogonal sequences. In the examples that follow, all three targets (protein #1-#3) are present in the sample.
  • An exemplary multiplexed target detection method follows.
  • a sample contains, or is suspected of containing, three target species—protein #1, protein #2, and protein #3.
  • Three docking strands are designed such that: the first, containing imager binding domain A, binds to protein #1; the second, containing imager binding domain B, binds to protein #2; and the third, containing imager binding domains A and B, binds to protein #3.
  • Complementary imager strand A′ binds to imager binding domain A of a docking strand and is labeled with a blue fluorophore
  • imager strand B′ binds to imager binding domain B of a docking strand and is labeled with a red fluorophore.
  • the sample is first contacted with the docking strands, and subsequently contacted with the imager strands A′ and B′.
  • the sample is then imaged.
  • the sample containing the docking strands and the imager strands is first imaged under conditions that detect the blue fluorophore. Imaging the blue fluorophore detects protein #1 and protein #3, each bound by an imager strand labeled with the blue fluorophore.
  • Imaging the red fluorophore detects protein #2 and protein #3, each bound by an imager strand labeled with the red fluorophore. Overlapping images of the red and blue fluorophores detects protein #3 only, the only protein bound by an imager strand labeled with a red fluorophore and an imager strand labeled with a blue fluorophore. Thus, the identification and location of proteins #1-#3 are identified by the overlay of images respectively detecting the red and blue fluorophores.
  • a sample contains, or is suspected of containing, three target species—protein #1, protein #2, and protein #3.
  • Three docking strands are designed such that: the first, containing imager binding domain A, binds to protein #1; the second, containing imager binding domain B, binds to protein #2; and the third, containing imager binding domains A and B, binds to protein #3.
  • Complementary imager strand A′ binds to imager binding domain A of a docking strand and is labeled with a blue fluorophore
  • imager strand B′ binds to imager binding domain B of a docking strand and is also labeled with a blue fluorophore.
  • the sample is first contacted with the docking strands, and subsequently contacted with imager strands A′.
  • the sample is then imaged under conditions that detect the blue fluorophore. Imaging the blue fluorophore detects protein #1 and protein #3, each bound by imager strand A′ labeled with the blue fluorophore.
  • the sample is then washed to remove imager strands A′.
  • the sample is contacted with imager strands B′.
  • the sample is then imaged again under conditions that detect the blue fluorophore.
  • Imaging the blue fluorophore now detects protein #2 and protein #3, each bound by imager strand B′ labeled with the blue fluorophore.
  • Overlapping images of the blue fluorophores detects protein #3 only, the only protein bound by two imager strands labeled with a blue fluorophore.
  • the identification and location of proteins #1-#3 are identified by the overlay of images detecting the blue fluorophores and is based on signal intensity.
  • a sample contains, or is suspected of containing, fifteen target species.
  • the docking strands are designed such that each target species binds to a docking strand, each docking strand containing a single distinct domain or a distinct combination of domains A-D (e.g., A, or A and B (i.e., A/B), or A/C, or A/D, or A/B/C, or A/B/D, or A/C/D, or A/B/C/D, or B, or B/C, or B/D, or B/C/D, or C, or C/D, or D).
  • A-D e.g., A, or A and B (i.e., A/B), or A/C, or A/D, or A/B/C, or A/B/D, or A/C/D, or A/B/C/D, or B, or B/C, or B/C/D, or C, or C/D, or D).
  • the imager strands are divided into two sets: the first set (set #1) contains imager strand A′ labeled by a red fluorophore and imager strand B′ labeled by a blue fluorophore; the second set contains imager strand C′ labeled with a red fluorophore and imager strand D′ labeled with a blue fluorophore.
  • the sample is first contacted with the docking strands, and subsequently contacted with imager strand set #1.
  • the sample is then imaged under conditions that detect blue and red fluorophores. Targets bound by imager strands A′ will be detected red and targets bound by imager strands B′ will be detected blue.
  • each of the 15 target species can be identified using only four imager strands and two fluorophores. It should be understood that more than four imager strands can be used as well as more than two fluorophores, depending on, for example, the number of targets.
  • the disclosure contemplates contacting target species with different docking strands domain sequence and different lengths of those sequences.
  • the length of a docking strand imager binding domain affects the duration of transient binding to an imager strand. Docking strands with longer binding domains bind to respectively complementary imager strands for longer durations relative to shorter binding domains.
  • a sample contains, or is suspected of containing, four target species.
  • Four docking strands are designed such that: the first, containing binding domain A of 10 nucleotides in length (A10), binds to protein #1; the second, containing imager binding domain A10 and imager binding domain B of 8 nucleotides in length (B8), binds to protein #2; the third, containing imager binding domain A of 8 nucleotides in length (A8) and imager binding domain B of 10 nucleotides in length (B10), binds to protein #3; and four, containing imager strand binding domain B10.
  • Imager strand A′ is 10 nucleotides in length, binds to both A8 and A10, and is labeled with a blue fluorophore.
  • Imager strand B′ is 10 nucleotides in length, binds to both B8 and B10, and is labeled with a red fluorophore.
  • the sample is first contacted with the docking strands, and subsequently contacted with imager strands A′ and B′.
  • the sample is then imaged under conditions that detect the blue fluorophore.
  • Imaging the blue fluorophore detects protein #3 and protein #4 with a longer bound time (i.e., time of binding between imager strand and docking strand) and protein #2 with a shorter bound time.
  • Imaging the red fluorophore detects protein #1 and protein #2 with a longer bound time and protein #3 with a shorter bound time.
  • Overlapping images of the blue and red fluorophores detects each of the four protein targets.
  • the present disclosure also contemplates combining multiplexed detection based on spectral resolution and duration, exchange and duration, and spectral resolution, exchange and duration.
  • a “sample” may comprise cells (or a cell), tissue, or bodily fluid such as blood (serum and/or plasma), urine, semen, lymphatic fluid, cerebrospinal fluid or amniotic fluid.
  • a sample may be obtained from (or derived from) any source including, without limitation, humans, animals, bacteria, viruses, microbes and plants.
  • a sample is a cell lysate or a tissue lysate.
  • a sample may also contain mixtures of material from one source or different sources.
  • a sample may be a spatial area or volume (e.g., a grid on an array, or a well in a plate or dish).
  • a sample includes target(s), BP-NA conjugate(s) and imager strand(s).
  • a “target” is any moiety that one wishes to observe or quantitate and for which a binding partner exists.
  • a target in some embodiments, may be non-naturally occurring.
  • the target in some embodiments, may be a biomolecule.
  • a “biomolecule” is any molecule that is produced by a living organism, including large macromolecules such as proteins, polysaccharides, lipids and nucleic acids (e.g., DNA and RNA such as mRNA), as well as small molecules such as primary metabolites, secondary metabolites, and natural products.
  • biomolecules include, without limitation, DNA, RNA, cDNA, or the DNA product of RNA subjected to reverse transcription, A23187 (Calcimycin, Calcium Ionophore), Abamectine, Abietic acid, Acetic acid, Acetylcholine, Actin, Actinomycin D, Adenosine, Adenosine diphosphate (ADP), Adenosine monophosphate (AMP), Adenosine triphosphate (ATP), Adenylate cyclase, Adonitol, Adrenaline, epinephrine, Adrenocorticotropic hormone (ACTH), Aequorin, Aflatoxin, Agar, Alamethicin, Alanine, Albumins, Aldosterone, Aleurone, Alpha-amanitin, Allantoin, Allethrin, ⁇ -Amanatin, Amino acid, Amylase, Anabolic steroid, Anethole, Angiotensinogen, Anisomycin,
  • a target may be a protein target such as, for example, proteins of a cellular environment (e.g., intracellular or membrane proteins).
  • proteins include, without limitation, fibrous proteins such as cytoskeletal proteins (e.g., actin, arp2/3, coronin, dystrophin, FtsZ, keratin, myosin, nebulin, spectrin, tau, titin, tropomyosin, tubulin and collagen) and extracellular matrix proteins (e.g., collagen, elastin, f-spondin, pikachurin, and fibronectin); globular proteins such as plasma proteins (e.g., serum amyloid P component and serum albumin), coagulation factors (e.g., complement proteins,C1-inhibitor and C3-convertase, Factor VIII, Factor XIII, fibrin, Protein C, Protein S, Protein Z, Protein Z-related protease inhibitor, thrombin, Von Willebrand
  • a target may be a nucleic acid target such as, for example, nucleic acids of a cellular environment.
  • a nucleic acid refers to a polymeric form of nucleotides of any length, such as deoxyribonucleotides or ribonucleotides, or analogs thereof.
  • a nucleic acid may be a DNA, RNA or the DNA product of RNA subjected to reverse transcription.
  • Non-limiting examples of nucleic acids include coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • loci locus
  • locus defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • nucleic acids include, without limitation, cDNA, aptamers, peptide nucleic acids (“PNA”), 2′-5′ DNA (a synthetic material with a shortened backbone that has a base-spacing that matches the A conformation of DNA; 2′-5′ DNA will not normally hybridize with DNA in the B form, but it will hybridize readily with RNA), locked nucleic acids (“LNA”), and nucleic acids with modified backbones (e.g., base- or sugar-modified forms of naturally-occurring nucleic acids).
  • PNA peptide nucleic acids
  • 2′-5′ DNA a synthetic material with a shortened backbone that has a base-spacing that matches the A conformation of DNA; 2′-5′ DNA will not normally hybridize with DNA in the B form, but it will hybridize readily with RNA
  • LNA locked nucleic acids
  • nucleic acids with modified backbones e.g., base- or sugar-modified forms of naturally-occurring nucleic acids
  • a nucleic acid may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs (“analogous” forms of purines and pyrimidines are well known in the art). If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer.
  • a nucleic acid may be a single-stranded, double-stranded, partially single-stranded, or partially double-stranded DNA or RNA.
  • a nucleic acid (e.g., a nucleic acid target) is naturally-occurring.
  • a “naturally occurring” refers to a nucleic acid that is present in organisms or viruses that exist in nature in the absence of human intervention.
  • a nucleic acid naturally occurs in an organism or virus.
  • a nucleic acid is genomic DNA, messenger RNA, ribosomal RNA, micro-RNA, pre-micro-RNA, pro-micro-RNA, viral DNA, viral RNA or piwi-RNA.
  • a nucleic acid target is not a synthetic DNA nanostructure (e.g., two-dimensional (2-D) or three-dimensional (3-D) DNA nanostructure that comprises two or more nucleic acids hybridized to each other by Watson-Crick interactions to form the 2-D or 3-D nanostructure).
  • a synthetic DNA nanostructure e.g., two-dimensional (2-D) or three-dimensional (3-D) DNA nanostructure that comprises two or more nucleic acids hybridized to each other by Watson-Crick interactions to form the 2-D or 3-D nanostructure.
  • nucleic acid docking strands and imager strands described herein can be any one of the nucleic acids described above (e.g., DNA, RNA, modified nucleic acids, nucleic acid analogues, naturally-occurring nucleic acids, synthetic nucleic acids).
  • the present disclosure also provides methods for quantitating fluorescent moieties or emitters in a dense cluster that cannot be spatially resolved using prior art imaging techniques. Prior to the invention, no systematic model existed that describes the kinetics of photoswitching of fluorescent signals.
  • Stochastic super-resolution imaging using transient binding of short oligonucleotides (e.g., imager strands) to their targets offers a unique possibility to quantitatively count integer numbers of labeled molecules in a diffraction-limited area.
  • “Switching” molecules from a fluorescent OFF- to an ON-state in the method of the present disclosure is facilitated by single-molecule nucleic acid (e.g., DNA) hybridization events, which are governed by a very predictable kinetic model with a second order association rate k on and a first order dissociation rate k off :
  • the kinetic parameters k on and k off are now directly linked to fluorescent ON- and OFF-times ( ⁇ b and ⁇ d , respectively) depicted in FIG. 7A .
  • the fluorescence OFF-time ⁇ d is determined by the association rate k on , the concentration of imager strands in solution c imager , and the number of observed binding sites bs:
  • the number of binding sites for an unknown molecule or area can be obtained according to the equation:
  • the quantification of a fluorescence image may be done automatically using binding kinetics analysis software.
  • a typical image is recorded in a time-lapsed fashion (e.g., 15000 frames with a frame rate of 10 Hz).
  • Fluorescence spot detection and fitting e.g., Gaussian fitting, Centroid fitting, or Bessel fitting
  • a calibration marker is selected (e.g., a DNA origami structure with a defined number of spots as in FIG. 7C ).
  • the software automatically calculates the fluorescence dark time ⁇ d by fitting the OFF-time distribution to a cumulative distribution function. Using the equations described above, the product of k on ⁇ c imager can be calculated. This product is used to calculate the number of docking sites, and thus targets in the imaged area.
  • the selection of areas of interest in the resolved (e.g., super-resolved) imaged can be performed automatically by applying a second spot detection step, e.g., to calculate the number of targets in a cluster.
  • fluorescence spot detection and fitting e.g., Gau
  • fitting function refers to a mathematical function used to fit the intensity profile of molecules.
  • fitting functions include, without limitation, Gaussian fitting, Centroid fitting, and Bessel fitting. It should be understood that while many aspects and embodiments of the present disclosure refer to Gaussian fitting, other fitting functions may be used instead of, or in addition to, Gaussian fitting.
  • compositions that comprise at least one or at least two (e.g., a plurality) BP-NA conjugate(s) (e.g., protein-nucleic acid conjugate(s)) of the present disclosure.
  • the BP-NA conjugates may be bound to a target of interest (e.g., biomolecule) and/or transiently bound to a complementary fluorescently-labeled imager strand.
  • a composition may comprise a plurality of the same species or distinct species of BP-NA conjugates.
  • a composition may comprise at least 10, 50, 100, 500, 1000, 2000, 3000, 4000, 5000, 10 4 , 50000, 10 5 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 BP-NA conjugates.
  • a composition may comprise at least 10, 50, 100, 500, 1000, 2000, 3000, 4000, 5000, 10 4 , 50000, 10 5 , 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 complementary fluorescently-labeled imager strands.
  • a composition may contain 1 to about 200 or more distinct species of BP-NA conjugates and/or imager strands.
  • a composition may contain at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200 or more distinct species.
  • a composition may contain less than about 5 to about 200 distinct species of BP-NA conjugates and/or imager strands.
  • a composition may contain less than 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175 or 200 distinct species.
  • the number of complementary fluorescently-labeled imager strands imager stands in a composition may be less than, equal to or greater than the number of BP-NA conjugates in the composition.
  • kits comprising one or more components as provided herein.
  • the kits may comprise, for example, a BP-NA conjugate and/or a fluorescently-labeled imager strands.
  • the kits may also comprise components for producing a BP-NA conjugate or for labeling an imager strand.
  • the kits may comprise a binding partner (e.g., antibody), docking strands and intermediate linkers such as, for example, biotin and streptavidin molecules, and/or imager strands.
  • the kits can be used for any purpose apparent to those of skill in the art, including, those described above.
  • kits may include other reagents as well, for example, buffers for performing hybridization reactions.
  • the kit may also include instructions for using the components of the kit, and/or for making and/or using the BP-NA conjugates and/or labeled imager strands.
  • a kit comprises at least one docking strand and at least one labeled imager strand that is capable of transiently binding to a docking strand.
  • the docking strands may or may not be conjugated to a binding partner.
  • the docking strands are conjugated to “generic” non-target-specific affinity molecule (e.g., biotin or streptavidin), which may be used to link a docking strand to binding partner chosen by an end user.
  • the affinity molecule is a secondary antibody.
  • a kit comprises at least one docking strand, at least one affinity molecule such as a secondary antibody, and at least one imager strand.
  • a kit comprises (a) at least one docking strand linked to a binding partner such as a protein (e.g., a protein that binds to a target) and (b) at least one (e.g., at least 2, at least 3, at least 4, at least 5, at least 10, at least 100) labeled imager strand that is capable of transiently binding (e.g., transiently binds) to a docking strand.
  • a docking strand may comprise, for example, at least two domains or at least three domain, wherein each domain binds to a respective complementary labeled imager strand.
  • the number of labeled imager strands may be, for example, less than, greater than or equal to the number of docking strands.
  • the binding partner may be a protein such as, for example, an antibody (e.g., monoclonal antibody), an antigen-binding antibody fragment, or a peptide aptamer.
  • a kit comprises at least two different binding partners (e.g., proteins), each specific for a different target.
  • a binding partner e.g., protein
  • a docking strand is modified to contain an affinity molecule that can be used to link the docking strand to a binding partner.
  • the affinity molecule is a secondary antibody.
  • An imager strand in some embodiments, is labeled with at least one fluorescent label (e.g., at least one fluorophore).
  • the length of an imager strand is 4 to 30 nucleotides, or longer.
  • the length of an imager strand may be 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides.
  • the length of an imager strand is 8 to 10 nucleotides.
  • a kit comprises at least two imager strands, each different from one another.
  • the thermal stability of a docking strand transiently bound to its complementary labeled imager strand is within 0.5 kcal/mol of the thermal stability of other docking strands transiently bound to their respective labeled imager strands.
  • a kit comprises (a) at least one docking strand linked to a monoclonal antibody or an antigen binding fragment thereof (e.g., a monoclonal antibody or an antigen binding fragment thereof that binds to a target) and (b) at least one (e.g., at least 2, at least 3, at least 4, at least 5, at least 10, at least 100) labeled imager strand that is capable of transiently binding (e.g., transiently binds) to a docking strand.
  • a docking strand may comprise, for example, at least two domains, wherein each domain binds to a respectively complementary labeled imager strand.
  • a kit comprises at least two different monoclonal antibodies or antigen binding fragments thereof, each specific for a different target.
  • a monoclonal antibody or an antigen binding fragment thereof in some embodiments, is linked to a docking strand through an intermediate linker that includes biotin and streptavidin (e.g., a biotin-streptavidin-biotin linker).
  • An imager strand in some embodiments, is labeled with at least one fluorescent label (e.g., at least one fluorophore).
  • the length of an imager strand is 4 to 30 nucleotides, or longer.
  • the length of an imager strand may be 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides.
  • the length of an imager strand is 8 to 10 nucleotides.
  • a kit comprises at least two imager strands, each different from one another.
  • the thermal stability of a docking strand transiently bound to a complementary labeled imager strand is within 0.5 kcal/mol of the thermal stability of other docking strands transiently bound to their respective labeled imager strands.
  • BP-NA conjugates e.g., protein-nucleic acid conjugates or antibody-nucleic acid conjugates
  • BP-NA conjugates can be used, inter alia, in any assay in which existing target detection technologies are used.
  • assays include detection assays including diagnostic assays, prognostic assays, patient monitoring assays, screening assays, biowarfare assays, forensic analysis assays, prenatal genomic diagnostic assays and the like.
  • the assay may be an in vitro assay or an in vivo assay.
  • the present disclosure provides the advantage that many different targets can be analyzed at one time from a single sample using the methods of the present disclosure, even where such targets are spatially not resolvable (and thus spatially indistinct) using prior art imaging methods. This allows, for example, for several diagnostic tests to be performed on one sample.
  • the BP-NA conjugates can also be used to simply observe an area or region.
  • the methods of the present disclosure may be applied to the analysis of samples obtained or derived from a patient so as to determine whether a diseased cell type is present in the sample and/or to stage the disease.
  • a blood sample can be assayed according to any of the methods described herein to determine the presence and/or quantity of markers of a cancerous cell type in the sample, thereby diagnosing or staging the cancer.
  • the methods described herein can be used to diagnose pathogen infections, for example infections by intracellular bacteria and viruses, by determining the presence and/or quantity of markers of bacterium or virus, respectively, in the sample.
  • the targets detected using the methods, compositions and kits of the present disclosure may be either patient markers (such as a cancer marker) or markers of infection with a foreign agent, such as bacterial or viral markers.
  • the quantitative imaging methods of the present disclosure may be used, for example, to quantify targets (e.g., target biomolecules) whose abundance is indicative of a biological state or disease condition (e.g., blood markers that are upregulated or downregulated as a result of a disease state).
  • targets e.g., target biomolecules
  • a biological state or disease condition e.g., blood markers that are upregulated or downregulated as a result of a disease state.
  • compositions and kits of the present disclosure may be used to provide prognostic information that assists in determining a course of treatment for a patient.
  • the amount of a particular marker for a tumor can be accurately quantified from even a small sample from a patient.
  • overexpression of certain proteins, such as Her2-neu indicate a more aggressive course of treatment will be needed.
  • the methods of the present disclosure may also be used for determining the effect of a perturbation, including chemical compounds, mutations, temperature changes, growth hormones, growth factors, disease, or a change in culture conditions, on various targes, thereby identifying targets whose presence, absence or levels are indicative of a particular biological states.
  • the present disclosure is used to elucidate and discover components and pathways of disease states. For example, the comparison of quantities of targets present in a disease tissue with “normal” tissue allows the elucidation of important targets involved in the disease, thereby identifying targets for the discovery/screening of new drug candidates that can be used to treat disease.
  • the sample being analyzed may be a biological sample, such as blood, sputum, lymph, mucous, stool, urine and the like.
  • the sample may be an environmental sample such as a water sample, an air sample, a food sample and the like.
  • the assay may be carried out with one or more components of the binding reaction immobilized.
  • the targets or the BP-NA conjugates may be immobilized.
  • the assay may be carried out with one or more components of the binding reaction non-immobilized.
  • the assays may involve detection of a number of targets in a sample, essentially at the same time, in view of the multiplexing potential offered by the BP-NA conjugates and fluorescently-labeled imager strands of the present disclosure.
  • an assay may be used to detect a particular cell type (e.g., based on a specific cell surface receptor) and a particular genetic mutation in that particular cell type. In this way, an end user may be able to determine how many cells of a particular type carry the mutation of interest, as an example.
  • the device is a polymer-based (e.g., polydimethylsiloxane (PDMS)) device comprising first and second channels, each connected at one end to a sample chamber.
  • PDMS polydimethylsiloxane
  • This configuration permits one or more fluid(s) to be sequentially administered to the sample at a controlled rate.
  • a syringe may be used to administer a first fluid to the sample through a first channel of the device.
  • the syringe may then be used to administer a second fluid, which passes through the first channel of the device into the sample chamber, thereby forcing the first fluid out of the sample chamber, passing through a second channel and into, for example, a reservoir connected to the second channel ( FIG. 23A ).
  • the device is positioned on a glass slide to permit viewing from a microscope objective positioned below the device.
  • Super-resolution imaging with increased spatial resolution may be achieved, in some embodiments, by increasing the number of photons per localization event using one of two strategies, depicted in FIG. 11A .
  • the first strategy the maximum number of photons from single, replenishable fluorophores is extracted.
  • High laser excitation power, in combination with fluorophore stabilization buffers ( 16 , 17 ) may be used to “bleach” transiently bound fluorophores at docking sites (or sites of docking strands), thus extracting the maximal number of photons per binding event and dye ( FIG. 11A ).
  • a fluorescent DNA nanostructure or “metafluorophore,” may be constructed by decorating a compact DNA nanostructure with many fluorophores (FIG. 11 B 3 ). The sum of the individual dye emissions from a metafluorophore are interpreted as originating from the same point source, and thus, using the metafluorophore in place of a standard fluorophore (e.g., Cy3) further improves the localization precision.
  • a standard fluorophore e.g., Cy3
  • FIG. 11 B 4 A more advanced version of the metafluorophore with active background suppression is depicted in FIG. 11 B 4 .
  • the clam-shell-like structure acts as a conditional fluorophore that only fluoresces when it is bound to the docking strand.
  • the present disclosure also provides algorithms used for spot detection, fitting and drift correction, as described below.
  • Some embodiments are directed to methods and apparatus for correcting drift in images recorded in a time sequence.
  • a non-limiting application of the techniques for performing drift correction is to correct for drift in molecular scale DNA-based imaging described herein involving transiently binding between docking strands and imaging strands.
  • the techniques described herein may alternatively be used to correct for drift in other imaging applications where one or more transient imaging events are recorded during a time sequence of images, and embodiments related to drift correction are not limited to molecular scale DNA-based imaging.
  • a DNA nanostructure can be used as a drift marker.
  • Any suitable DNA nanostructure see, e.g., (Rothemund US-2007/0117109 A1), single-stranded tiles (Yin et al., “Programming DNA Tube Circumferences,” Science (2008): 321: 824-826), DNA hairpins (Yin et al. US-2009/0011956 A1; Yin et al., “Programming biomolecular self-assembly pathways,” Nature (2008) 451:318-323) may be used, and may be made using, e.g., DNA origami techniques.
  • Drift correction using DNA nanostructure-based drift markers in combination with advanced analysis and post-processing techniques has the advantage of high precision correction, compatibility with long time imaging and simplicity of implementation.
  • Conventional nucleic acid-based imaging techniques incorporating drift markers based on fluorescent beads suffer from the limited length of imaging time before the beads are bleached; whereas bright field imaging requires specialized equipment, e.g. dual-field camera view.
  • Drift correction techniques in accordance with some embodiments described herein may include a plurality of stages, where each of the stages uses a different technique to perform drift correction.
  • the output from one stage is provided as input to a subsequent stage for additional drift correction processing.
  • a coarse drift correction is performed by comparing localizations from neighboring frames.
  • a single drift marker is selected and its time trace is used as a different coarse correction.
  • a group of drift markers is selected, either automatically or with user input, and their time traces are then combined to compute a more precise drift correction.
  • a fourth stage localizations are pooled from template-based drift markers displaying spots in a defined and spatially resolvable geometry (e.g., 4 ⁇ 3 grid points).
  • a smoothing of the drift correction is performed to further reduce noise and enabling the resolution of the final image to approach molecular-scale resolution.
  • an amount of drift in the time sequence of images may be characterized using a quality measure, and based, at least in part, on the quality measure, one or more of the stages may be eliminated.
  • all five stages may be performed, as embodiments are not limited in this respect.
  • additional drift correction stages used in combination with at least one of the stages described herein may also be used.
  • FWHM Full Width at Half Maximum
  • the recorded image stack is referred to herein as a “movie” and each of the individual images as a “frame.”
  • Each frame of the movie is operated on with a spot finding algorithm, and then a local Gaussian fitting algorithm may be used for each identified spot; the spot and its fitted center position localization are interchangeably referred to herein as a “localization.”
  • the frames of the movie capture one or more transient events that are present in some frames but not others.
  • binding events are discussed in further detail below as one illustrative transient event that may be analyzed using the techniques described herein for performing drift correction, it should be appreciated that other types of transient events imaged in a time sequence may alternatively be used.
  • time trace the collection of all localizations throughout the entire movie is collectively referred to as the “time trace,” which reflects the movement of an observed structure, and is used for drift correction in several different ways, as described in more detail below.
  • FIG. 12 illustrates a schematic overview of five stages of a drift correction procedure that may be performed in accordance with the techniques described herein. The stages are illustrated as being performed consecutively in an order from an unprocessed image to a final image that has been processed using the techniques of each of the five stages. Each of these stages will be discussed in more detail below.
  • FIG. 12A (i) illustrates schematics showing the principle of each stage of drift correction. In each image, black markers and lines indicate source data, and red values and curves indicate the calculated drift correction.
  • FIG. 12A (ii) shows a schematic drawing of the major type of drift markers (e.g., DNA drift markers) used in each stage.
  • FIG. 12B (i) illustrates an example structure showing the imaging quality after each stage or correction, and FIG.
  • FIG. 12B (ii) shows a zoomed image of the corresponding green rectangle in FIG. 12B (i) at each stage.
  • the scale bars shown in FIGS. 12 B(i) and 12 B(ii) correspond to 50 nm.
  • FIG. 12C (i) illustrates an example drift trace after each stage of correction
  • FIG. 12C (ii) shows a zoomed image of the corresponding green rectangle in FIG. 12C (i) at each stage.
  • the scale bars in FIG. 12C (i) correspond to x: 500 nm, t: 500 s
  • the scale bars in FIG. 12C (ii) correspond to x: 10 nm, t: 10 s.
  • FIG. 18 illustrates an alternate representation of stages in a drift correction process in accordance with some embodiments.
  • an image resolution output from the first stage may be on the order of 1 ⁇ m.
  • an image resolution output from the second stage may be on the order of 200 nm.
  • an image resolution output from the third stage may be on the order of 20 nm.
  • an image resolution output from the fourth stage may be on the order of 5 nm.
  • an image resolution output from the fourth stage may be on the order of less than 5 nm.
  • DNFL Distance between Neighboring Frame Localizations
  • the procedure for calculating the DNFL for an image is outlined as follows. For each pair of NF (Neighboring Frames, e.g. frame #1 and #2), all localizations from both frames are pooled and the distance between every pair of localizations from different frames (e.g. one localization from frame #1 versus another from frame #2) is calculated, assuming no drift between the frames. The resulting distances from all NF pairs are pooled to provide a bimodal distribution. The first mode of the bimodal distribution is broad, high in amplitude, and spans the width of the field of view. The second mode of the bimodal distribution is sharp, low in amplitude, and close to zero, and corresponds to localizations from the same binding event.
  • the quality of a final drift-corrected image may assessed by characterizing the Point Spread Function (PSF) of a single binding site.
  • PSF Point Spread Function
  • a statistical overlay of images of more than thousands of single docking sites may be produced as the reference for the PSF distribution.
  • image supported resolution sigma*2.35.
  • the isolation and overlay of single isolated docking sites may be performed with the help of an auxiliary DNA nanostructure.
  • This structure has a known pattern of well-separated docking sites (e.g., a lattice grid pattern), and may be the same structure used for the template-based drift correction stage, discussed in more detail below.
  • a lattice grid pattern e.g., a lattice grid pattern
  • the above determined image quality of the whole image may not reflect the true imaging quality for each single sample object in the imaging field.
  • structures closer to the center of the imaging field and better fixed to the optical surface are better illuminated, and show better resolution than those that are on the periphery and are less well fixed.
  • the image quality and resolution of a single molecule may be determined in a procedure similar to the one above.
  • a projection of a single molecule of an auxiliary DNA nanostructure may be taken along a direction that best separates the docking sites (in the case of lattice grid structures, this will be along any of the lattice directions), and a multi-Gaussian fit may be performed on the projected 1-D distribution.
  • the standard deviation of the fitted Gaussian peaks may then be determined and similarly used to infer the resolution of a single-molecule image.
  • the five stages incorporating techniques for performing drift correction operate in series to reduce the drift of an unprocessed image, where each consecutive stage reduces the drift further, and low enough for the successful operation of the next stage.
  • less than all five stages may be used. For example, if it is determined that there is low drift in the original image, the localizations in each frame may be separable, and processing may begin from the second stage without requiring processing by first stage. If it is determined that there is even lower drift in the original image, processing may be begin from the third stage without significant loss of final image quality.
  • drift correction Due to the complex origin of drift, which may involve, among other things, thermal fluctuation and expansion, microscope stage movement due to electric motor activation, vibration from the building and optical table complex, controlling drift in the original image tends to be difficult, and including the first two stages is often useful in producing a final image with desired resolution. For example, including all five stages described herein provides a robust strategy for drift correction that is applicable to images taken in most biology labs, without the requirement of specialized hardware or building requirements.
  • the amount of drift and overall image quality of the original unprocessed image may be determined using any suitable technique, and the determined image quality may be used to select a choice of drift correction stages to use in performing drift correction.
  • a technique for determining image quality may compare different temporal segments of the same image.
  • the original image may be divided into two halves by separately pooling localizations from the first half and the second half of the movie, respectively.
  • the cross-correlation between the two images may be calculated and a best offset may be estimated to provide an indication of the overall drift.
  • the indication of overall drift may be compared to one or more threshold values to determine whether one or more of the drift correction stages may be skipped in performing drift correction in accordance with the techniques described herein.
  • FIG. 13 illustrates a process for performing drift correction in accordance with some embodiments.
  • drift correction is performed by considering differences in localizations across neighboring frames of a movie.
  • the process then proceeds to act 220 , where a single drift marker is selected, a time trace describing the movement of the drift marker over time during the movie is determined, and the time trace for the single drift marker is used to perform drift correction of the image.
  • the process then proceeds to act 230 , where time traces are determined for each of a plurality of drift markers identified in the image. As discussed in more detail below, differences between the time traces may be used to provide a further drift correction in the final image.
  • the process then proceeds to act 240 , where drift correction using geometrically-constrained templates is performed.
  • act 250 where the image is further drift corrected by smoothing the drift trace using suitable smoothing techniques, as discussed in more detail below.
  • suitable smoothing techniques as discussed in more detail below.
  • Each of the five stages for performing drift correction in accordance with the techniques described herein are described in further detail below. As should be appreciated from the foregoing discussion, not all embodiments require the use of all five stages for drift correction processing. For example, in some embodiments, only acts 230 and 240 may be performed. In other embodiments, acts 230 , 240 , and 250 may be performed. In yet other embodiments, acts 220 , 230 , 240 and 250 may be performed without including act 210 .
  • a first stage of drift correction (e.g., act 210 of FIG. 13 ) operates by comparing localizations from neighboring frames in a movie.
  • a procedure similar to the DNFL calculation described above (or any other suitable technique) may be used to identify pairs of localizations originating from the same transient event (e.g., a single binding event). All pairs of localizations originating from the same transient event may be pooled to create a bimodal distribution. After creating a bimodal distribution of the localizations from neighboring images, a cutoff value may be automatically determined to separate those pairs of localizations from the same event (close localizations), from those that are different.
  • the first stage of drift correction typically corrects for global drift with high amplitude (farther than 1 ⁇ m in offset), which effectively removes interference between different drift markers and allows for incorporation of the next stage.
  • the first stage of processing may be omitted. A determination of whether the first stage of processing may be omitted may be made using an image quality factor analysis, as discussed above, or using any other suitable technique (e.g., manual inspection).
  • a second stage of drift correction operates on a single drift marker or sample object.
  • the single drift marker for use in this stage of drift correction processing may be selected in any suitable way.
  • the single drift marker may be randomly selected from the set of all identified drift markers.
  • a particular drift marker associated with desirable qualities e.g., an average amount of drift over the entire movie
  • After selecting the single drift marker its time trace is automatically determined, smoothed, and output as the drift correction.
  • a drift trace may be manually drawn in cases where separation between drift markers is hard to identify automatically.
  • the second stage of drift correction further reduces global drift in the movie (typically ⁇ 200 nm), and allows automatic batch identification of drift markers in the following stages.
  • a third stage of drift correction (e.g., stage 230 of FIG. 2 ) combines the time traces of a plurality of drift markers to compute drift correction with a finer resolution than the second stage of drift correction.
  • Each drift marker has a large number of docking sites to allow a high temporal coverage; and a large number of these drift markers are deposited onto the imaging surface together with the samples.
  • the number of binding sites on each drift marker and the concentration of drift markers on the surface may be selected appropriately to ensure a high quality drift correction, as the improvement in drift correction in performing this stage is primarily determined by the spread of each drift marker in the image and the effective number of drift markers per frame.
  • FIG. 14 illustrates a process for performing drift correction corresponding to stage 230 of FIG. 2 .
  • locations of a plurality of drift markers are identified. Identifying locations of the plurality of drift markers may include pooling localizations from all frames of the movie to calculate a two-dimensional (2D) histogram. Then, the locations of drift markers may be identified by appropriately tuning the histogram binning size and a combination of other selection criteria. For example, the binning size of the histogram may be tuned to reflect the feature size of the drift marker, e.g., a fourth or third of their overall size.
  • the range of selection criteria includes, but it is not limited to, a lower-bound threshold of the histogram value and filtering based on geometrical properties (e.g., area, dimensions). Adequate separation between nearby drift markers is often necessary to exclude false localizations, which, for example, arise from spurious localizations of double-binding events.
  • the process to act 320 where the time trace for each drift marker is determined and the relative time trace determined as the offset of each time trace from the center of the combined trace is computed. Because the images capture transient events (e.g., nucleic acid-binding events), not all time traces for a drift marker may cover all time points in the movie. In such cases, the time traces may be linearly interpolated at the “missing points” to achieve a finer and smoother result.
  • the process proceeds to act 330 , where the drift correction for the image is determined based on the time traces determined for each drift marker. Any suitable combination of the time traces may be used to determine the drift correction, and embodiments are not limited in this respect.
  • a weighted average of the time traces is used to determine the drift correction output from this stage. For example, a weighted average of the pool of relative time traces may be computed as the result of drift correction, where the correction is weighted by the quality of drift marker traces.
  • the quality of drift marker traces may be determined in any suitable way including, but not limited to, determining the quality by assessing drift marker quality or individual localization quality.
  • the quality of each drift marker trace is computed by taking the standard deviation (sigma) of the trace over time.
  • the inverse of this measure e.g., 1/sigma
  • the quality of each individual localization within the time traces may be computed as the localization uncertainty given by the formula in Thomson, 2002.
  • the inverse of the standard deviation of this calculation may be used as the weight factor for each time trace.
  • This stage of drift correction may be performed any number of times. In some embodiments, this stage of drift correction is iteratively performed with different parameters used for each iteration. As drift correction proceeds, the remaining drift amplitude is decreased further and further, the spatial spread-out of drift markers becomes smaller and smaller, and selection of drift markers may be performed more and more stringently. Consequently, in initial iterations, the threshold histogram count may be set to a lower value, and this value may be adjusted during later iterations to higher values. Additionally, in some embodiments, the valid area and dimensions of drift markers may be set to larger values in initial iterations, and later adjusted to smaller values during subsequent iterations. Yet further, in some embodiments, separation between drift markers may be shifted from larger values to smaller values in later iterations. In some embodiments, an interactive quality check (either manually or automatically performed) may be determined between iterations to facilitate a determination of further operations.
  • this stage of drift correction typically brings the obtained image resolution to within a factor of two from the best allowed resolution (i.e. if the precision of each individual localization supports resolution of ⁇ 5 nm, then this stage usually yields ⁇ 10 nm resolution).
  • this stage usually yields ⁇ 10 nm resolution.
  • a resolution ⁇ 10 nm may be obtained following processing with this stage.
  • a fourth stage of drift correction uses drift marker “templates,” and thus this stage is termed “templated drift correction.”
  • One or more drift marker templates e.g., DNA nanostructures with docking sites in a known and well-separated geometric arrangement
  • the separation between these docking sites is preferably chosen not to be not smaller than twice the resulting resolution from the previous stage (e.g., stage three), allowing easy separation between localizations from different docking sites.
  • the number of docking sites on these templates as well as the concentration of the docking sites on the surface is preferably chosen to achieve effective template correction, similar that described for the third stage.
  • FIG. 15 illustrates a process for performing drift correction corresponding to stage 240 of FIG. 2 .
  • act 410 a plurality of drift correction templates are identified from a 2-D histogram of localizations pooled across all frames of the movie. To distinguish the drift templates from the drift markers used in the third stage, an extra upper-bound threshold in histogram count may be incorporated in addition to the range of selection criteria as mentioned above.
  • act 420 the time trace of each drift template is determined. Because the docking sites are designed to be well separated in the templates, several non-overlapping time traces from individual docking sites may be isolated from each time trace of a full drift template. This identification and separation step may be carried out in a similar manner as the identification of drift markers from the entire image. For example, a combination of local histogram thresholding and filtering on standard deviation of the individual time traces for each drift template may be used.
  • the process proceeds to act 430 , where the combination of time traces is used to determine a drift correction for this stage. In some embodiments, this is accomplished by computing relative time traces for each time trace, and the relative time traces are used, at least in part, to determine the drift correction.
  • the relative time traces may be used in any suitable way to determine the drift correction. For example, in some embodiments, a weighted average of all the time traces of individual docking sites may be averaged to produce the final drift correction.
  • the weight factors may be determined in any suitable way. For example, the weight factors may be based on the quality of each individual site, or the quality of each individual localization in the time trace.
  • the process proceeds to act 440 where the image is corrected using the determined drift correction.
  • this stage of drift correction may result in a resolution of the final image being close to the best possible resolution. That is, if the precision of each individual localization supports a resolution of ⁇ 5 nm, performing template drift correction in accordance with the techniques described herein may achieve a resolution close to ⁇ 6 nm.
  • a DNA nanostructure with 12 docking sites arranged in a 4 ⁇ 3 grid of lattice spacing 20 nm may be used as the drift correction template. Template-based drift correction using the techniques described in this section may enable the achievement of 6-7 nm resolution after this stage.
  • a fifth stage of drift correction performs smoothing of the drift correction trace, and the smoothed drift correction trace may be used to perform drift correction.
  • the resultant drift correction may be smoothed using any suitable technique to produce the final drift correction result. Smoothing effectively increases the number of drift markers or drift templates in each frame, by taking the localizations in neighboring frames into account. Smoothing may be performed in any suitable manner using any suitable window period. For example, in some embodiments, smoothing is performed with a robust local regression method that operates over a window period determined by the characteristic drift time scale. A non-limiting example of a smoothing window period may be 10-30 s.
  • All stages described above can be directly applied to correct a 3D image (e.g., super-resolution image) as well.
  • a 3D image e.g., super-resolution image
  • an astigmatism lens may be introduced in the imaging path and the ellipticity of the resulting Gaussian emission profile may be used to determine a z-position of a molecule.
  • the above-described origami drift marker structures e.g., geometric-constrained templates
  • a DNA origami structure with a defined 3D shape e.g., a tetrahedron
  • FIG. 16 illustrates 3D tetrahedrons used as templates for 3D drift correction.
  • the four corners are labeled with docking sites.
  • FIG. 16A shows that the four corners are clearly resolved.
  • FIG. 16B illustrates the X-Z projection of the structures with a height of ⁇ 85 nm.
  • the above-described techniques for correcting drift in a plurality of time sequence images is described with respect to imaging a transient event identified using a single color in the images.
  • these techniques may be extended to multicolor imaging in which different transient events (e.g., binding of different nucleic acid drift markers with docking sites) are labeled with different colors that can be identified in the same image.
  • the geometric templates discussed above for template-based drift correction may include information describing a particular known geometry for the different transient events that correspond to the different colors.
  • the computer system 600 may include one or more processors 610 and one or more computer-readable non-transitory storage media (e.g., memory 620 and one or more non-volatile storage media 630 ).
  • the processor 610 may control writing data to and reading data from the memory 620 and the non-volatile storage device 630 in any suitable manner, as the aspects of the present disclosure described herein are not limited in this respect.
  • the processor 610 may execute one or more instructions stored in one or more computer-readable storage media (e.g., the memory 620 ), which may serve as non-transitory computer-readable storage media storing instructions for execution by the processor 610 .
  • computer-readable storage media e.g., the memory 620
  • the embodiments can be implemented in any of numerous ways.
  • the embodiments may be implemented using hardware, software or a combination thereof.
  • the software code can be executed on any suitable processor or collection of processors, whether provided in a single computer or distributed among multiple computers.
  • any component or collection of components that perform the functions described above can be generically considered as one or more controllers that control the above-discussed functions.
  • the one or more controllers can be implemented in numerous ways, such as with dedicated hardware, or with general purpose hardware (e.g., one or more processors) that is programmed using microcode or software to perform the functions recited above.
  • one implementation of the embodiments of the present disclosure comprises at least one non-transitory computer-readable storage medium (e.g., a computer memory, a floppy disk, a compact disk, a tape, etc.) encoded with a computer program (i.e., a plurality of instructions), which, when executed on a processor, performs the above-discussed functions of the embodiments of the present disclosure.
  • the computer-readable storage medium can be transportable such that the program stored thereon can be loaded onto any computer resource to implement the aspects of the present disclosure discussed herein.
  • the reference to a computer program which, when executed, performs the above-discussed functions is not limited to an application program running on a host computer. Rather, the term computer program is used herein in a generic sense to reference any type of computer code (e.g., software or microcode) that can be employed to program a processor to implement the above-discussed aspects of the present disclosure.
  • inventive embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed.
  • inventive embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein.
  • a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.
  • the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements.
  • This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified.
  • “at least one of A and B” can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.
  • FIG. 2 Multiplexed super-resolution imaging of intra-cellular components in fixed cells was achieved by linking docking strands to antibodies ( FIG. 2 ). These antibody-DNA conjugates were formed by first reacting biotinylated docking strands with streptavidin, and then incubating with a biotinylated antibody against the protein of interest. Fixed HeLa cells were then immunostained using a preassembled antibody-DNA conjugate against beta-tubulin. Prior to imaging, ATTO655-labeled imager strands were introduced to the sample in hybridization buffer (1 ⁇ PBS supplemented with 500 mM NaCl), and single-molecule imaging was carried out using oblique illumination (9).
  • the resulting super-resolution images show a clear increase in spatial resolution in contrast to the diffraction-limited representation ( FIGS. 3 a -3 c ).
  • a cross-sectional profile taken at position ⁇ i> in FIG. 3B yields a distance of ⁇ 79 nm between two adjacent microtubules with an apparent width of ⁇ 47 and ⁇ 44 nm for each of the microtubules, which is in agreement with earlier reports for immunostained microtubules (13).
  • the antibody-DNA conjugation approach of the present disclosure yields a high labeling density, and little to no non-specific binding of imager strands to non-labeled cellular components occurs.
  • the microtubule network in a fixed HeLa cell was labeled with a preassembled antibody-DNA conjugate carrying a docking sequence for Cy3b-labeled strands, and mitochondria were stained using a second antibody linked to an orthogonal sequence for ATTO655 imager sequences. While both Cy3b- and ATTO655-labeled imager strands were present in solution at the same time, imaging was carried out sequentially in the Cy3b and ATTO655 channels and the resulting super-resolution images showed a clear increase in spatial resolution as compared to the diffraction-limited representation ( FIGS.
  • FIG. 5A shows a single DNA nanostructure, displaying four distinct sets of DNA sequences, designed to resemble the digits from 0 to 3, respectively. Imaging was performed sequentially using a simple flow chamber setup, first flushing in imager strands complementary to the docking strands of the number 0, and then exchanging the solution for imager strands with a sequence complementary to docking strands of the number 1 and so forth. The resulting images were pseudo-colored to represent the respective imaging rounds. The demonstration using DNA origami structures showed the high imaging efficiency as well as no crosstalk between consecutive imaging runs.
  • FIG. 5B (iii) shows a combined image of all ten rounds, demonstrating specific interaction of imager strands with respective targets with no observable crosstalk between cycles. Digits 8 and 9 are not present in the selected area. An apparent “green” digit 5 instead of 2 was observed ( ⁇ i> in FIG. 5B (iii)). This is likely not a falsely imaged digit 5 from crosstalk, but rather a “mirrored” digit 2. A mirrored image likely results from an origami immobilized upside-down, with docking strands trapped underneath, yet still accessible to imager strands.
  • the fluidic setup is designed to minimize sample movement by “decoupling” the fluid reservoir and syringe from the actual flow chamber via flexible tubing. To avoid sample distortion, special care was taken to ensure gentle fluid flow during washing steps. To verify that the sample indeed exhibited little movement and little-to-no distortion, a ten-round Exchange-PAINT experiment was performed. The DNA origami was imaged for digit 4 in the first round and reimaged after ten rounds of buffer exchange. The total sample movement (physical movement of the fluidic chamber with respect to the objective) was less than 2 ⁇ m, which could easily be corrected using fiducial markers. Normalized cross-correlation analysis for select structures produced a correlation coefficient 0.92, demonstrating almost no sample distortion (also see the discussion in the cellular imaging section).
  • Exchange-PAINT four different digit patterns were successfully imaged on the same DNA origami structure ( FIG. 5B (iv)).
  • Exchange-PAINT is not limited to spatially separate species and can resolve sub-diffraction patterns on the same structure with no observable crosstalk or sample distortion. Aligning images from different Exchange-PAINT rounds is straightforward using DNA origami-based drift markers. Additionally, because imaging is performed using the same dye, no chromatic aberration needs to be corrected between imaging rounds.
  • FIG. 7C a DNA origami nanostructure with 13 binding sites in a grid-like arrangement was used ( FIG. 7C ).
  • the incorporation efficiency for docking sites was not 100%, leading to a distribution of actually incorporated sites ( FIGS. 7C and 7 D 1 ). Nonetheless, the structures were an ideal test system because the number of available sites could be determined visually by counting the number of spots (“direct”) and comparing it with the corresponding number of sites calculated using the proposed binding kinetic analysis (“kinetics”).
  • FIG. 7 D 1 shows the binding site distribution for 377 origami structures obtained by direct counting.
  • the binding site distribution for the same structures obtained by binding kinetic analysis is shown in FIG. 7 D 2 .
  • the “offset” between direct and kinetic counting was calculated for each structure. The counting “error” or uncertainty for the method was less than 7% (determined by the coefficient of variation of the Gaussian distribution) with an imaging time of ⁇ 25 min.
  • binding frequency analysis rather than geometrical or spectral encoding.
  • Binding frequencies of BP-NA conjugates, or docking strands, to a molecule of interest is linearly dependent on the number of binding sites on this molecule.
  • binding frequency scales linearly with the number of binding sites, and can thus be used for identification.
  • 124 distinct dynamic “blinking signatures” were created using 3 colors and 4 levels of binding frequency per color ( FIG. 8 ). Compared to geometrical encoding, this approach features much more compact, unstructured probes.
  • the method of the present disclosure is more cost effective, scalable, and easier to implement. Only 3 fluorescently-labeled imager strands are required in this frequency encoding method, making it very cost-efficient for high-throughput screening experiments.
  • In vitro tests on a DNA origami test structure are shown in FIG. 8C .
  • the fluorescence ON-time or ⁇ b and thus the dissociation constant k off can also be used to encode information.
  • k off can be precisely tuned by the base-composition and/or length of the duplex of docking and imager strand.
  • the feasibility of this approach is illustrated in FIG. 9 : 1/ ⁇ d and 1/ ⁇ b are plotted vs. the length of the docking/imaging duplex. 1/ ⁇ d , and thus k on , is independent of the duplex stability.
  • extending the imaging/docking duplex from 9 to 10 nt by adding a single CG base pair reduces the kinetic OFF-rate by almost one order of magnitude.
  • a “microbarcode,” a minimal barcode that uses our ability to detect differences in thermodynamic stability of the imager/docking duplex was produced to identify a large number of molecules using a short, economical and unstructured probe.
  • the barcode contains only of a single DNA molecule, roughly 50 nt in length, which is used to tag a molecule of interest using a 21 nt target detection domain t* ( FIG. 10A ) followed by a ⁇ 30 nt long “barcode” region with a combination of 8, 9, or 10 nt long binding domain for red, green, or blue imager strands.
  • FIG. 10 illustrates a8, 9, or 10 nt long docking strands for three colors with a k off of 10, 1 and 0.1 per second, respectively.
  • FIG. 10A shows an example barcode consisting of an 8 nt long binding domain for a red imager strand, two 9 nt long binding domains for the green, and blue imager strand, respectively. This produces characteristic intensity vs. time traces with increased fluorescence ON-times ⁇ b for the 9 nt interaction domain compared to the 8 nt interaction domain ( FIG. 10B ). Stochastic simulations show that it is clearly possible to distinguish between k off values of 10, 1 and 0.1 per second, respectively ( FIG. 10C ).
  • a significant advantage of fluorescence imaging lies in its potential to visualize biomolecular processes in living cells.
  • One such challenge is in the delivery of a sufficient concentration of synthetic imaging probes to living cells in a biocompatible manner while also allowing for proper imaging conditions.
  • Another challenge is the extent of background fluorescence for unbound probes in the context of a live cell environment where macromolecular crowding may be more of a significant factor compared to fixed cell environments, and “live” helicases may influence binding kinetics.
  • RNA probe that can specifically bind to a target molecule in a living cell, and only then start to fluoresce and blink to enable super-resolution imaging of the specific target.
  • This conditional “blinking” probe is a small single-stranded RNA ( ⁇ 100 nt) with a target binding domain (TBD) and a conditional blinking domain (CBD).
  • TBD target binding domain
  • CBD conditional blinking domain
  • the CBD is under mechanical control of the TBD and is dark when the TBD is not bound to a target T.
  • the binding of TBD with target “T” results in a reconfiguration of the CBD and enables it to blink with an intensity and frequency suitable for the super-resolution imaging of T.
  • the blinking RNA probe is based on the Spinach aptamer system (ref. 19), a fluorescent RNA mimic of GFP ( FIG. 19 ).
  • Spinach can turn on the fluorescence of an initially dark small molecule DFHBI (similar to DMHBI), which is non-toxic and cell-permeable.
  • DFHBI dark small molecule
  • DFHBI binds and unbinds Spinach, it will alternate between a fluorescence ON- and OFF-state. The resulting blinking behavior is used to perform super-resolution fluorescence microscopy, which is referred to herein as “Spinach-PAINT” ( FIG. 20 ). Unlike most live cell super-resolution imaging techniques, Spinach-PAINT needs no special imaging conditions such as special buffer systems or external photoswitching or activation. More importantly, DFHBI is a small, cell-permeable molecule and has been shown to provide non-toxic imaging for living cells.
  • the necessary “blinking” behavior for super-resolution imaging can be obtained by altering the fluorescence ON- and OFF-times by adjusting the DFHBI concentration in solution and modifying/mutating Spinach to enhance/weaken the binding of DFHBI to it in the same spirit as one would tune the DNA-DNA binding interaction of an imaging strand with its partner. It is possible to characterize and optimize the binding kinetics of DFHBI to surface-immobilized Spinach based on single-molecule measurements ( FIG. 20 ). The binding kinetics are checked for compatibility with super-resolution microscopy based on transient binding.
  • a “doped” library of Spinach variants will be prepared, using a dNTP mixture containing the dNTP that is found in Spinach for each position and the other three dNTPs in a 2:1:1:1 ratio. This approach is typically used to optimize aptamer sequences (SELEX) (ref. 23). The Spinach variants will then be screened for variants with shorter DFHBI residence times. After 5-10 rounds of SELEX, clones will be individually characterized. A first step is to confirm that all the Spinach variants still exhibit Spinach-like fluorescence with comparable quantum yield and extinction coefficient upon binding DFHBI. It is generally easy to weaken rather than to strengthen the binding interaction between an aptamer and a small molecule.
  • a second step involves measuring the binding and unbinding rate constants of these Spinach variants by single-molecule imaging.
  • Spinach variants that exhibit binding durations that provide sufficient photon counts for obtaining precise super-resolution imaging will be chosen.
  • the DNA origami substrate has the advantage of providing a programmable environment for placing multiple Spinach molecules in a defined distance and geometry. This nanoscopic ruler system will enable us to precisely quantify the obtainable resolution of this super-resolution imaging technique ( FIG. 21 ).
  • RNAs that Exhibit Blinking upon Binding Tubulin for Super-Resolution Imaging of Cytoskeleton Proteins Spinach-based sensors that are activated by metabolites (ref. 24) and by proteins (ref. 25) have been generated. The approach of this disclosure will be used to generate Spinach-based sensors that are activated by binding tubulin, using tubulin-binding aptamers and the blinking Spinach variants described herein.
  • the allosteric form of Spinach is compromised of the modified Spinach aptamer domain fused to a “control” or “sensing” module consisting of an aptamer that binds a target of interest (ref. 24). Binding of the target results in the allosteric folding of the modified Spinach aptamer into an “active” conformation, enabling DFHBI binding and fluorescence ( FIG. 22 ).
  • a “control” or “sensing” module consisting of an aptamer that binds a target of interest
  • Binding of the target results in the allosteric folding of the modified Spinach aptamer into an “active” conformation, enabling DFHBI binding and fluorescence ( FIG. 22 ).
  • Several tubulin-binding DNA aptamers have been described (ref. 26). This disclosure provides for the evolution of control modules for Spinach capable of sensing tubulin using previously established protocols. Briefly, candidate aptamers will be fused to Spinach to
  • Spinach-PAINT can be used for, for example, super-resolution imaging of microtubules in live mammalian cells.
  • FIG. 23A shows an example of an experimental setup used for in vitro DNA origami experiments, as provided herein.
  • the sample is immobilized on a glass coverslip in a PDMS channel.
  • Imaging and washing buffers are added to a reservoir and pulled through the channel by a syringe.
  • Reservoirs and syringes are connected to the PDMS channel via flexible tubing and are, thus, mechanically decoupled.
  • FIG. 23B shows an experimental setup used for in situ cell imaging. Cells are imaged in a Lab-Tek II chamber. One syringe supplies new buffer solution, the second one removes the previous buffer.
  • Unmodified DNA oligonucleotides were purchased from Integrated DNA Technologies. Fluorescently modified DNA oligonucleotides were purchased from Biosynthesis. Biotinylated monoclonal antibodies against ⁇ -tubulin (9F3; Catalog number: 6181) and COX IV (3E11; Catalog number: 6014) were purchased from Cell Signaling. Anti-PMP70 (Catalog number: ab28499) was purchased from Abcam. Anti-TGN46 (Catalog number: NBP1-49643B) was purchased from VWR. Streptavidin was purchased from Invitrogen (Catalog number: S-888). Bovine serum albumin (BSA), and BSA-biotin was obtained from Sigma Aldrich (Catalog Number: A8549).
  • Buffer A (10 mM Tris-HCl, 100 mM NaCl, 0.05% Tween-20, pH 7.5
  • buffer B (5 mM Tris-HCl, 10 mM MgCl2, 1 mM EDTA, 0.05% Tween-20, pH 8)
  • buffer C (1 ⁇ PBS, 500 mM NaCl, pH 8).
  • Optical setup Fluorescence imaging was carried out on an inverted Nikon Eclipse Ti microscope (Nikon Instruments) with the Perfect Focus System, applying an objective-type TIRF configuration using a Nikon TIRF illuminator with an oil-immersion objective (CFI Apo TIRF 100 ⁇ , NA 1.49, Oil). For 2D imaging an additional 1.5 magnification was used to obtain a final magnification of ⁇ 150-fold, corresponding to a pixel size of 107 nm. Three lasers were used for excitation: 488 nm (200 mW nominal, Coherent Sapphire), 561 nm (200 mW nominal, Coherent Sapphire) and 647 nm (300 mW nominal, MBP Communications).
  • the laser beam was passed through cleanup filters (ZT488/10, ZET561/10, and ZET640/20, Chroma Technology) and coupled into the microscope objective using a multi-band beam splitter (ZT488rdc/ZT561rdc/ZT640rdc, Chroma Technology). Fluorescence light was spectrally filtered with emission filters (ET525/50m, ET600/50m, and ET700/75m, Chroma Technology) and imaged on an EMCCD camera (iXon X3 DU-897, Andor Technologies).
  • DNA origami self-assembly The microtubule-like DNA origami structures were formed in a one-pot reaction with 40 ⁇ l total volume containing 10 nM scaffold strand (p8064), 500 nM folding staples and biotin handles, 750 nM biotin anti-handles and 1.1 ⁇ M DNA-PAINT docking strands in folding buffer (1 ⁇ TAE Buffer with 20 mM MgCl 2 ). The solution was annealed using a thermal ramp13 cooling from 80° C. to 14° C. over the course of 15 h.
  • monomeric structures were purified by agarose gel electrophoresis (1.5% agarose, 0.5 ⁇ TBE, 10 mM MgCl 2 , 1 ⁇ SybrSafe) at 4.5 V/cm for 1.5 h. Gel bands were cut, crushed and filled into a ‘Freeze ‘N Squeeze’ column and spun for 5 min at 1000 ⁇ g at 4° C. Polymerization was carried out at 30° C. for 48 h with a 5-fold excess of polymerization staples in folding buffer. Polymerized structures were used for imaging without further purification.
  • DNA origami drift markers were self-assembled in a one-pot reaction (40 ⁇ l total volume, 20 nM M13mp18 scaffold, 100 nM biotinylated staples, 530 nM staples with DNA-PAINT docking sites, 1 ⁇ TAE with 12.5 mM MgCl2). Self-assembled structures were purified as described before.
  • DNA origami structures for the 4-“color” in vitro Exchange-PAINT demonstration were self-assembled in a one-pot reaction (40 ⁇ l total volume, 30 nM M13mp18 scaffold, 470 nM biotinylated staples, 400 nM staples with docking sites for number imaging, 370 nM core structure staples, 1 ⁇ TAE with 12.5 mM MgCl2). Self-assembled structures were purified as described before.
  • DNA origami structures for the 10-“color” in vitro Exchange-PAINT demonstration were self-assembled in a one-pot reaction (40 ⁇ l total volume, 30 nM M13mp18 scaffold, 36 nM biotinylated staples, 750 nM staples with docking sites for number imaging, 300 nM core structure staples, 1 ⁇ TAE with 12.5 mM MgCl2). Structures were not purified. Excessive staples are washed out of the sample after immobilization of the structure on the surface.
  • DNA strand sequences for the microtubule-like DNA origami structures can be found in Table 1.
  • DNA strand sequences for DNA origami drift markers can be found in Table 2.
  • DNA strand sequences for DNA origami structures for 10-“color” in vitro Exchange-PAINT demonstration can be found in Tables 3 and 4 for odd and even digits, respectively.
  • DNA strand sequences for DNA origami structures for in vitro Exchange-PAINT demonstration (digits 0 to 3) can be found in Table 5.
  • the scaffold sequence for p8064 and M13mp18 correspond to SEQ ID NO: 882 and 883, respectively.
  • DNA-PAINT imager and docking sequences as well as sequences for surface attachment via Biotin are listed in Table 6.
  • Antibody-DNA conjugates used to specifically label proteins of interest with DNA-PAINT docking sites were preassembled in two steps: First, 3.2 ⁇ l of 1 mg/ml streptavidin (dissolved in buffer A) was reacted with 0.5 ⁇ l biotinylated DNA-PAINT docking strands at 100 ⁇ M and an additional 5.3 ⁇ l of buffer A for 30 min at room temperature (RT) while gently shaking. The solution was then incubated in a second step with 1 ⁇ l of monoclonal biotinylated antibodies at 1 mg/ml against the protein of interest for 30 min at RT. Filter columns (Amicon 100 kDa, Millipore) were used to purify the preassembled conjugates from unreacted streptavidin-oligo conjugates.
  • HeLa and DLD1 cells were cultured with Eagle's minimum essential medium fortified with 10% FBS with penicillin and streptomycin and were incubated at 37° C. with 5% CO2. Approximately 30% confluence cells per well were seeded into Lab-Tek II chambered cover glass 24 h before fixation.
  • Microtubules, mitochondria, Golgi complex, and peroxisomes were immunostained using the following procedure: washing in PBS; fixation in a mixture of 3% paraformaldehyde and 0.1% glutaraldehyde in PBS for 10 min; 3-times washing with PBS; reduction with ⁇ 1 mg/ml NaBH4 for 7 min; 3-times washing with PBS; permeabilization with 0.25% (v/v) Triton X-100 in PBS for 10 min; 3-times washing with PBS; blocking with 3% (w/v) bovine serum albumin for 30 min and staining over night with the preassembled antibody-DNA conjugates against ⁇ -tubulin, COX IV, PMP70, or TGN46 (conjugates were diluted to 10 ⁇ g/ml in 5% BSA); 3-times washing with PBS; post-fixation in a mixture of 3% paraformaldehyde and 0.1% glutaraldehyde in PBS for 10 min; and 3-times
  • Imaging was performed using TIR illumination with an excitation intensity of 166 W/cm2 at 561 nm (Ten-“color” Exchange-PAINT with 3 nM Cy3b-labeled imager strands in buffer B, FIG. 5B (iii) and 5 B(v)) and 600 W/cm2 at 647 nm (Four-“color” Exchange-PAINT with 3 nM ATTO655-labeled imager strands in buffer B, FIG. 5B (iv)).
  • FIG. 3A 700 pM ATT0655-labeled imager strands in buffer C.
  • FIGS. 6B and 6C Super-resolution Exchange-PAINT imaging of cells.
  • a Lab-Tek II chamber was adapted for fluid exchange.
  • 2D images ( FIGS. 6B and 6C ) were acquired with an EMCCD readout bandwidth of 5 MHz at 14 bit, 5.1 preamp gain and 255 EM gain.
  • 3D images ( FIG. 6 ) were acquired with a CCD readout bandwith of 3 MHz at 154 bit, 5.1 pre-amp gain and no EM gain. Imaging was performed using HILO illumination in both cases. Sequential imaging was done as described for the 2D origami nanostructures, but the washing steps were performed using buffer C.
  • 3D DNA-PAINT imaging 3D images were acquired with a cylindrical lens in the detection path (Nikon).
  • the N-STORM analysis package for NIS Elements (Nikon) was used for data processing. Imaging was performed without additional magnification in the detection path, yielding 160 nm pixel size. 3D calibration was carried out according to the manufacturer's instructions.
  • Imager strand concentration determination Optimal imager concentrations are determined empirically according to the labeling density. Generally, a high enough fluorescence OFF/ON-ratio has to be ensured in order to guarantee binding of only a single imager strand per diffraction-limited area. Additionally, a sufficient imager strand concentration (and thus sufficiently low fluorescence OFF-time) is necessary to ensure sufficient binding events and thereby robust detection of every docking strand during image acquisition.
  • Normalized cross-correlation analysis Normalized cross-correlation coefficients were obtained by first normalizing the respective reconstructed gray-scale super-resolution images and subsequently performing a cross-correlation analysis in MATLAB R2013b (MathWorks, Natick, Mass., USA).
  • DNA origami structures are used for drift correction and as alignment markers in in vitro DNA-PAINT and Exchange-PAINT imaging. Drift correction was performed by tracking the position of each origami drift marker throughout the duration of each movie. The trajectories of all detected drift markers were then averaged and used to globally correct the drift in the final super-resolution reconstruction. For channel alignment between different imaging cycles in Exchange-PAINT, these structures are used as alignment points by matching their positions in each Exchange-PAINT image. For cellular imaging, 100 nm gold nanoparticles (Sigma Aldrich;10 nM in buffer C, added before imaging) were used as drift and alignment markers. The gold nanoparticles adsorb non-specifically to the glass bottom of the imaging chambers.
  • Drift correction and alignment is performed in a similar fashion as for the origami drift markers. Again, the apparent movement of all gold nanoparticles in a field of view is tracked throughout the movie. The obtained trajectories are then averaged and used for global drift correction of the final super-resolution image. For the dual-color image of mitochondria and microtubules in FIG. 3D-3F , the gold particles are visible in both color channels. The same gold nanoparticles are also used for drift-correction and re-alignment of the different imaging rounds in the in situ Exchange-PAINT experiments ( FIG. 6 ).
  • Imaging 3.5 ⁇ l of undiluted microtubules-like DNA structures were adsorbed for 2 minutes onto glow-discharged, carbon-coated TEM grids. The grids were then stained for 10 seconds using a 2% aqueous ultra-filtrated (0.2 ⁇ m filter) uranyl formate solution containing 25 mM NaOH. Imaging was performed using a JEOL JEM-1400 operated at 80 kV.
  • Atomic force microscopy imaging Imaging was performed using tapping mode on a Multimode VIII atomic force microscope (AFM) with an E-scanner (Bruker). Imaging was performed in TAE/Mg2+ buffer solution with DNP-S oxide-sharpened silicon nitride cantilevers and SNL sharp nitride levers (Bruker Probes) using resonance frequencies between 7-9 kHz of the narrow 100 ⁇ m, 0.38 N/m force constant cantilever. After self-assembly of the origami structure ⁇ 20 ⁇ l of TAE/Mg2+ buffer solution was deposited onto a freshly cleaved mica surface (Ted Pella) glued to a metal puck (Ted Pella).
  • the mica surface was dried using a gentle stream of N2 and 5 ⁇ l of the origami solution was deposited onto the mica surface. After another 30 s, 30 ⁇ l of additional buffer solution was added to the sample. Imaging parameters were optimized for best image quality while maintaining the highest possible setpoint to minimize damage to the samples. Images were post-processed by subtracting a 1st order polynomial from each scan line. Drive amplitudes were approximately 0.11 V, integral gains ⁇ 2, and proportional gains ⁇ 4.
  • each oligonucleotide position in a described structure is set forth.
  • Each oligonucleotide position (e.g., n[n]n[n]) in the first column is separated by a comma and corresponds respectively to a sequence identification number in the second column within the same row.
  • Each sequence identification number identifies a corresponding oligonucleotide sequence in the attached sequence listing, incorporated by reference herein.
  • position 0[39]21[39] corresponds to the oligonucleotide represented by SEQ ID NO: 1
  • position 0[79]1[79] corresponds to the oligonucleotide represented by SEQ ID NO: 2 and so forth.

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