WO2000055372A1 - Procedes et dispositif servant a detecter des polymorphismes d'acides nucleiques - Google Patents

Procedes et dispositif servant a detecter des polymorphismes d'acides nucleiques Download PDF

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Publication number
WO2000055372A1
WO2000055372A1 PCT/US2000/006841 US0006841W WO0055372A1 WO 2000055372 A1 WO2000055372 A1 WO 2000055372A1 US 0006841 W US0006841 W US 0006841W WO 0055372 A1 WO0055372 A1 WO 0055372A1
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Prior art keywords
sample
nucleic acid
light
primer
polarization
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PCT/US2000/006841
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English (en)
Inventor
Todd E. French
Douglas N. Modlin
John C. Owicki
James S. Richey
Lev J. Leytes
Enal S. Razvi
Yan Zhang-Klompus
Peter R. Panfili
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Ljl Biosystems, Inc.
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Priority claimed from PCT/US1999/008410 external-priority patent/WO1999054711A1/fr
Priority claimed from PCT/US2000/000895 external-priority patent/WO2000042209A1/fr
Priority claimed from US09/494,407 external-priority patent/US6297018B1/en
Application filed by Ljl Biosystems, Inc. filed Critical Ljl Biosystems, Inc.
Priority to AU37488/00A priority Critical patent/AU3748800A/en
Publication of WO2000055372A1 publication Critical patent/WO2000055372A1/fr
Priority to US09/770,720 priority patent/US20010046673A1/en
Priority to US10/445,292 priority patent/US6992761B2/en

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    • C—CHEMISTRY; METALLURGY
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • C—CHEMISTRY; METALLURGY
    • 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
    • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
    • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase
    • C—CHEMISTRY; METALLURGY
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C—CHEMISTRY; METALLURGY
    • 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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00279—Features relating to reactor vessels
    • B01J2219/00306—Reactor vessels in a multiple arrangement
    • B01J2219/00313—Reactor vessels in a multiple arrangement the reactor vessels being formed by arrays of wells in blocks
    • B01J2219/00315—Microtiter plates
    • B01J2219/00317—Microwell devices, i.e. having large numbers of wells
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277—Apparatus
    • B01J2219/00497—Features relating to the solid phase supports
    • B01J2219/00527—Sheets
    • B01J2219/00529—DNA chips
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B60/00—Apparatus specially adapted for use in combinatorial chemistry or with libraries
    • C40B60/14—Apparatus specially adapted for use in combinatorial chemistry or with libraries for creating libraries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/91—Transferases (2.)
    • G01N2333/912—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • G01N2333/91205—Phosphotransferases in general
    • G01N2333/9121—Phosphotransferases in general with an alcohol group as acceptor (2.7.1), e.g. general tyrosine, serine or threonine kinases

Definitions

  • the invention relates to nucleic acids. More particularly, the invention relates to methods and apparatus for detecting nucleic acid polymorphisms in luminescence-based assays.
  • Nucleic acids are linear polymers composed of covalently linked nucleotides.
  • nucleotides are small organic compounds composed of phosphoric acid, a carbohydrate, and a purine such as adenine (A) or guanine (G) or a pyrimidine such as cytosine (C), thymidine (T), or uracil (U).
  • Nucleic acids may be single-stranded or double-stranded, where double- stranded nucleic acids are composed of two single-stranded nucleic acids bound to one another through noncovalent base-pairing interactions to form a hybrid. Such binding or hybridization will occur if the sequences of the single- stranded nucleic acids are "complementary" (or nearly complementary), so that for example wherever there is an A in one strand there is a T or a U in the other, and wherever there is a G in one strand there is a C in the other.
  • Nucleic acids in the form of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) encode genetic information that controls cellular function and heredity in biological systems.
  • DNA encodes information at least in part in the form of genes, where genes are sequences of nucleotides that encode information for constructing a polypeptide.
  • the sequence of nucleotides in a gene may vary due to insertions, deletions, repeats, inversions, translocations, and/or single and multiple nucleotide substitutions, among others. These variations may be termed polymorphisms, and genes that differ by polymorphisms may be termed alleles.
  • Polymorphisms and other genetic factors appear to contribute to virtually every human disease, conferring susceptibility or resistance and affecting both progression and severity.
  • variations in the apoE gene are associated with Alzheimer's disease
  • variations in the CCR5 chemokine receptor gene are associated with resistance to HIV infection
  • variations in the hemoglobin gene are associated with sickle cell anemia
  • variations in glycosyltransferase genes are associated with the ABO blood groups.
  • an understanding of the genetic contribution to disease may greatly impact the diagnosis, treatment, and prevention of disease.
  • an understanding of this genetic contribution also may help in identifying and understanding nongenetic (e.g., environmental) influences on disease.
  • DNA sequence variations are becoming increasingly important in identifying the genes involved in both disease and normal biological processes, including development, aging, and reproduction. For example, to understand disease, it is important to understand how genetic variation affects gene function. Response to therapies also can be affected by genetic differences. Thus, information about variations in DNA sequence may assist in the analysis of disease and in the development of diagnostic, therapeutic, and preventative strategies.
  • SNPs single nucleotide polymorphisms
  • SNPs single nucleotide polymorphisms
  • SNPs have many properties that make them attractive as the primary analytical reagent for the study of human sequence variation. In addition to their frequency, SNPs are stable, having much lower mutation rates than repeat sequences. More importantly, SNPs will be often be the nucleotide sequence variations that are responsible for functional changes of interest.
  • SNPs are very common in human DNA. Any two random chromosomes differ at about 1 in 1000 bases. However, only about half or fewer of random pairs of chromosomes will differ for any particular polymorphic base (i.e., for any base for which the least common variant has a frequency of at least 1% in the population). Thus, there actually are more polymorphic sites in the human population, viewed in its entirety, than there are sites that differ in any particular pair of chromosomes. Altogether, there may be anywhere from 6 million to 30 million nucleotide positions in the genome at which variation can occur in the human population. Thus, overall, approximately one in every 100 to 500 bases in human DNA may be polymorphic.
  • SNPs are biallelic. Each allele contains one of two nucleotides, for example, A or C.
  • a or C nucleotides
  • three genotypes are possible: homozygous AA, homozygous CC, or heterozygous AC.
  • SNPs can be used as genetic markers in mapping studies.
  • SNPs can be used for whole-genome scans in pedigree-based linkage analysis of families; for this purpose, a map of about 2000 SNPs has the same analytical power as a map of about 800 microsatellite markers, currently the most frequently used type of marker.
  • haplotype distributions and linkage disequilibria can be used to map genes by association methods. For this purpose, it has been estimated that 30,000 to as many as 300,000 mapped SNPs will be needed.
  • SNPs genetic analysis can be used in case-control studies to identify functional SNPs contributing to a particular phenotype. Most SNPs are located outside of coding sequences, because only three to five percent of the human DNA sequence encodes proteins. However, SNPs located within protein-coding sequences ("cSNPs") are of particular interest because they are more likely than a random SNP to have functional significance. It also is likely that some of the SNPs in noncoding DNA will have functional consequences, such as those in sequences that regulate gene expression. Discovery of SNPs that affect biological function should become increasingly important over the next several years, and should be greatly facilitated by the availability of a large collection of SNPs, from which candidates for polymorphisms with functional significance can be identified. Accordingly, SNPs discovery is an important objective of SNPs research.
  • SNPs will be particularly important for mapping and discovering the genes associated with common diseases.
  • Many processes and diseases are caused or influenced by complex interactions among multiple genes and environmental factors. These include processes such as development and aging, and diseases such as diabetes, cancer, cardiovascular and pulmonary disease, neurological diseases, autoimmune diseases, psychiatric illnesses, alcoholism, common birth defects, and susceptibility to infectious diseases, teratogens, and environmental agents.
  • Many of the alleles associated with health problems are likely to have a low penetrance, meaning that only a small percentage of individuals carrying the alleles will develop disease.
  • Examples of common polymorphisms associated with an increased risk of disease include the ApoE4 allele and Alzheimer's disease, and the APC I1307K allele and colon cancer.
  • association studies that do have the power to identify such loci efficiently require new approaches, techniques, and scientific resources to make them as robust and powerful as positional cloning.
  • Among the resources needed is a genetic map of much higher density than the existing, microsatellite-based map.
  • Association studies using a dense map should allow the identification of disease alleles even for complex diseases. SNPs are well suited to be the basis of such a map.
  • U.S. Patent No. 5,888,819 to Goelet et al. describes a technique involving first binding a primer to a single-stranded polynucleotide immediately adjacent a polymorphic site of interest, and extending the primer by a terminating nucleotide such as a labeled ddNTP. Incorporation of the labeled base is then detected indicating what allele is present in the sample at the polymorphic site.
  • a similar technique is described in U.S. Patent No. 5,302,509 to Cheeseman.
  • the invention provides methods and apparatus for detecting nucleic acid polymorphisms in luminescence-based assays. Brief Description of the Drawings
  • Figure 1 is a schematic view of (A) an incorporation assay and (B) a ligation assay provided by the invention.
  • Figure 2 is a schematic view of a surface-based incorporation assay showing how primer mobility can be reduced by attachment to a surface.
  • Figure 3 is a schematic view of an incorporation assay showing how luminescence polarization can be used in a two-dye assay for SNPs detection.
  • Figure 4 is a graph showing results obtained in detecting a two-allele SNP using a template-directed dye-terminator incorporation assay and high- efficiency luminescence polarization detection.
  • Figure 5 is a schematic view of a procedure for determining the sequence of a DNA at the site of a known polymorphism.
  • Figure 6 is a flowchart summarizing the genotyping assay of Figure 5.
  • Figure 7 is an apparatus for performing dichroic (or multi-dichroic) genomics assays in accordance with the invention.
  • Figure 8 is a schematic view of transmission profiles for a dichroic beamsplitter and complementary excitation and emission filters.
  • Figure 9 is a graph of transmission profiles for (A) a double-dichroic beamsplitter and (B) complementary pairs of excitation and emission filters, all suitable for fluorescein and Texas Red, or spectrally similar luminophores.
  • Figure 10 is a graph showing results of a genotyping assay obtained using fluorescein and Texas Red luminescent labels in combination with (A) a 50:50 beamsplitter, and (B) a fluorescein / Texas Red double-dichroic beamsplitter.
  • Figure 11 is a schematic view of a multiplexed genotyping assay employing multiple primers and multiple tails.
  • Figure 12 is a schematic view of luminescently labeled molecules, showing how molecular reorientation affects luminescence polarization.
  • Figure 13 is a schematic view of a frequency-domain time-resolved measurement, showing the definitions of phase angle (phase) ⁇ and demodulation factor (modulation) M.
  • Figure 14 is a schematic view of an apparatus for detecting light in accordance with the invention.
  • Figure 15 is a schematic view of an alternative apparatus for detecting light in accordance with the invention.
  • Figure 16 is a partially schematic perspective view of the apparatus of Figure 15.
  • Figure 17 is a schematic view of photoluminescence optical components from the apparatus of Figure 15.
  • Figure 18 is a schematic view of chemiluminescence optical components from the apparatus of Figure 15.
  • Figure 19 is a partially exploded perspective view of a housing for the apparatus of Figure 15.
  • Figure 20 is a schematic view of another alternative apparatus for detecting light in accordance with the invention.
  • Figure 21 is a graph of polarization versus fluorescein concentration measured in 96-well and 384-well microplates, showing the sensitivity of the apparatus.
  • Figure 22 is a graph of the standard deviation of polarization versus fluorescein concentration measured in 384-well microplates, determined after 4-minute and 9-minute whole microplate read times, showing the sensitivity of the apparatus.
  • Figure 23 is a top view of a 96-well microplate constructed in accordance with the invention.
  • Figure 24 is a cross-sectional view of the microplate in Figure 23, taken generally along line 17-17 in Figure 23.
  • Figure 25 is a first enlarged portion of the cross-sectional view in Figure 24, showing details of a sample well.
  • Figure 26 is a second enlarged portion of the cross-sectional view in Figure 24, showing details of a reference fiducial.
  • Figure 27 is a top view of a 384-well microplate constructed in accordance with the invention.
  • Figure 28 is a cross-sectional view of the microplate in Figure 27, taken generally along line 21-21 in Figure 27.
  • Figure 29 is an enlarged portion of the cross-sectional view in Figure 27, showing details of a sample well.
  • Figure 30 is an enlarged cross-sectional view of the microplate in Figure 27, taken generally along line 30-30 in Figure 27, showing details of a reference fiducial.
  • Figure 31 is a perspective view of a 1536-well microplate constructed in accordance with the invention.
  • Figure 32 is a top view of the microplate in Figure 31.
  • Figure 33 is an enlarged portion of the top view in Figure 32, showing details of the sample wells.
  • Figure 34 is a cross-sectional view of the microplate in Figure 31, taken generally along line 34-34 in Figure 31.
  • Figure 35 is an enlarged portion of the cross-sectional view in Figure 34, showing details of the sample wells.
  • Figure 36 is a partially schematic cross-sectional view of a standard microplate well.
  • Figure 37 is a partially schematic cross-sectional view of a sample holder constructed in accordance with the invention.
  • Figure 38 is a partially schematic cross-sectional view of an alternative sample holder constructed in accordance with the invention.
  • Figure 39 is a partially schematic cross-sectional view of another alternative sample holder constructed in accordance with the invention.
  • Figure 40 is a partially schematic cross-sectional view of three sample wells, showing alternative positions of a sensed volume.
  • Figure 41 is a partially schematic cross-sectional view of four sample wells, showing how the meniscus affects the shape and position of the sensed volume within a sample well.
  • Figure 42 is a partially schematic cross-sectional view of a sample well, showing how the geometry of the sample well affects the position of the sensed volume.
  • Figure 43 is a graph showing the relationships between critical Z-height and microplate well height.
  • Figure 44 is a graph of experimental results showing that short-lifetime background with low polarization does not significantly affect performance of FLAMe methods.
  • Figure 45 is a phasor diagram showing phase and modulation phasors for a system having an analyte and background.
  • Figure 46 is a graph of simulation results showing how the invention discriminates between an analyte and background for three zeroth-order embodiments of the invention, as described in Equations 13 (LDI, M x -based), 15 (LDI, ⁇ -based), and 16 (LRI).
  • Figure 47 is a graph of experimental results showing how the invention discriminates between a long-lifetime ruthenium-complex analyte and a short- lifetime R-phycoerythrin background, for a constant concentration of analyte and an increasing concentration of background. Results are shown for embodiments described under Figure 46.
  • Figure 48 is a graph of experimental results showing how the invention discriminates between a long-lifetime ruthenium-complex analyte and a short- lifetime R-phycoerythrin background, for a constant concentration of background and an increasing concentration of analyte. Results are shown for embodiments described under Figure 46.
  • Figure 49 is a graph of simulation results showing how binding affects differential phase (Panel A) and modulated anisotropy (Panel B) in the presence of 0% background in a frequency-domain binding experiment, for 0- 100%o binding as shown.
  • Figure 50 is a graph of simulation results showing how binding affects differential phase (Panel A) and modulated anisotropy (Panel B) in the presence of 50% background in the frequency-domain binding experiments shown in Figure 49.
  • Figure 51 is a graph of simulation results showing how binding affects ⁇ ⁇ in the presence of 0% (solid lines) and 50% (dashed lines) background in the frequency-domain experiments of Figure 49, for 0-100% binding as shown.
  • ⁇ ⁇ is defined and evaluated in accordance with the invention.
  • Figure 52 is a graph of simulation results showing how binding affects K ⁇ in the presence of 0% (solid lines) and 90% (dashed lines) background in the frequency- domain binding experiments of Figure 49.
  • K ⁇ is defined and evaluated in accordance with the invention.
  • Figure 53 is a graph of computed lifetime versus signal-to-background fluorescence intensities for simulated parameters, showing how the FLDL method improves the accuracy of lifetime measurement with strong backgrounds.
  • the invention provides methods and apparatus for detecting nucleic acid targets in luminescence assays.
  • These targets may include nucleic acid polymorphisms, such as single nucleotide polymorphisms (SNPs).
  • the methods may include (1) allele-specific hybridization, using luminescence detection, (2) allele-specific oligonucleotide ligation, using dye-labeled oligonucleotide ligation with luminescence resonance energy transfer (FRET) detection, and (3) allele-specific nucleotide incorporation, using primer extension with luminescence polarization (FP) detection.
  • FRET luminescence resonance energy transfer
  • the methods may include (1) locating a sample containing a nucleic acid material at an examination site, (2) illuminating the sample, (3) detecting light transmitted from the sample, and (4) determining the presence, absence, and/or identity of a nucleic acid target in the sample using the light transmitted from the sample.
  • the steps of illuminating and detecting may be performed on a single sample or (serially and/or simultaneously) on a plurality of samples.
  • Figure 1 is a schematic view of (A) an incorporation assay and (B) a ligation assay provided by the invention. These assays may be used to identify a SNP in a target sequence.
  • a single- stranded nucleic-acid primer 50 is hybridized to a target sequence 51, one base pair upstream of a SNP position 52.
  • a dye-labeled dideoxy nucleoside triphosphate (ddNTP) 53, or dye terminator, corresponding to the SNP is included in the sample, so that it will be enzymatically incorporated onto the primer by a polymerase if the SNP allele in question is on the target sequence.
  • ddNTP dideoxy nucleoside triphosphate
  • first 55 and second 56 single-stranded nucleic-acid primers are hybridized to a target sequence 57, first primer 55 one base pair upstream of a SNP position 58 and second primer 56 one base pair downstream of the SNP position.
  • a deoxy nucleoside triphosphate (dNTP) 59 corresponding to the SNP is included in the sample, so that it will be ligated between the two primers by a ligase if the SNP allele in question is on the target sequence.
  • dNTP deoxy nucleoside triphosphate
  • the incorporation of free nucleotide into the primer(s) in Panels A and B may be determined using luminescence.
  • the ddNTP may be luminescently labeled, and the incorporation of the ddNTP into the primer may be determined by observing an increase in polarization, or an increase in energy transfer to or from an energy transfer partner associated with the primer.
  • the dNTP may be luminescently labeled, and the incorporation of the dNTP into (either or both of) the two primers may be determined by observing an increase in polarization or energy transfer, as described above.
  • the dNTP may be unlabeled, and the incorporation of the dNTP may be determined by observing an increase in energy transfer between energy transfer partners associated with each of the two primers brought together by the ligation.
  • Energy transfer may be observed using any suitable mechanism; preferred methods and apparatus for energy transfer are described in subsequent sections.
  • energy transfer may be observed using intensity-based methods, by observing decreases in donor intensity, increases in acceptor intensity (if the acceptor is luminescent), or changes in the ratio of the two intensities.
  • energy transfer may be observed using lifetime-based methods, by observing decreases in donor lifetime, increases in acceptor lifetime (for luminescent acceptors), or changes in the ratio of the two lifetimes. Lifetime-based detection can be carried out using frequency-domain methods (e.g., phase/modulation detection), time- domain methods (e.g., pulse excitation with gated integration), or hybrid methods combining features of both.
  • Polarization also may be observed using any suitable mechanism; preferred methods and apparatus for polarization are described in subsequent sections.
  • Polarization assays exploit the decrease in rotational mobility that accompanies incorporation of a free nucleotide into a primer. Specifically, free luminescent ligands undergo relatively rapid rotation and produce relatively depolarized emission following excitation with polarized light, whereas incorporated luminescent ligands undergo relatively slow rotation and produce relatively polarized emission following excitation. These differences may be observed by measuring intensities of luminescence emissions parallel and perpendicular to an excitation polarization, and then using these quantities to evaluate a suitable mathematical function, such as polarization or anisotropy.
  • aspects of the invention include mechanisms that augment the increase in polarization upon inco ⁇ oration, so that it can be measured more easily.
  • the change in polarization upon incorporation into the primer can be increased by making any linker between the luminophore and terminator as short and/or rigid as possible, while maintaining relevant substrate properties for the enzymes involved in the assay.
  • Short and/or rigid linkers will restrict luminophore motion relative to the terminator, reducing the "propeller effect" so that the luminophore more accurately reports the motion of both the incorporated and free terminator.
  • the rigidity of the linker may be increased by avoiding using hexanoic acid linkers, which typically are long and flexible, and by using amide groups in place of methylene groups, among other mechanisms.
  • the change in polarization upon inco ⁇ oration into the primer also can be increased by decreasing the lifetime of the terminator.
  • lifetime can be decreased by including an appropriately positioned energy transfer acceptor on the primer, so that energy transfer occurs from the luminophore to the acceptor upon inco ⁇ oration.
  • Lifetime also can be decreased by including an appropriately positioned quencher on the primer. Energy transfer and quenching will shorten the lifetime of the luminophore by providing additional mechanisms for depleting the excited state.
  • the change in polarization upon inco ⁇ oration into the primer also can be increased by decreasing the mobility of the primer (i.e., by increasing the rotational correlation time).
  • Mobility can be decreased by increasing the size of the primer, either directly or by forming a complex with a mass label.
  • Suitable mass labels include other molecules and beads, among others. The use of mass labels is described in detail in PCT Patent Application Serial No. PCT/US99/24707, which is inco ⁇ orated herein by reference.
  • Mobility also can be decreased by attaching the primer to a surface, such as the surface of the sample holder. Attachment to other molecules, beads, and/or surfaces may be accomplished using any of a number of well-known reactive groups.
  • Figure 2 shows how primer mobility can be reduced by attachment of the primer to a surface.
  • a substrate e.g., microplate
  • a substrate e.g., microplate
  • the primer would be designed, as for the solution- based case, to come within one base of the SNP 64.
  • Inco ⁇ oration of the ddNTP 65 by a polymerase 66 would result in a dramatic polarization change, taking the free nucleotide label to a surface-immobilized state.
  • the spectral properties of the label would identify which of up to four nucleotides were actually inco ⁇ orated.
  • Quantities such as energy transfer and polarization may be monitored using lifetime-based and intensity-based methods.
  • Lifetime-based methods have several advantages over intensity-based methods. For example, lifetime-based detection increases precision by monitoring an intensive quantity, luminescence lifetime, rather than an extensive quantity, luminescence intensity.
  • lifetime-based detection is able to reject background interference from light scattering and luminescent contaminants that have a lifetime different from that of the label being analyzed. This becomes increasingly important as sample volume and hence signal-to-background ratios are decreased. Decreasing sample volume is advantageous for various reasons, including economy of reagent consumption and the ability to utilize smaller biological samples.
  • two- to four-lifetime detection methods may be constructed that require only one excitation and one emission wavelength. For example, call a series of four luminescent labels with similar excitation and emission spectra but distinguishable luminescence lifetimes FI, F2, F3, and F4. Using the four dideoxy terminators, create the dye terminators ddATP-Fl, ddTTP-F2, ddCTP- F3, and ddGTP-F4. The one-base-pair-extension/termination procedure with a labeled primer is carried out as described above, but with all four dye terminators present.
  • the amount of energy transfer corresponding to the interactions of each of the four luminophores with the label on the primer can be assessed to determine the SNP (or SNPs, if heterozygous) that were present in the sample.
  • a similar approach may be used in the ligation assay, using multiple labeled dNTPs.
  • the number of required labeled-nucleotides depends on the number of alleles corresponding to the polymo ⁇ hism of interest. For example, if there are four alleles, each differing by a single nucleotide substitution (A, T, G, C), then a four-lifetime method is appropriate. Alternatively, if there are only three or two alleles, then a three-lifetime or two-lifetime method is appropriate, respectively.
  • polarization labels preferably are chosen to minimize energy transfer, which decreases polarization, and because polarization labels must be selected to obtain spectral separation while maintaining good polarization properties.
  • Suitable sets of labels may be constructed using novel luminescent labels and/or novel combinations of pre-existing luminescent labels.
  • Suitable sets of dyes can be constructed by selecting one label from each of up to the following four groups of labels, among others: (1) Cascade blue or aminomethyl coumarin, (2) fluorescein or rhodamine green, (3) rhodamine 6G or tetramethyl rhodamine, and (4) sulforhodamine 101 or lissamine rhodamine B. Such a selection could result in 16 different quartets, 32 different triplets, and 48 different pairs, based on combinatorics.
  • Dyes can be distinguished by using wavelength and lifetime sequentially. For example, F 1 through F3 could be distinguished from F4 by wavelength, and F 1 through F3 could be distinguished among themselves by lifetime. Dyes also can be distinguished by using wavelength and lifetime simultaneously. For example, FI through F4 could be distinguished among themselves in a two- dimensional space based on wavelength and lifetime. It may be more reliable to use both wavelength and lifetime than either alone, depending on the refinements in spectral and lifetime properties of dyes that are possible.
  • Figure 3 shows how luminescence polarization can be used in a two-dye assay for SNP detection.
  • luminescently labeled dideoxy- mononucleotides are used to detect and identify a particular SNP.
  • This SNP involves a DNA fragment in which a particular base may be G (the G-allele) or A (the A- allele).
  • a primer may be added to an amplified DNA fragment including the polymo ⁇ hism, so that it binds with the DNA fragment.
  • the primer is complementary to a sequence of DNA up to but not including the polymo ⁇ hism.
  • An appropriate polymerase such as DNA polymerase
  • appropriate mononucleotides such as ROX-labeled dideoxy-cytosine (ddC) mononucleotides and TAMRA-labeled dideoxy-uracil (ddU) mononucleotides
  • ROX denotes 6-carboxy- X-rhodamine
  • TAMRA denotes N,N,N',N'-tetramethyl-6- carboxyrhodamine.
  • the polymo ⁇ hism includes G, the ROX-labeled ddC mononucleotide will be added to the primer by the polymerase, increasing its luminescence polarization by reducing its rotation rate. If the polymo ⁇ hism includes A, the TAMRA-labeled ddU mononucleotide will be added to the primer, increasing its luminescence polarization by reducing its rotation rate.
  • the polymo ⁇ hism may be identified by determining which luminescence experiences an increase in luminescence polarization.
  • Figure 4 and the following table show results obtained at LJL BioSystems, Inc. by applying the assay of Figure 3 to score the A/C SNP of Figure 3.
  • DNA samples were obtained from 24 different individuals and interrogated for genotype. The results show that the homozygous A/A genotype was present in one individual (-5% of the population), the heterozygous A/C genotype was present in five individuals ( ⁇ 24%o of the population), and the homozygous C/C genotype was present in fifteen individuals (-71% of the population), with three individuals uninterro gated due to PCR failure.
  • the energy transfer and polarization assays presented above are homogeneous, i.e., there are no separation steps in these assays. It is possible to perform these assays in an inhomogeneous fashion with the same labeled nucleotides described above by using unlabeled primers, separating inco ⁇ orated from uninco ⁇ orated labeled nucleotides, and measuring the luminescence intensity at each lifetime for the inco ⁇ orated labeled nucleotides.
  • the separation might be accomplished, for example, by washing following capture of the sample or primers on a solid phase, such as a bead or microplate surface, using hybridization or other biospecific interaction. It sometimes may be advantageous to attach or immobilize other reagents to a solid surface.
  • polymerase which is used to add the labeled ddNTP onto an end of the primer
  • ligase which is used to ligate the labeled dNTP between two primers
  • the polymerase or ligase may be chemically linked to the solid support and/or stabilized in dry form, for example, in a film or by lyophilization, so that it will solubilize and recover enzymatic activity in an aqueous sample.
  • all required reagents may be stabilized in a microplate well so that the assay can be run simply by adding an appropriate buffer and sample nucleic acid to the well and performing the luminescence assay.
  • nucleic acids include target and primer nucleic acids.
  • these nucleic acids may include deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs), and peptide nucleic acids (PNAs), among others, as well as fragments, derivatives, and analogs thereof, so long as each is enzymatically recognizable.
  • the nucleic acids may be single stranded, double stranded, or multiply stranded.
  • the method may include treating (e.g., heating or otherwise denaturing) the nucleic acids to permit access and/or binding to the nucleic acid (e.g., target) by a complementary nucleic acid (e.g., primer).
  • the nucleic acids may be of any length, from oligonucleotides having fewer than about 100 bases to long chromosomes having millions of bases.
  • the nucleic acids can be characterized by their sequences. These sequences may be created de novo or copied or patterned after a natural sequence, such as that found in all or part of an exon, intron, gene, gene family, plasmid, cosmid, virus, virion, or chromosome, among others.
  • the nucleic acids can be isolated, synthesized, and/or manipulated using standard techniques from molecular biology. Suitable techniques are described in William Bains, Biotechnology from A to Z (1993), which is inco ⁇ orated herein by reference.
  • target and primer nucleic acids can be labeled and/or amplified using the polymerase chain reaction (PCR), among others.
  • PCR polymerase chain reaction
  • the target and primer nucleic acids may be brought into contact using any method for effectuating such contact.
  • a preferred method is by mixing the materials in solution, although other methods also may be used, such as attaching one or more components to a solid support such as a bead or surface, so long as the nucleic acids retain at least some specificity and binding affinity following such coupling.
  • the target and primer nucleic acids may be brought into contact under conditions conducive to hybridization. These conditions will vary with the nucleic acids due to the unique melting temperatures and hybridization properties of different polynucleotides. Melting temperature is determined largely by guanine/cytosine concentration in the hybrid. Generally, lower temperature and higher ionic strengths favor hybridization.
  • concentration of primer nucleic acid it is preferable for the concentration of primer nucleic acid to be at least about as great as the concentration of target nucleic acid. In PCR assays, it is preferable for the concentration of primer to exceed the concentration of target, so that multiple primers can be labeled during multiple PCR cycles, enhancing signal.
  • Additional agents can be used to facilitate hybridization by destabilizing single-stranded nucleic acids, lowering melting temperatures, concentrating nucleic acids, and/or blocking and reducing nonspecific binding to substrate.
  • formamide lowers melting temperatures, so hybridizations can be performed at lower temperatures.
  • Blocking agents such as bovine serum albumin, sheared/denatured DNA, casein, and nonfat dry milk
  • Blocking agents reduce nonspecific binding, although they may spuriously increase polarization if they act by binding labeled polynucleotides.
  • Excluding agents (such as dextran) effectively concentrate polynucleotides by excluding them from solution, thereby enhancing hybridization.
  • the detection of nucleic acid polymo ⁇ hisms can be enhanced using high-sensitivity luminescence methods, including luminescence resonance energy transfer, luminescence polarization, and luminescence lifetime, among others.
  • the detection also can be enhanced by improving (1) the assay system, including the assay chemistry,
  • Signal may be enhanced in several ways, including (1) using a high color temperature light source, such as a xenon arc lamp, in a continuous illumination mode, (2) using a dichroic or multi-dichroic beamsplitter in combination with complementary photoluminescent dideoxy terminators, and
  • the high color temperature light source increases the number of usable photons, which is important because the lower limit of the signal-to-noise ratio is set by the square root of the total number of photons collected in the measurement.
  • Signal-to-background ratios can be enhanced in several ways, including
  • Sample volumes can be reduced by matching the shape of the sample holder to the shape of the optical beam of the instrument. Simple calculations show that the number of luminescent molecules obtained from a typical PCR reaction is sufficiently high that the resulting luminescence signal will be considerably above the lower detection limit for polarization measurements in the light detection device described below, even after the sample is aliquoted in 1-10 ⁇ L amounts between 96, 384, 1536, or more sample wells. Specifically, samples taken from humans typically contain about 10 6 cells, and PCR amplification factors typically are in the range 10 6 - 10 12 . If the PCR gain is about 10 6 , the concentration of luminescent label will be about 0.2 ⁇ M in a 10 ⁇ L sample, high enough readily to detect expected polarization changes.
  • the methods and apparatus presented for detecting SNPs may reduce the required amounts of sample and reagents, and allow the use of conventional microplate technology, while avoiding the higher error rates associated with SNPs detection using DNA chips.
  • DNA chips generally attempt to detect SNPs by measuring the extent of hybridization of DNA targets to DNA probes immobilized on the chip surface. Single-base mismatches are difficult to detect when the immobilized DNA probes are relatively long compared to the mismatch, e.g., DNA chips often use 10-mers or 20-mers to achieve sequence uniqueness.
  • microplate technology also can be expected to increase turnaround time for custom DNA arrays.
  • the methods and apparatus provided by the invention may be used for the discovery and/or scoring of SNPs, among other applications. These methods and apparatus also may be combined with other approaches, including "wet bench", computational, and/or multiplexing approaches, to generate additional information regarding a genome of interest (e.g. a map location or haplotype).
  • the invention may be used for drug research and accelerated drug discovery, combinatorial chemistry, life science research, DNA sequencing, genome studies, and genetic screening, among others.
  • aspects of the invention may include SNPs discovery. These aspects may focus on finding SNPs throughout the genome, or in or adjacent regulatory and coding regions, or in particular types or sets of genes within the coding regions. These aspects also may focus on finding SNPs related to particular processes, organs, or diseases, or functional variants of genes.
  • aspects of the invention also may include SNPs scoring.
  • SNPs "scoring” is used to determine the genotypes of individuals for particular SNPs that already have been discovered. SNPs may be "scored” to stratify a population based on genotype. SNPs may be scored using various mechanisms. For example, as described above, SNPs may be scored by taking a DNA template, annealing a complementary primer, and then performing an extension reaction using dye-labeled ddNTPs. The dye-labeled ddNTP tumbles freely in solution if uninco ⁇ orated, but is restricted in its tumbling if inco ⁇ orated into a polynucleotide chain.
  • the difference in tumbling may be measured using luminescence polarization, together with combinations of sample holders and/or detection optics and methods as described herein. Additional aspects of the invention are described below and in patent applications cross-referenced above and incorporated herein by reference.
  • the invention may include combining the sample and reference polynucleotides with a luminescent reference compound, and determining the intensity of light emitted from the labeled nucleotide as a function of the intensity of light emitted from the reference compound.
  • amplicons were amplified from purified genomic DNA containing the SNP of interest.
  • Luminescent ddNTPs were then added in the primer extension reaction. Identification of the specific luminescent ddNTP inco ⁇ orated at the polymo ⁇ hic site was determined in a homogenous luminescent polarization assay. Covalent linkage of the luminophore onto the primer increases the molecular weight of ddNTP labels at least tenfold, resulting in increased polarization. Polarization is calculated in a ratiometric formula with the units of mP.
  • Figure 5 is a schematic showing a procedure for determining the sequence of a DNA at the site of a known polymo ⁇ hism. It is a three-step enzymatic procedure, which can be performed in a single well of a microplate.
  • the genomic region of interest is amplified using conventional PCR.
  • su ⁇ lus PCT primers and dNTPs are removed using Exonuclease I and Shrimp Alkaline Phosphatase.
  • the genotype is determined.
  • the PCR product amplicon
  • an oligonucleotide primer that is complementary to the region immediately upstream of the polymo ⁇ hism.
  • a DNA polymerase enzyme and four fluorescently labeled ddNTPs are added to the primer- amplicon complex. Each of the four ddNTPs is labeled with a different luminophore, and the luminophores are chosen to have minimal spectral overlap.
  • the polymerase enzyme inco ⁇ orates the labeled ddNTP complementary to the nucleotide just downstream from the primer.
  • Inco ⁇ oration of a luminescently labeled ddNTP into a larger molecule causes a decrease in the rotational rate of the luminophore in solution, allowing for specific detection by fluorescence polarization (e.g., by HEFPTM methods).
  • fluorescence polarization e.g., by HEFPTM methods.
  • the color of the label in the depolarized state positively identifies the inco ⁇ orated base.
  • PCR Amplification of Template DNA • Mix contains PCR primers, regular dNTPs, and source DNA (usually genomic DNA) and polymerase • Goal: obtaining sufficient PCR product with the minimal amount of PCR primers and dNTPs 2. Degradation of PCR Primers and dNTPs
  • ROX-ddGTP 100 ⁇ M (NEN, Cat.# NEL-479)
  • TAMRA-ddCTP 100 ⁇ M (NEN, Cat.# NEL-473)
  • BFL-14-ddATP 100 ⁇ M (NEN, Cat.# NLP-999E001)
  • R6G denotes rhodamine 6G
  • ROX denotes 6-carboxy-X- rhodamine
  • TAMRA denotes N,N,N',N'-tetramethyl-6- carboxyrhodamine
  • BFL denotes bodipy-fluorescein.
  • extension primers bind just upstream from the polymo ⁇ hic site. Because we used a two-step cycling primer-extension reaction with annealing and extension occurring at 60 °C, the extension primers were designed to have annealing temperatures of 70 °C or higher. The sequence is as follows: ApoE- 112 extension primer:
  • reaction buffer Tris-HCl, pH 9.0 250 mM
  • Labeled-ddNTP Mix To use all four labels, mix equal volumes of four ddNTPs for a final concentration of 25 ⁇ M for each dye; adjust concentrations if only one or two colors will be detected simultaneously. To use only three or two dye-ddNTPs, supplement unlabeled ddNTPs for the other one or two nucleotides to reduce misinco ⁇ oration. Labeled ddNTPs may be stored in a refrigerator or freezer and should not be repeatedly frozen and thawed. We store aliquoted 100 ⁇ M stock solutions and mixed working solutions at -20 °C. Reaction Mix (final volume is 20 ⁇ L):
  • samples can be read on the AnalystTM (or other suitable light detection device). Samples may be read directly in the PCR plate or in a microplate or other sample holder following transfer.
  • the average polarization of luminophores inco ⁇ orated into extension primers should be 70 mP or larger than the average polarization of free luminophores for reliable inte ⁇ retation.
  • the standard deviation of replicate samples should be less than 10 microplate, indicating reproducibility of the procedure/technique and stability of the instrument. The most accurate measurements will be obtained following high inco ⁇ oration of the free ddNTPs; with an efficiency >50%. Therefore, it is preferable to use conditions that ensure the near depletion of free ddNTPs in the primer-extension reaction. For initial evaluation and assay optimization, it is helpful to quantify the inco ⁇ oration efficiency by running the reaction mixture on a sequencer in parallel.
  • the length of the extension primer may not contribute significantly to the magnitude of the polarization as long as the extension primer is equal to or longer than about 20 nucleotides. In particular, 20-, 22-, and 25-mers were used for primer extension without significant differences in mP changes. Instead, appropriate cycling conditions should be chosen to ensure efficient annealing of the extension primer onto the template.
  • Black and clear 96- or 384-well plates can be used without significant compromise in signal intensity. Clear plates can be stacked in the stacker and registered by the stacker's plate sensor. Black PCR plates are stackable in the magazines. However, to be detected by the plate sensor on the AnalystTM detection platform, a 1 cm x 0.5 cm opaque is required near the center of the plate's short edge facing the instrument. A suitable opaque area may be produced using paint or a barcode sticker, among others. Unfortunately, current MJTM 96-well PCR plates expand after thermocycling and may be caught in the instrument's stacker. Sample Data Using ApoE 112 Synthetic Templates
  • BDF is routinely the weakest. Using the reduced label may require background subtraction for BDF, especially if the signal-to-noise ratio will be below 5: 1. Alternatively, BDF can be mixed with half of the concentration of all other luminophores. 2. Primer Extension, or use conditions that best suit the extension primer.
  • the invention provides methods and apparatus for dichroic and multi- dichroic detection of nucleic acid polymo ⁇ hisms in luminescence-based assays.
  • Dichroic refers to an ability selectively to reflect and transmit light as a function of wavelength, generally regardless of plane of polarization.
  • Multi- dichroic refers to an ability selectively to reflect and transmit light of two or more specific wavelengths (or ranges of wavelengths).
  • selectively refers to an ability to reflect or transmit, as desired, substantially more than half of the incident light
  • multi-dichroic refers to double dichroic, triple dichroic, and so on.
  • Dichroic and multi-dichroic detection may be used to enhance assay sensitivity, while reducing assay cost by reducing reagent requirements.
  • Figure 7 shows an apparatus 1000 for performing dichroic (or multi- dichroic) genomics assays in accordance with the invention.
  • the apparatus includes a light source 1001 for producing excitation light, a detector 1002 for detecting emission light, and a dichroic (or multi-dichroic) beamsplitter 1003 for directing excitation light toward a sample 1004 and emission light toward the detector.
  • the apparatus also may include an excitation filter 1005 for filtering the excitation light and an emission filter 1006 for filtering the emission light.
  • Apparatus 1000 is used as follows. Excitation light 1011 produced by light source 1001 is selectively reflected off a surface of beamsplitter 1003 and onto sample 1004. The excitation light excites luminophores such as luminescent terminators in sample 1004, which respond by emitting longer- wavelength emission light 1012. The emission light is then selectively transmitted through the surface of beamsplitter 1003 and toward detector 1002. In other embodiments, excitation light may be transmitted through a surface of a beamsplitter and onto the sample, and emission light may be reflected off the surface of the beamsplitter and toward a detector. Excitation filter 1005 can be used to filter excitation light output by the light source, so that light having only preselected wavelengths is directed toward the sample. Emission filter 1006 can be used (together with the dichroic beamsplitter) to filter emission light emitted by the sample, so that excitation and other stray light is not directed into the detector.
  • Excitation filter 1005 can be used to filter excitation light output by the light
  • the invention may be used with various combinations of luminophores.
  • a single dichroic may be used with one suitable luminophore
  • a double dichroic may be used with two suitable luminophores
  • a triple dichroic may be used with three suitable luminophores, and so on.
  • a double dichroic also may be used with only one suitable luminophore
  • a triple dichroic also may be used with only one or two suitable luminophores, and so on.
  • a suitable luminophore is a luminophore having excitation and emission spectra that will result in one of excitation and emission being reflected off the beamsplitter, and the other of excitation and emission being transmitted through the beamsplitter.
  • a suitable pair of luminophores is a pair of luminophores having excitation and emission spectra that are distinguishable from one another, and matched to the reflection and transmission properties of the multi-dichroic as with the single suitable luminophore.
  • Preferred pairs include fluorescein and Texas Red, and fluorescein and Tamra, as well as pairs, triplets, and quartets described above.
  • Suitable multi-dichroic beamsplitters are able selectively to transmit incident light for exciting each of the chosen luminophores toward a sample, and selectively to reflect incident luminescence emission light emitted by each of the chosen luminophores toward a detector, or vice versa.
  • Preferred multi- dichroic beamsplitters block most other light.
  • Appropriate excitation filters are able selectively to transmit light for exciting one of the chosen luminophores, and appropriate emission filters are able selectively to transmit luminescence light emitted by one of the chosen luminophores.
  • Figure 8 is a schematic view of transmission profiles for a dichroic beamsplitter and complementary excitation and emission filters.
  • the beamsplitter is substantially reflective where the percent transmission is low and substantially transmissive where the percent transmission is high.
  • the excitation filter is chosen to transmit (excitation) light with wavelengths (EX) that will be reflected by the beamsplitter, and the emission filter is chosen to transmit (emission) light with wavelengths (EM) that will be transmitted by the beamsplitter.
  • Figure 9 is a graph of transmission profiles for a double-dichroic beamsplitter and complementary pairs of excitation and emission filters. These components are designed for imaging of fluorescein and Texas Red, or spectrally similar luminophores. Dichroic and multi-dichroic beamsplitters have several potential advantages over standard beamsplitters. In particular, the throughput of standard 50:50 beamsplitters is about 25%, because only about half of the excitation light incident on the beamsplitter is reflected toward the sample, and only about half of the emission light incident on the beamsplitter is transmitted toward the detector.
  • the throughput of a dichroic beamsplitter with suitable luminophores may be about 75%, and the throughput of a multi- dichroic beamsplitter may be higher than the throughput of a 50:50 beamsplitter, though lower than the throughput of a single dichroic.
  • the background rejection of a dichroic or multi-dichroic beamsplitter also may be better than that of a 50:50 beamsplitter.
  • Dichroic and multi-dichroic beamsplitters have several potential disadvantages relative to standard beamsplitters. In particular, they will provide enhanced performance relative to standard beamsplitters only with suitable luminophores, and they will provide diminished performance relative to standard beamsplitters with unsuitable luminophores.
  • the two-dye mix was diluted with unlabeled ddNTPs.
  • Rl lO-ddATP was used in combination with ROX-ddGTP to detect an A/G SNP, and equal volumes of 100 ⁇ M of Rl lO-ddATP, 100 ⁇ M ROX-ddGTP, 100 ⁇ M unlabeled ddTTP, and 100 ⁇ M unlabeled ddCTP were mixed to obtain the original stock concentration of dye.
  • 0.05 ⁇ L of this stock mix was then used in each reaction, to yield 30 mL of final volume.
  • an unlabeled ddNTP mix was prepared by mixing equal volumes of 100 ⁇ M solutions of all four ddNTPs, which was used as the dilution buffer of the dyes.
  • Reaction products were read on LJL's AnalystTM light-detection platform, with wavelength-specific double dichroics as indicated above to achieve higher sensitivity in the presence of reduced reagent cost.
  • Results Figure 10 shows results of a genotyping assay using fluorescein and
  • Texas Red luminescent labels in combination with (A) a 50:50 beamsplitter, and (B) a fluorescein / Texas Red double-dichroic beamsplitter.
  • SNP 69805 was typed with Rl lO-ddCTP and ROX-ddGTP in twenty-four individuals. 1/8 of the original label was used, and the plate was read on an Analyst platform using a 50:50 beamsplitter or a fluorescein/Texas Red double dichroic beamsplitter, as indicated.
  • Polarization values detected in R110 or ROX channels were plotted for each individual on a scatter plot, so that each genotype appears as a point on the plot.
  • Data may be reliably inte ⁇ reted if points for each individuals fall into one of the four distinct clusters on the scatter plot: (1) the lower-left corner shows PCR failures with no inco ⁇ oration (and no-DNA controls) resulting in low polarizations in both channels, (2) the upper-left corner shows homozygote GGs, (3) the lower-right corner shows homozygote CCs, and (4) the upper-right corner shows heterozygote GCs resulting in high polarizations in both channels.
  • the results with the 50:50 beamsplitter do not show distinct clusters, which are important or necessary for accurate base-calling, depending on the amount of dye used.
  • the results with the double dichroic beamsplitter show distinct clusters for the same plate, which are clearly inte ⁇ retable.
  • the increased sensitivity provided by multi-dichroics and compatible dye combinations can increase sensitivity because the increased wavelength specificity results in a better signal-to-background ratio.
  • Rl 10-ddCTP and ROX-ddGTP were used and diluted 1 :8 from the original concentration in the unlabeled ddNTP dilution buffer.
  • the S channel intensity for Rl lO-ddCTP yielded a signal-to-background ratio of 5: 1 when read with the 50:50 beamsplitter, and 24: 1 when read with the specific fluorescein/Texas Red double dichroic beamsplitter.
  • the S channel intensity for ROX-ddGTP yielded a signal-to-background ratio of 2: 1 and 19: 1 with the 50:50 beamsplitter and the double dichroic beamsplitter, respectively.
  • the fluorescein/rhodamine double dichroic improved the signal-to-background ratio for R110 and Tamra dyes from 4: 1 and 8: 1 to 13: 1 and 72: 1, respectively.
  • Such improved sensitivity permits at least an eightfold reduction in dye concentration, and likely more, resulting in a significant reduction in cost.
  • Example 4 Multiplexed SNPs Genotyping Assay Employing Multiple Primers With Multiple Tails
  • the invention provides methods and apparatus for multiplexed detection of SNPs using multiple primers with multiple tails.
  • the assay is shown schematically in Figure 11.
  • the assay may be performed using a sample nucleic acid that includes a polymo ⁇ hism.
  • Suitable sample nucleic acids include genomic DNA templates, and suitable polymo ⁇ hisms include single nucleotide polymorphisms (SNPs).
  • SNPs single nucleotide polymorphisms
  • the sample nucleic acid is subjected to two rounds of amplification, for example, using polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • the sample is mixed with a first primer for binding to one side of the template, and a set of second primers for binding to the other side of the template.
  • Each of the second primers includes a binding portion having a cognate base of one of the SNP alleles potentially present in the template, and a unique tail portion different from the template and different from the tail portion of any other primer in the set of second primers. The tail portions will not bind specifically to any components of the assay.
  • the first primer is shown on the right, and the set of second primers is shown on the left.
  • the number of second primers to be used is determined by (1) the number of alleles per SNP, and (2) the number of SNPs to be assayed in each sample. Depending on which SNP allele is present in the sample, the primer with the complementary binding portion and unique tail will bind to the sample, participate in the PCR process, and be amplified.
  • the product of the first amplification is mixed with a set of third primers for binding to the tails of the amplified set of second primers.
  • This mixing step may proceed in situ following the first amplification or after a cleanup step.
  • Each of the third primers includes a portion complementary to one of the tails of the second primers, and each is labeled with a unique spectroscopically distinguishable luminophore Li, L 2 , etc.
  • the primer that was expanded in the first amplification determines which of the set of third primers will undergo second-stage amplification, and therefore which of the luminophores Lj, L 2 , etc. will go from being attached to a small primer to being attached to a large amplification product.
  • This increase in size may be monitored using any technique suitable for monitoring such an increase.
  • a preferred detection method is fluorescence polarization, which can monitor an increase in size by a concomitant increase in polarization.
  • Luminescence is the emission of light from excited electronic states of luminescent atoms or molecules, as described above. Luminescence generally refers to all kinds of light emission, except incandescence, and may include photoluminescence, chemiluminescence, and electrochemiluminescence, among others. In photoluminescence, including fluorescence and phosphorescence, the excited electronic state is created by the abso ⁇ tion of electromagnetic radiation.
  • chemiluminescence which includes bioluminescence
  • electrochemiluminescence the excited electronic state is created by an electrochemical process.
  • photoluminescence may be used interchangeably with luminescence and fluorescence
  • luminophore may be used interchangeably with fluorophore.
  • luminescence is emitted by luminophores associated with the terminator or other base inco ⁇ orated during the assay.
  • Luminophores may have short (0.1-10 nanosecond) or long (10 nanosecond-l+ second) luminescence lifetimes and be intrinsic or extrinsic to the terminator.
  • such luminophores will be extrinsic, such as cyanine dyes, phenanthridines (such as ethidium bromide), acridines (such as acridine orange), indoles (such as DAPI), imidazoles, psoralens, and luminescent metal-ligand and lanthanide complexes and cryptates, among others. Additional luminophores are listed in Richard P.
  • Extrinsic luminophores may be associated with the polynucleotides covalently or noncovalently. Luminophores may be associated covalently using various reactive groups, especially if amines or thiols are inco ⁇ orated into the nucleotides during their synthesis. Luminophores may be associated noncovalently via specific binding pairs, such as avidin and biotin, protein A and immunoglobulins, and lectins and sugars (e.g., concanavalin A and glucose). Luminophores also may be associated noncovalently by intercalating into the polynucleotide or by binding to grooves in the polynucleotide, if they so associate only after inco ⁇ oration of the terminator.
  • Luminophores may be used in a variety of luminescence assays, including fluorescence polarization (FP), fluorescence resonance energy transfer (FRET), fluorescence lifetime (FLT), total internal reflection (TIR) fluorescence, fluorescence correlation spectroscopy (FCS), and fluorescence recovery after photobleaching (FRAP), as well as their phosphorescence and higher-transition analogs, among others.
  • FP fluorescence polarization
  • FRET fluorescence resonance energy transfer
  • FLT fluorescence lifetime
  • TIR total internal reflection
  • FCS fluorescence correlation spectroscopy
  • FRAP fluorescence recovery after photobleaching
  • A intensity assays
  • B polarization assays
  • C energy transfer assays
  • D time- resolved assays
  • Luminescence intensity assays involve monitoring the intensity (or amount) of light emitted from a composition.
  • the intensity of emitted light will depend on the extinction coefficient, quantum yield, and number of luminophores in the composition, among others. These quantities, in turn, will depend on the environment of the luminophore, including the proximity and efficacy of quenchers and energy transfer partners. Thus, luminescence intensity assays may be used to study binding reactions, among other applications.
  • Luminescence polarization assays involve monitoring the intensity of polarized light emitted from a composition. (Polarization describes the direction of light's electric field, which generally is pe ⁇ endicular to the direction of light's propagation.) Luminescence polarization assays may be homogeneous and ratiometric, making them relatively insensitive to sample-to- sample variations in concentration, volume, and meniscus shape.
  • Luminescence polarization assays typically are used to study molecular rotation.
  • Figure 12 shows how luminescence polarization is affected by molecular rotation.
  • specific molecules 65 within a composition 66 are labeled with one or more luminophores.
  • the composition then is illuminated with polarized excitation light, which preferentially excites luminophores having abso ⁇ tion dipoles aligned parallel to the polarization of the excitation light. These molecules subsequently decay by preferentially emitting light polarized parallel to their emission dipoles.
  • the extent of polarization of the total emitted light depends on the extent of molecular reorientation during the time interval between luminescence excitation and emission, which is termed the luminescence lifetime, ⁇ .
  • the extent of molecular reorientation depends on the luminescence lifetime and the size, shape, and environment of the reorienting molecule.
  • luminescence polarization assays can be used to quantify hybridization/binding reactions and enzymatic activity, among other applications.
  • molecules commonly rotate via diffusion with a rotational correlation time ⁇ that is proportional to their size.
  • relatively large molecules will not reorient significantly, so that their total luminescence will be relatively polarized.
  • relatively small molecules will reorient significantly, so that their total luminescence will be relatively unpolarized.
  • the relationship between polarization and intensity is expressed by the following equation:
  • P is the polarization
  • L is the intensity of luminescence polarized pe ⁇ endicular to the polarization of the excitation light.
  • P generally varies from zero to one-half for randomly oriented molecules (and zero to one for aligned molecules). If there is little rotation between excitation and emission, / will be relatively large, L will be relatively small, and P will be close to one-half.
  • P may be less than one-half even if there is no rotation; for example, P will be less than one-half if the abso ⁇ tion and emission dipoles are not parallel.
  • A will be comparable to A, and P will be close to zero.
  • Polarization often is reported in milli-P (mP) units (1000 ⁇ ), which for randomly oriented molecules will range between 0 and 500, because P will range between zero and one-half.
  • r is the anisotropy.
  • Polarization and anisotropy include the same information, although anisotropy may be more simply expressed for systems containing more than one luminophore.
  • these terms may be used interchangeably, and a generic reference to one should be understood to imply a generic reference to the other.
  • P 0 is the polarization in the absence of molecular motion (intrinsic polarization)
  • ⁇ is the luminescence lifetime (inverse decay rate) as described above
  • ⁇ I0t is the rotational correlation time (inverse rotational rate) as described above.
  • the Perrin equation shows that luminescence polarization assays are most sensitive when the luminescence lifetime and the rotational correlation time are similar. Rotational correlation time is proportional to molecular weight, increasing by about 1 nanosecond for each 2,400 Dalton increase in molecular weight (for a spherical molecule).
  • luminescence polarization assays are most sensitive for molecular weights less than about 40,000 Daltons.
  • luminescence polarization assays are most sensitive for molecular weights between about 70,000 Daltons and 4,000,000 Daltons.
  • Energy transfer is the transfer of luminescence energy from a donor luminophore to an acceptor without emission by the donor.
  • a donor luminophore is excited from a ground state into an excited state by abso ⁇ tion of a photon. If the donor luminophore is sufficiently close to an acceptor, excited-state energy may be transferred from the donor to the acceptor, causing donor luminescence to decrease and acceptor luminescence to increase (if the acceptor is luminescent). The efficiency of this transfer is very sensitive to the separation R between donor and acceptor, decaying as 1/R " 6 .
  • Energy transfer assays use energy transfer to monitor the proximity of donor and acceptor, which in turn may be used to monitor the presence or activity of an analyte, among others.
  • Energy transfer assays may focus on an increase in energy transfer as donor and acceptor are brought into proximity. These assays may be used to monitor binding, as between two molecules X and Y to form a complex X : Y.
  • colon (:) represents a noncovalent interaction.
  • one molecule is labeled with a donor D, and the other molecule is labeled with an acceptor A, such that the interaction between X and Y is not altered appreciably.
  • D and A may be covalently attached to X and Y, or covalently attached to binding partners of X and Y.
  • Energy transfer assays also may focus on a decrease in energy transfer as donor and acceptor are separated. These assays may be used to monitor cleavage, as by hydrolytic digestion of doubly labeled substrates (peptides, nucleic acids).
  • doubly labeled substrates peptides, nucleic acids.
  • two portions of a polypeptide are labeled with D and A, so that cleavage of the polypeptide by a protease such as an endopeptidase will separate D and A and thereby reduce energy transfer.
  • two portions of a nucleic acid are labeled with D and A, so that cleave by a nuclease such as a restriction enzyme will separate D and A and thereby reduce energy transfer.
  • Energy transfer between D and A may be monitored in various ways. For example, energy transfer may be monitored by observing an energy- transfer induced decrease in the emission intensity of D and increase in the emission intensity of A (if A is a luminophore). Energy transfer also may be monitored by observing an energy-transfer induced decrease in the lifetime of D and increase in the apparent lifetime of A.
  • a long-lifetime luminophore is used as a donor, and a short-lifetime luminophore is used as an acceptor.
  • Suitable long-lifetime luminophores include metal-ligand complexes containing ruthenium, osmium, etc., and lanthanide chelates containing europium, terbium, etc.
  • the donor is excited using a flash of light having a wavelength near the excitation maximum of D. Next, there is a brief wait, so that electronic transients and/or short-lifetime background luminescence can decay. Finally, donor and/or acceptor luminescence intensity is detected and integrated.
  • the donor is excited using time-modulated light, and the phase and/or modulation of the donor and/or acceptor emission is monitored relative to the phase and/or modulation of the excitation light. In both assays, donor luminescence is reduced if there is energy transfer, and acceptor luminescence is observed only if there is energy transfer. D.
  • Steady-State Versus Time-Resolved Assays Apparatus 70, 90, and 160 may be used to conduct a variety of steady- state and time-resolved luminescence assays.
  • Steady-state assays measure luminescence under constant illumination, using the continuous light source.
  • Time-resolved assays measure luminescence as a function of time, using either the continuous light source, with its intensity appropriately modulated, or the time-varying light source. Time-resolved assays may be conducted in the time domain or in the frequency domain, both of which are functionally equivalent.
  • the time course of luminescence is monitored directly.
  • a composition containing a luminescent analyte is illuminated using a narrow pulse of light, and the time dependence of the intensity of the resulting luminescence emission is observed, although other protocols also may be used.
  • the luminescence commonly follows a single-exponential decay.
  • the time course of luminescence is monitored indirectly, in frequency space.
  • the composition is illuminated using light whose intensity is modulated sinusoidally at a single modulation frequency f although other protocols (such as transforming time- domain data into the frequency domain) also may be used.
  • the intensity of the resulting luminescence emission is modulated at the same frequency as the excitation light. However, the emission will lag the excitation by a phase angle (phase) ⁇ , and the intensity of the emission will be demodulated relative to the intensity of the excitation by a demodulation factor (modulation) M.
  • Figure 13 shows the relationship between emission and excitation in a single-frequency frequency-domain experiment.
  • the phase ⁇ is the phase difference between the excitation and emission.
  • the modulation M is the ratio of the AC amplitude to the DC offset for the emission, relative to the ratio of the AC amplitude to the DC offset for the excitation.
  • ⁇ is the angular modulation frequency, which equals 2 ⁇ times the modulation frequency.
  • the angular modulation frequency should be roughly the inverse of the luminescence lifetime. Lifetimes of interest in high-throughput screening vary from less than 1 nanosecond to greater than 1 millisecond. Therefore, instruments for high- throughput screening should be able to cover modulation frequencies from less than about 200 Hz to greater than about 200 MHz.
  • Luminescence Apparatus Figures 14-20 show apparatus 70, 90, 260 for detecting light transmitted from a composition. These apparatus may include a variety of components, some or all of which may be used in any given assay. These components include (1) a stage for supporting the composition, (2) one or more light sources for delivering light to a composition, (3) one or more detectors for receiving light transmitted from the composition and converting it to a signal, (4) first and second optical relay structures for relaying light between the light source, composition, and detector, and (5) a processor for analyzing the signal from the detector. These apparatus can be used for a variety of assays, including but not limited to the assays described above.
  • Components of the optical system can be chosen to optimize sensitivity and dynamic range for each assay supported by the apparatus. Toward this end, optical components with low intrinsic luminescence are preferred. In addition, some components may be shared by different modes, whereas other components may be unique to a particular mode. For example, in apparatus 90 and 260, absorbance, scattering, photoluminescence intensity and steady-state photoluminescence polarization modes share a light source; time-resolved absorbance and luminescence modes use their own light source; and chemiluminescence modes do not use a light source. Similarly, photoluminescence and chemiluminescence modes use different detectors. A. Apparatus 70
  • Figure 14 shows an apparatus 70 for detecting light (especially polarized light) transmitted from a composition.
  • Apparatus 70 includes a light source 72, an excitation polarizer 74, an emission polarizer 76, and a detector 78.
  • Light 80 produced by light source 72 is directed through excitation polarizer 74, which passes polarized excitation light (indicated by vertical arrow).
  • Polarized excitation light is directed onto a sample 82, which emits light 84 in response.
  • the emitted light may be either some fraction of the incident light or luminescence.
  • Emitted light 84 is directed through emission polarizer 76, which may have components oriented parallel (
  • emission polarizer 76 may have components oriented parallel (
  • Figures 15-19 show an alternative apparatus 90 for detecting light transmitted from a composition.
  • This apparatus includes (i) a photoluminescence optical system, (ii) a chemiluminescence optical system, and (iii) a housing.
  • FIGS 15-17 show the photoluminescence (or incident light-based) optical system of apparatus 90.
  • apparatus 90 includes a continuous light source 100 and a time-modulated light source 102.
  • Apparatus 90 includes light source slots 103a-d for four light sources, although other numbers of light source slots and light sources also could be provided.
  • Light source slots 103a-d function as housings that may surround at least a portion of each light source, providing some protection from radiation and explosion.
  • the direction of light transmission through the incident light-based optical system is indicated by arrows.
  • Continuous source 100 provides light for absorbance, scattering, photoluminescence intensity, and steady-state photoluminescence polarization assays.
  • Continuous light source 100 may include arc lamps, incandescent lamps, fluorescent lamps, electroluminescent devices, lasers, laser diodes, and light-emitting diodes (LEDs), among others.
  • a preferred continuous source is a high-intensity, high color temperature xenon arc lamp, such as a Model LX175F CERMAX xenon lamp from ILC Technology, Inc. Color temperature is the absolute temperature in Kelvin at which a blackbody radiator must be operated to have a chromaticity equal to that of the light source.
  • a high color temperature lamp produces more light than a low color temperature lamp, and it may have a maximum output shifted toward or into visible wavelengths and ultraviolet wavelengths where many luminophores absorb.
  • the preferred continuous source has a color temperature of 5600 Kelvin, greatly exceeding the color temperature of about 3000 Kelvin for a tungsten filament source.
  • the preferred source provides more light per unit time than flash sources, averaged over the flash source duty cycle, increasing sensitivity and reducing read times.
  • Apparatus 90 may include a modulator mechanism configured to vary the intensity of light incident on the composition without varying the intensity of light produced by the light source.
  • Time-modulated source 102 provides light for time-resolved absorbance and/or photoluminescence assays, such as photoluminescence lifetime and time-resolved photoluminescence polarization assays.
  • a preferred time- modulated source is a xenon flash lamp, such as a Model FX-1160 xenon flash lamp from EG&G Electro-Optics. The preferred source produces a "flash" of light for a brief interval before signal detection and is especially well suited for time-domain measurements.
  • Other time-modulated sources include pulsed lasers, electronically modulated lasers and LEDs, and continuous lamps and other sources whose intensity can be modulated extrinsically using a Pockels cell, Kerr cell, or other mechanism.
  • Such other mechanisms may include an amplitude modulator such as a chopper as described in U.S. Provisional Patent Application No. 60/094,276, which is inco ⁇ orated herein by reference.
  • Extrinsically modulated continuous light sources are especially well suited for frequency-domain measurements.
  • continuous source 100 and time-modulated source 102 produce multichromatic, unpolarized, and incoherent light.
  • Continuous source 100 produces substantially continuous illumination
  • time-modulated source 102 produces time-modulated illumination.
  • Light from these light sources may be delivered to the sample without modification, or it may be filtered to alter its intensity, spectrum, polarization, or other properties.
  • Light produced by the light sources follows an excitation optical path to an examination site or measurement region. Such light may pass through one or more "spectral filters,” which generally comprise any mechanism for altering the spectrum of light that is delivered to the sample. Spectrum refers to the wavelength composition of light.
  • a spectral filter may be used to convert white or multichromatic light, which includes light of many colors, into red, blue, green, or other substantially monochromatic light, which includes light of one or only a few colors.
  • spectrum is altered by an excitation interference filter 104, which preferentially transmits light of preselected wavelengths and preferentially absorbs light of other wavelengths.
  • excitation interference filters 104 may be housed in an excitation filter wheel 106, which allows the spectrum of excitation light to be changed by rotating a preselected filter into the optical path.
  • Spectral filters also may separate light spatially by wavelength. Examples include gratings, monochromators, and prisms.
  • excitation filter wheel 106 may be mounted in the optical path of some light source slots 103a,b, but not other light source slots 103c,d.
  • the filter wheel may include a blank station that does not affect light passage.
  • Light is transmitted through a fiber optic cable much like water is transmitted through a garden hose.
  • Fiber optic cables can be used easily to turn light around corners and to route light around opaque components of the apparatus. Moreover, fiber optic cables give the light a more uniform intensity profile.
  • a preferred fiber optic cable is a fused silicon bundle, which has low auto luminescence. Despite these advantages, light also can be delivered to the optics heads using other mechanisms, such as mirrors.
  • Excitation polarization filters may be included with the top and/or bottom optics head.
  • polarization is altered by excitation polarizers 114, which are included only with top optics head 112a for top reading; however, such polarizers also can be included with bottom optics head 112b for bottom reading.
  • Excitation polarization filters 114 may include an s-polarizer S that passes only s-polarized light, a p-polarizer P that passes only p-polarized light, and a blank O that passes substantially all light, where polarizations are measured relative to the beamsplitter.
  • Excitation polarizers 114 also may include a standard or ferro-electric liquid crystal display (LCD) polarization switching system. Such a system may be faster than a mechanical switcher. Excitation polarizers 114 also may include a continuous mode LCD polarization rotator with synchronous detection to increase the signal-to-noise ratio in polarization assays. Excitation polarizers 114 may be inco ⁇ orated as an inherent component in some light sources, such as certain lasers, that intrinsically produce polarized light.
  • LCD liquid crystal display
  • the confocal optics element includes a set of lenses 117a-c and an excitation aperture 116 placed in an image plane conjugate to the sensed volume, as shown in Figure 17.
  • Aperture 116 may be implemented directly, as an aperture, or indirectly, as the end of a fiber optic cable. Preferred apertures have diameters of 1 mm and 1.5 mm.
  • Lenses 117a,b project an image of aperture 116 onto the sample, so that only a preselected or sensed volume of the sample is illuminated. The area of illumination will have a diameter corresponding to the diameter of the excitation aperture.
  • Light traveling through the optics head is directed onto a beamsplitter 118, which reflects light toward a composition 120 and transmits light toward a light monitor 122.
  • the reflected light passes through lens 117b, which is operatively positioned between beamsplitter 118 and composition 120.
  • Beamsplitter 118 is used to direct excitation or incident light toward the sample and light monitor, and to direct light leaving the sample toward the detector.
  • the beamsplitter is changeable, so that it may be optimized for different assay modes or compositions. In some embodiments, switching between beamsplitters may be performed manually, whereas in other embodiments, such switching may be performed automatically. Automatic switching may be performed based on direct operator command, or based on an analysis of the sample by the instrument. If a large number or variety of photoactive molecules are to be studied, the beamsplitter must be able to accommodate light of many wavelengths; in this case, a "50:50" beamsplitter that reflects half and transmits half of the incident light independent of wavelength is optimal.
  • Such a beamsplitter can be used with many types of molecules, while still delivering considerable excitation light onto the composition, and while still transmitting considerable light leaving the sample to the detector. If one or a few related photoactive molecules are to be studied, the beamsplitter needs only to be able to accommodate light at a limited number of wavelengths; in this case, a "dichroic" or “multichroic” beamsplitter is optimal.
  • a beamsplitter can be designed with cutoff wavelengths for the appropriate sets of molecules and will reflect most or substantially all of the excitation and background light, while transmitting most or substantially all of the emission light in the case of luminescence. This is possible because the beamsplitter may have a reflectivity and transmissivity that varies with wavelength.
  • the beamsplitter more generally comprises any optical device for dividing a beam of light into two or more separate beams.
  • a simple beamsplitter (such as a 50:50 beamsplitter) may include a very thin sheet of glass inserted in the beam at an angle, so that a portion of the beam is transmitted in a first direction and a portion of the beam is reflected in a different second direction.
  • a more sophisticated beamsplitter (such as a dichroic or multi-dichroic beamsplitter) may include other prismatic materials, such as fused silica or quartz, and may be coated with a metallic or dielectric layer having the desired transmission and reflection properties, including dichroic and multi-dichroic transmission and reflection properties.
  • two right-angle prisms are cemented together at their hypotenuse faces, and a suitable coating is included on one of the cemented faces.
  • Light monitor 122 is used to correct for fluctuations in the intensity of light provided by the light sources. Such corrections may be performed by reporting detected intensities as a ratio over corresponding times of the luminescence intensity measured by the detector to the excitation light intensity measured by the light monitor.
  • the light monitor also can be programmed to alert the user if the light source fails.
  • a preferred light monitor is a silicon photodiode with a quartz window for low autoluminescence.
  • the composition may be held in a sample holder supported by a stage 123.
  • the composition can include compounds, mixtures, surfaces, solutions, emulsions, suspensions, cell cultures, fermentation cultures, cells, tissues, secretions, and/or derivatives and/or extracts thereof. Analysis of the composition may involve measuring the presence, concentration, or physical properties (including interactions) of a photoactive analyte in such a composition.
  • Composition may refer to the contents of a single microplate well, or several microplate wells, depending on the assay.
  • the stage may be intrinsic to the instrument.
  • the sample holder can include microplates, biochips, or any array of samples in a known format.
  • the preferred sample holder is a microplate 124, which includes a plurality of microplate wells 126 for holding compositions.
  • Microplates are typically substantially rectangular holders that include a plurality of sample wells for holding a corresponding plurality of samples. These sample wells are normally cylindrical in shape although rectangular or other shaped wells are sometimes used. The sample wells are typically disposed in regular arrays.
  • the "standard" microplate includes 96 cylindrical sample wells disposed in a 8x12 rectangular array on 9 millimeter centers.
  • the sensed volume typically has an hourglass shape, with a cone angle of about 25° and a minimum diameter ranging between 0.1 mm and 2.0 mm. For 96-well and 384-well microplates, a preferred minimum diameter is about 1.5 mm. For 1536-well microplates, a preferred minimum diameter is about 1.0 mm.
  • the size and shape of the sample holder may be matched to the size and shape of the sensed volume, as described in PCT Patent Application Serial No. PCT/US99/08410, which is inco ⁇ orated herein by reference.
  • the position of the sensed volume can be moved precisely within the composition to optimize the signal-to-noise and signal-to-background ratios.
  • the sensed volume may be moved away from walls in the sample holder to optimize signal-to-noise and signal-to-background ratios, reducing spurious signals that might arise from luminophores bound to the walls and thereby immobilized.
  • position in the X,Y-plane pe ⁇ endicular to the optical path is controlled by moving the stage supporting the composition, whereas position along the Z-axis parallel to the optical path is controlled by moving the optics heads using a Z-axis adjustment mechanism 130, as shown in Figures 15 and 16.
  • any mechanism for bringing the sensed volume into register or alignment with the appropriate portion of the composition also may be employed.
  • top and bottom optics permits assays to combine: (l) top illumination and top detection, or (2) top illumination and bottom detection, or (3) bottom illumination and top detection, or (4) bottom illumination and bottom detection.
  • Same-side illumination and detection, (1) and (4) is referred to as "epi” and is preferred for photoluminescence and scattering assays.
  • Opposite-side illumination and detection, (2) and (3) is referred to as "trans” and has been used in the past for absorbance assays.
  • epi modes are supported, so the excitation and emission light travel the same path in the optics head, albeit in opposite or anti-parallel directions. However, trans modes also can be used with additional sensors, as described below.
  • top and bottom optics heads move together and share a common focal plane. However, in other embodiments, top and bottom optics heads may move independently, so that each can focus independently on the same or different sample planes.
  • top optics can be used with any sample holder having an open top
  • bottom optics can be used only with sample holders having optically transparent bottoms, such as glass or thin plastic bottoms. Clear bottom sample holders are particularly suited for measurements involving analytes that accumulate on the bottom of the holder.
  • Light is transmitted by the composition in multiple directions. A portion of the transmitted light will follow an emission pathway to a detector. Transmitted light passes through lens 117c and may pass through an emission aperture 131 and/or an emission polarizer 132.
  • the emission aperture is placed in an image plane conjugate to the sensed volume and transmits light substantially exclusively from this sensed volume.
  • the emission apertures in the top and bottom optical systems are the same size as the associated excitation apertures, although other sizes also may be used.
  • the emission polarizers are included only with top optics head 112a. The emission aperture and emission polarizer are substantially similar to their excitation counte ⁇ arts. Emission polarizer 132 may be included in detectors that intrinsically detect the polarization of light.
  • Excitation polarizers 1 14 and emission polarizers 132 may be used together in nonpolarization assays to reject certain background signals.
  • Luminescence from the sample holder and from luminescent molecules adhered to the sample holder is expected to be polarized, because the rotational mobility of these molecules should be hindered.
  • Such polarized background signals can be eliminated by "crossing" the excitation and emission polarizers, that is, setting the angle between their transmission axes at 90°. As described above, such polarized background signals also can be reduced by moving the sensed volume away from walls of the sample holder.
  • beamsplitter 118 should be optimized for reflection of one polarization and transmission of the other polarization. This method will work best where the luminescent molecules of interest emit relatively unpolarized light, as will be true for small luminescent molecules in solution.
  • Transmitted light next passes through an emission fiber optic cable 134a,b to an emission optical shuttle (or switch) 136.
  • This shuttle positions the appropriate emission fiber optic cable in front of the appropriate detector.
  • these components are substantially similar to their excitation counte ⁇ arts, although other mechanisms also could be employed.
  • Emission neutral density filters 138 may include a high-density filter H that absorbs most incident light, a medium-density filter M that absorbs somewhat less incident light, and a blank O that absorbs substantially no incident light. These filters may be changed manually, or they may be changed automatically, for example, by using a filter wheel.
  • Intensity filters also may divert a portion of the light away from the sample without abso ⁇ tion.
  • Examples include beam splitters, which transmit some light along one path and reflect other light along another path, and diffractive beam splitters (e.g., acousto-optic modulators), which deflect light along different paths through diffraction. Examples also include hot mirrors or windows that transmit light of some wavelengths and absorb light of other wavelengths.
  • Light next may pass through an emission interference filter 140, which may be housed in an emission filter wheel 142. In apparatus 90, these components are substantially similar to their excitation counte ⁇ arts, although other mechanisms also could be employed.
  • Emission interference filters block stray excitation light, which may enter the emission path through various mechanisms, including reflection and scattering.
  • Emission interference filters can separate photoluminescence from excitation light because photoluminescence has longer wavelengths than the associated excitation light. Luminescence typically has wavelengths between 200 and 2000 nanometers.
  • filters used here in only one optical path such as intensity filters
  • filters used here in only top or bottom optics such as polarization filters
  • filters used here in only top or bottom optics such as polarization filters
  • the optimal positions and combinations of filters for a particular experiment will depend on the assay mode and the composition, among other factors.
  • Light last passes to a detector, which is used in absorbance, scattering and photoluminescence assays.
  • a detector which is used in absorbance, scattering and photoluminescence assays.
  • a preferred detector is a photomultiplier tube (PMT).
  • Apparatus 90 includes detector slots 145a-d for four detectors, although other numbers of detector slots and detectors also could be provided. More generally, detectors comprise any mechanism capable of converting energy from detected light into signals that may be processed by the apparatus, and by the processor in particular. Suitable detectors include photomultiplier tubes, photodiodes, avalanche photodiodes, charge-coupled devices (CCDs), and intensified CCDs, among others. Depending on the detector, light source, and assay mode, such detectors may be used in a variety of detection modes.
  • These detection modes include (1) discrete (e.g., photon- counting) modes, (2) analog (e.g., current-integration) modes, and/or (3) imaging modes, among others, as described in PCT Patent Application Serial No. PCT/US99/03678.
  • Chemiluminescence optical system Figures 15, 16, and 18 show the chemiluminescence optical system of apparatus 90. Because chemiluminescence follows a chemical event rather than the abso ⁇ tion of light, the chemiluminescence optical system does not require a light source or other excitation optical components. Instead, the chemiluminescence optical system requires only selected emission optical components. In apparatus 90, a separate lensless chemiluminescence optical system is employed, which is optimized for maximum sensitivity in the detection of chemiluminescence.
  • chemiluminescence optical system performs the same functions and are subject to the same caveats and alternatives as their counte ⁇ arts in the incident light-based optical system.
  • the chemiluminescence optical system also can be used for other assay modes that do not require illumination, such as electrochemiluminescence.
  • the chemiluminescence optical path begins with a chemiluminescent composition 120 held in a sample holder 126.
  • the composition and sample holder are analogous to those used in photoluminescence assays; however, analysis of the composition involves measuring the intensity of light generated by a chemiluminescence reaction within the composition rather than by light- induced photoluminescence.
  • a familiar example of chemiluminescence is the glow of the firefly.
  • Chemiluminescence light typically is transmitted from the composition in all directions, although most will be absorbed or reflected by the walls of the sample holder. A portion of the light transmitted through the top of the well is collected using a chemiluminescence head 150, as shown in Figure 15, and will follow a chemiluminescence optical pathway to a detector. The direction of light transmission through the chemiluminescence optical system is indicated by arrows.
  • the chemiluminescence head includes a nonconfocal mechanism for transmitting light from a sensed volume within the composition. Detecting from a sensed volume reduces contributions to the chemiluminescence signal resulting from "cross talk," which is pickup from neighboring wells.
  • the nonconfocal mechanism includes a chemiluminescence baffle 152, which includes rugosities 153 that absorb or reflect light from other wells.
  • the nonconfocal mechanism also includes a chemiluminescence aperture 154 that further confines detection to a sensed volume.
  • Fiber optic cable 156 is analogous to excitation and emission fiber optic cables 110a,b and 134a,b in the photoluminescence optical system.
  • Fiber optic cable 156 may include a transparent, open-ended lumen that may be filled with fluid. This lumen would allow the fiber optic to be used both to transmit luminescence from a microplate well and to dispense fluids into the microplate well. The effect of such a lumen on the optical properties of the fiber optic could be minimized by employing transparent fluids having optical indices matched to the optical index of the fiber optic.
  • chemiluminescence intensity filters which generally comprise any mechanism for reducing the intensity of light.
  • intensity is altered by chemiluminescence neutral density filters 158.
  • Light also may pass through other filters, if desired.
  • Light last passes to a detector, which converts light into signals that may be processed by the apparatus.
  • chemiluminescence detector 160 there is one chemiluminescence detector 160. This detector may be selected to optimize detection of blue/green light, which is the type most often produced in chemiluminescence.
  • a preferred detection is a photomultiplier tube, selected for high quantum efficiency and low dark count at chemiluminescence wavelengths (400-500 nanometers).
  • FIG. 19 shows a housing 200 and other accessories for the apparatus of Figures 15-18.
  • Housing 200 substantially encloses the apparatus, forming (together with light source slots 103a-d) two protective layers around the continuous high color temperature xenon arc lamp.
  • Housing 200 permits automated sample loading and switching among light sources and detectors, further protecting the operator from the xenon arc lamp and other components of the system.
  • Figure 20 shows another alternative apparatus 260 for detecting light transmitted from a composition 262, where the detection and/or processing may be performed in the frequency-domain.
  • Apparatus 260 includes substantial portions of apparatus 90, including its fiber-optic-coupled optics head 264, excitation 266 and emission 268 filters, dichroic beam splitter 270, and mechanisms for sample positioning and focus control.
  • apparatus 260 also may include alternative light sources 272, sample ('S') detectors 274, reference ('R') detectors 276, and detection electronics 278.
  • alternative components 272-278 are shown outside apparatus 90, but they readily may be included inside housing 250 of apparatus 90, if desired.
  • Apparatus 260 may provide incident light in various ways, as described above. For example, analytes absorbing blue light may be excited using a NICHIA-brand bright-blue LED (Model Number NSPB500; Mountville, PA). This LED produces broad-spectrum excitation light, so excitation filter 266 may be selected to block the red edge of the spectrum. If analytes are excited using a laser diode, an excitation filter is not necessary.
  • NICHIA-brand bright-blue LED Model Number NSPB500; Mountville, PA. This LED produces broad-spectrum excitation light, so excitation filter 266 may be selected to block the red edge of the spectrum. If analytes are excited using a laser diode, an excitation filter is not necessary.
  • Apparatus 260 may detect emitted light and convert it to a signal in various ways. This demodulation/deconvolution may be internal to the photodetector, or it may be performed with external electronics or software.
  • emitted light can be detected using sample detector 274, which may be an ISS-brand gain-modulated PMT (Champaign, IL).
  • High-frequency emitted light can be frequency down-converted to a low-frequency signal using a technique called heterodyning.
  • the phase and modulation of the low- frequency signal can be determined using a lock-in amplifier 280, such as a STANFORD RESEARCH SYSTEMS brand lock-in amplifier (Model Number SR830; Sunnyvale, CA).
  • Lock-in amplifier 280 is phase locked using a phase- locked loop 282 to the modulation frequency of light source 272.
  • the output of light source 272 may be monitored using reference detector 276, which may be a HAMAMATSU-brand PMT (Model Number H6780; Bridgewater, NJ). If reference detector 276 can respond to high-frequency signals, the heterodyning step can be performed using an external mixer 284.
  • the phase and modulation of reference detector 276 also may be captured by lock-in amplifier 280 and used to normalize the signal from sample detector 274.
  • Apparatus 260 may be controlled by a computer or processor.
  • the computer may direct sample handling and data collection.
  • phase and modulation data will be collected at one or more frequencies appropriate for the lifetime of the analyte.
  • phase and modulation may be measured at one or a few frequencies and processed by the computer or processor to help reduce detected background.
  • photoluminescence assays include illuminating a sample with light from a light source, and detecting light emitted from the sample.
  • Photoluminescence detection devices typically employ one of various light sources for illuminating the sample.
  • light sources for luminescence polarization assays have included lasers and arc lamps (e.g., xenon arc lamps).
  • arc lamps e.g., xenon arc lamps.
  • the power supplies for lasers and xenon arc lamps operate at very high currents (about 25 amps) and voltages (about 20,000 to 40,000 volts), so that electrocution and other health hazards are always a danger.
  • the power supplies for arc lamps can deliver a lethal shock when the lamps are started.
  • the power supplies also may produce transients that can damage other electronic components of the system.
  • the light emitted by lasers and xenon arc lamps is very intense, so that eye damage is always a danger. In particular, the extreme brightness may damage the retina, and ultraviolet light emitted by xenon arc lamps and some lasers may damage the cornea.
  • the spectral output of lasers and some (e.g., mercury) arc lamps is very limited, so that desired excitation wavelengths may not be available.
  • the lifetime of arc lamps may be very short, typically around 300 hours, so that the lamp must be changed frequently, further exposing the operator to dangers posed by the lamp and power supply.
  • the short-wavelength light produced by some (e.g., xenon) arc lamps may produce ozone.
  • the light source may be used nearly continuously, so that the dangers posed by lasers and arc lamps are ever present.
  • the light source also may be used by relatively unskilled operators, who may be unfamiliar with or unreceptive to safety issues.
  • incandescent lamps are relatively common and inexpensive, and include lamps from overhead projectors. Incandescent lamps put out broad- spectrum light, so that they may be used with a variety of luminescent compounds. Flash lamps are more exotic, but provide some advantages over incandescent lamps. In particular, flash lamps may be used for both time-resolved and steady-state measurements. This flexibility allows the same light source to be used in instruments that perform multiple assays, such as steady-state and time-resolved luminescence polarization assays. Moreover, flash lamps may have long lifetimes, as long as 10,000 hours. Aspects of the invention may address some or all of these shortcomings by using a high color temperature light source.
  • incandescent lamps e.g., tungsten lamps
  • flash lamps are relatively common and inexpensive, and include lamps from overhead projectors. Incandescent lamps put out broad- spectrum light, so that they may be used with a variety of luminescent compounds. Flash lamps are more exotic, but provide some advantages over incandescent lamps. In particular, flash lamps may
  • the above-disclosed apparatus can be used to conduct a variety of steady-state and time-resolved luminescence assays, including polarization assays.
  • Steady-state assays measure luminescence under constant illumination, using the continuous light source.
  • Time-resolved polarization assays measure luminescence as a function of time under time-varying illumination, using either the continuous light source, with its intensity appropriately modulated, or the time-varying light source.
  • Intensity assays can be conducted by monitoring the intensity of the luminescence emitted by the composition.
  • Polarization assays can be conducted as follows. Excitation light from the continuous light source is directed through an excitation filter, low- luminescence fiber optic cable, and excitation polarization filter. Excitation light then is directed to a beamsplitter, which reflects most of the light onto a composition and transmits a little of the light into a light monitor. Emitted light from the composition is directed back through the beamsplitter and then is directed through another low-luminescence fiber optic cable, an emission filter, and a polarization filter (in either the S or P orientation) before detection by a photomultiplier tube or other detector. Two measurements are performed for each composition, one with excitation and emission polarizers aligned and one with excitation and emission polarizers crossed.
  • Either polarizer may be static or dynamic, and either polarizer may be set in the S or P orientation, although typically the excitation polarizer is set in the S orientation.
  • polarized light may be transmitted to and detected from a fixed assay or examination site as successive samples are automatically, serially aligned in an optical path intersecting the examination site.
  • Additional luminescence assays can be conducted using procedures outlined in various patent applications cross-referenced above, Joseph R. Lakowicz, Principles of Fluorescence Spectroscopy (2 nd Ed. 1999) and/or generally known to persons of ordinary skill in the art.
  • additional assays include fluorescence resonance energy transfer (FRET), fluorescence lifetime (FLT), total internal reflection fluorescence (TIR), fluorescence correlation spectroscopy (FCS), and fluorescence recovery after photobleaching (FRAP), as well as their analogs based on phosphorescence and higher-order electronic transitions. 5.
  • FRET fluorescence resonance energy transfer
  • FLT fluorescence lifetime
  • TIR total internal reflection fluorescence
  • FCS fluorescence correlation spectroscopy
  • FRAP fluorescence recovery after photobleaching
  • Enhancements of signal-to-noise and signal-to-background ratios may be important in polarization and other luminescence assays, especially those involving dilute samples.
  • binding assays can be used to probe binding between molecules having subnanomolar dissociation coefficients, if acceptable signal-to-noise and signal-to-background ratios can be obtained from compositions having subnanomolar luminophore concentrations.
  • the methods for enhancing signal-to-noise and signal-to-background ratios described below are especially useful with such dilute samples, thereby minimizing reagent cost that otherwise can be considerable.
  • Sensitivity and dynamic range can be enhanced by selecting optical components having low intrinsic luminescence and high intrinsic throughput; such as the fiber optic cables and beamsplitters described above.
  • some components may be shared by different modes, whereas other components may be unique to a particular mode.
  • photoluminescence intensity and steady-state photoluminescence polarization modes may share a continuous light source; time-resolved luminescence modes may share a time-varying light source, and chemiluminescence modes may not use a light source.
  • photoluminescence and chemiluminescence modes may use different detectors, each selected for the application.
  • Sensitivity also can be enhanced by reducing the contribution of noise to the measurements.
  • various factors contribute to noise, such as (1) background noise and (2) intensity noise.
  • Background noise refers to contributions to the signal from luminescent species other than the luminescent species of interest, including luminescent species in the apparatus and sample holder.
  • Intensity noise refers to fluctuations in light intensity, including those arising from photon noise.
  • the apparatus may use low luminescence components, such as fused silica fiber optic cables.
  • the sample holder or substrate may be constructed of low luminescence materials, such as black polystyrene.
  • Background noise also can be reduced by reducing detection of luminescence from components of the sample that are bound to the sample holder and immobilized, spuriously increasing polarization.
  • the walls of the sample holder may be constructed or treated to reduce binding.
  • the sensed volume may be positioned near the center of the composition, away from the walls of the sample holder.
  • Intensity noise can be reduced by correcting for fluctuations in light source intensity, among others.
  • Light source fluctuations arise due to fluctuations in power from the power supply and drift in the position of the arc in arc lamps, among others.
  • Light source fluctuations can lead to luminescence fluctuations, because the amount of luminescence is proportional to the amount of excitation light.
  • Luminescence fluctuations are especially problematic in luminescence polarization assays, because such assays involve comparing the magnitude of successively measured luminescence signals.
  • Light source fluctuations can be reduced by choosing a stable light source and by rescaling the luminescence signal using information obtained from a light source monitor, as described above.
  • Intensity noise also can be reduced by increasing the number of photons (i.e., the amount of light) detected, which reduces photon noise.
  • Photon (or shot) noise arises due to the statistical nature of light and can be described by the same statistical law used to describe radiation decay. In particular, if an average of N photons are detected during a given time interval, the standard deviation in that number due to photon noise will be VN .
  • the limit set by photon noise can never be overcome; however, the significance of photon noise can be reduced by increasing the number of photons collected by the detector.
  • the number of photons collected can be increased by increasing the intensity of the light source, the efficiency of the detector, and/or the throughput of components of the optical relay structure, such as the beamsplitter, among others.
  • Photon noise creates noise in luminescence polarization assays.
  • the noise in the polarization is proportional to the noise in the luminescence intensities from which the polarization is calculated and corresponds to seven mP standard deviation in polarization for every one percent standard deviation in intensity. This relationship essentially is independent of the degree of polarization.
  • Photon noise puts a premium on simply collecting enough light, especially in rapid high-throughput screening measurements using the optically restrictive microplate format. For additional information, see the calculation in U.S. Provisional Patent Application Serial No. 60/063,811, which is inco ⁇ orated herein by reference.
  • Figure 21 is a graph showing polarization in a serial dilution of fluorescein in 96- and 384-well microplates. The graph demonstrates that the polarization of fluorescein can be measured with adequate accuracy and precision down to, or below, 100 pM, because the measured value is substantially independent of concentration down to, or below, this concentration.
  • Figure 22 is a graph showing the noise (or standard deviation) in polarization in a serial dilution of fluorescein in 384-well microplates. As described above, noise below 5-10 mP is sufficiently small for most practical polarization assays.
  • Photon noise can be reduced by using a sufficiently high-intensity light source, such as a continuous high color temperature xenon arc lamp or a laser, among others, as described above.
  • a sufficiently high-intensity light source such as a continuous high color temperature xenon arc lamp or a laser, among others, as described above.
  • the following table compares the preferred continuous and time-varying light sources used in apparatus 90 and 260.
  • the lifetime of the continuous lamp is only 1/33 the lifetime of the flash lamp.
  • the lifetime of the continuous lamp was taken directly from the manufacturer's specifications.
  • the lifetime of the flash lamp was computed using the manufacturer's specification. Specifically, the flash lamp is run at 100 flashes per second, using 250 mJ of electrical power per flash; at this power level, the lifetime of the flash lamp is rated at l xlO 9 - l x lO 10 flashes, corresponding to a lifetime of about 10,000 hours (5xl0 9 flashes / [100 flashes/sec x 3600 sec/hour]).
  • the continuous lamp provides about 20 times more light than the flash lamp.
  • the total optical power of the continuous lamp (collected by a F/1.0 optical system) is 13 W over the wavelength range 300-4000 nm.
  • the total optical power of the flash lamp (collected by a F/1.0 optical system) is 830 mW over the wavelength range 100-4000 nm.
  • the total optical power of the flash lamp was derived from the electrical energy, the electrical-to-optical conversion efficiency, the optical collection efficiency, and the repetition rate (250 mJ x 50%) x 6.6% x 100 Hz).
  • the optical powers of the different spectra of the flash lamp were derived by multiplying the total optical power of the flash lamp by the fraction of the power in each wavelength range, i.e., ultraviolet (300-390 nm) 8.3%, visible (390-770 nm) 28%, and infrared (770+ nm) 24%.
  • the optical power in the preferred apparatus was determined after passage through a bandpass filter (center 485 nm, bandwidth 20 nm).
  • High-throughput screening requires that light be collected quickly and efficiently, so that assays can be accurately and rapidly performed.
  • a 1% error in intensity, corresponding to a 7 mP error in polarization, requires collection of at least 10,000 photons, as described above.
  • these photons should be collected within 100 ms, corresponding to a collection rate of 100,000 photons/sec.
  • Both lamps produce more than 100,000 photons/sec, but the criterion is to collect 100,000 luminescence photons/sec, not to produce 100,000 excitation photons/sec.
  • the criterion is to count at least 10,000 photons in 100 msec (l xlO 5 photon/sec) for low concentrations of luminophore (less than 1 nM).
  • the preferred apparatus achieves this photon limit at roughly 10-100 pM for polarization assays.
  • the detection efficiency is given by the product of an emission efficiency, a collection efficiency, a transmission efficiency, and a detector quantum efficiency, as calculated below.
  • the emission efficiency is determined by a product of the fractional abso ⁇ tion and quantum yield.
  • the molar extinction coefficient of typical luminophores is about 50,000 per molar per centimeter, and the path length in typical microplates is about 5 mm.
  • the fraction of photons absorbed is about 6xl0 "3 in a 1 nM solution and about 6 xlO "7 in a 10 pM solution.
  • the quantum yield (ratio of photons emitted to photons absorbed) of typical luminophores is 0.9, so that about 5xl0 "5 of the incoming photons are converted to luminescence emission photons (at 1 nM). This is effectively the emission efficiency.
  • the collection efficiency is determined by numerical aperture.
  • the optical collection efficiency is about 3% for an NA of 0.39 and about 1% for an NA of 0.22.
  • the transmission efficiency is determined by the optics through which the light passes between the sample and detector.
  • the transmission efficiency in the preferred apparatus probably is about 2%.
  • the detector quantum efficiency is determined by the detector.
  • the detector quantum efficiency of a photomultiplier tube (PMT) typically is about 20-25%
  • the detector quantum efficiency of a photodiode or other solid-state device typically is about 80%.
  • the preferred detector may vary with experimental conditions. At low light levels, a PMT may be preferred, because a PMT typically will have a lower background (i.e., dark count) and so contribute less noise to the system under these conditions. At higher light levels, a photodiode may be preferred, because a photodiode typically has a higher detector quantum efficiency and because any shortcoming in background relative to a PMT should be offset by a higher quantum efficiency.
  • the overall detection efficiency assumes values as follows:
  • the detection efficiency was multiplied by the excitation flux to yield an estimated measurable flux at 1 nM and 10 pM (measured in photons/sec).
  • the estimated measurable flux shows that the continuous lamp fails the criterion of 100,000 photons per second somewhere below 10 pM for a typical luminophore, whereas the flash lamp fails the criterion somewhere near 200 pM (roughly 20 times higher).
  • the continuous lamp satisfies the collection criteria, whereas the flash lamp does not.
  • the flash lamp has enough optical power to make statistically significant measurements at 1 nM, but not at 10 pM, where it leads to the collection of fewer than lxlO 5 photons/sec.
  • the continuous lamp has a power of greater than 1 watt over the visible wavelength range of 390 to 770 nm, and is sufficient to reduce photon noise to less than 1 percent of a light signal emitted from a 100 picomolar fluorescein solution at pH 7.5.
  • Samples may be supported by any substrate or material capable of supporting the sample for luminescence analysis at one or more examination or assay sites.
  • suitable substrates include microplates, PCR plates, DNA arrays (such as biochips), and hybridization chambers, among others, where features such as microplate wells and DNA array sites may comprise assay sites.
  • Preferred microplates are described below.
  • Preferred PCR plates would include the same (or a similar) footprint, well spacing, and well shape as the preferred microplates, while possessing a stiffness adequate for automated handling and a thermal stability adequate for PCR.
  • Preferred DNA arrays are described in Bob Sinclair, Everything's Great When It Sits on a Chip: A Bright Future for DNA Arrays, 13 THE SCIENTIST, May 24, 1999, at 18.
  • Preferred hybridization chambers are described in PCT Patent Application Serial No. PCT/US99/03678, which is inco ⁇ orated herein by reference.
  • Figures 23-35 show preferred microplates for supporting samples for luminescence assays in a plurality of wells or assay sites. These microplates differ in their well shape, well size, and well density, among other parameters.
  • the remainder of this section describes microplates constructed in accordance with aspects of the invention, including (A) 96-well microplates, (B) 384-well microplates, (C) 1536-well microplates, and (D) miscellaneous microplates.
  • Figure 23 is a top view of a 96-well microplate 200 constructed in accordance with aspects of the invention. Microplate 200 includes a frame 202 and a plurality of sample wells 204 disposed in the frame.
  • microplate 200 may include one or more reference fiducials 206 disposed in the frame.
  • Frame 202 is the main structural component of microplate 200.
  • the frame may have various shapes and various dimensions.
  • frame 202 is substantially rectangular, with a major dimension X of about 127.8 mm and a minor dimension Y of about 85.5 mm.
  • Frame 202 may be adapted for ease of use and manufacture.
  • frame 202 may include a base 208 to facilitate handling and/or stacking, and frame 202 may include notches 210 to facilitate receiving a protective lid.
  • Frame 202 may be constructed of a material, such as a thermoplastic, that is sturdy enough for repeated, rugged use and yet minimally photoluminescent to reduce background upon illumination.
  • Frame 202 includes a sample well region 212 and an edge region 214 forming a perimeter 216 around the sample well region.
  • Sample wells may be disposed in the sample well region in various configurations.
  • sample wells 204 are disposed in sample well region 212 in a substantially rectangular 8 x 12 array, with a pitch (i.e., center-to-center interwell spacing) along both X and Y of about 9 mm. This pitch corresponds to a density of wells of about one well per 81 mm 2 .
  • Reference fiducials 206 may be used for identification, alignment, and/or calibration of the microplate. Reference fiducials may be disposed in the sample well region and/or the edge region in various configurations. In microplate 200, reference fiducials 206 are disposed in edge region 214, substantially aligned with a row of sample wells along the X dimension. Reference fiducials preferentially are positioned in corners of the microplate, near where optical analysis begins, so that they may quickly be identified and analyzed. Reference fiducials may be positioned in rotationally symmetric positions, so that microplates may be loaded into an optical device and analyzed backwards without difficulty. Further aspects of reference fiducials are described in U.S. Patent Application Serial No. 09/156,318 and PCT Patent Application Serial No. PCT/US99/08410, which are inco ⁇ orated herein by reference.
  • Figure 24 is a cross-sectional view of microplate 200, showing sample wells 204, reference fiducial 206, and base 208.
  • frame 202 has a top 218, a substantially parallel bottom 220, and substantially pe ⁇ endicular sides 222.
  • Top 218 may have various shapes, although it typically is flat. (Top 218 may be surrounded by a raised edge to facilitate stacking.)
  • Frame 202 has a height H of about 12 mm, corresponding generally to the separation between top 218 and bottom 220. This height is large enough to facilitate handling by sample handlers and/or a stage, and yet small enough to permit optical analysis of the entire well.
  • Sample wells 204 are disposed with open, optically transparent ends 224 directed toward top 218, and closed, optically opaque ends 226 directed toward bottom 220. In some embodiments, optically opaque ends 226 may be replaced by optically transparent ends to permit bottom illumination and/or detection.
  • Reference fiducial 206 is disposed on top 218, although reference fiducials also may be disposed on bottom 220 and/or sides 222.
  • FIG 25 is a first enlarged portion of the cross-sectional view in Figure 24, showing details of sample wells 204.
  • Sample wells may have various shapes and various dimensions, as described in detail in subsequent sections.
  • sample wells 204 are substantially frusto-conical, with substantially straight side walls 228 and a substantially flat bottom wall 230.
  • optically opaque ends 226 are positioned about 6.7 mm below top 218, and about 5.3 mm above bottom 220.
  • Sample well 204 is characterized by a top diameter D ⁇ 96 , a bottom diameter D B>9 6, a height H 96 , and a cone angle ⁇ 96 .
  • ⁇ 96 is the included angle between side walls 228.
  • D ⁇ >96 is about 4.5 mm
  • D B ,96 is about 1.5 mm
  • H 96 is about 6.7 mm
  • ⁇ 96 is about 25.4°.
  • Sample well 204 has a total volume of about 50 ⁇ L, and a smallest practical working volume of about 1-20 ⁇ L.
  • Figure 26 is a second enlarged portion of the cross-sectional view in
  • reference fiducial 206 is substantially frusto-conical, with substantially straight side walls 232 and a substantially flat bottom wall 234.
  • Reference fiducial 206 is characterized by a top diameter D T;RF) 9 6 , a bottom diameter D B ,RF,96, a height H RF , 9 6, and a cone angle ⁇ RF ⁇ .
  • D B , RF ,96 and ⁇ RF J96 are substantially equal to D B 96 and ⁇ 96 , the corresponding values for sample well 204.
  • H 96 is about 1 mm
  • D TJRF,96 is specified by the other parameters.
  • FIGS. 27-30 are views of a 384-well microplate 300 constructed in accordance with aspects of the invention.
  • Microplate 300 is similar in many respects to microplate 200 and includes a frame 302 and a plurality of sample wells 304 disposed in a sample well region 312 of the frame.
  • microplate 300 may include one or more reference fiducials 306 disposed in an edge region 314 or other region of the frame.
  • microplate 300 The external dimensions of microplate 300 are similar to the external dimensions of microplate 200. However, the density of sample wells in microplate 300 is four times higher than the density of sample wells in microplate 200. Consequently, the pitch (i.e., the center-to-center interwell spacing) in microplate 300 is about 4.5 mm, or about one-half the pitch in microplate 200. This pitch corresponds to a density of wells of about four wells per 81 mm 2 .
  • reference fiducial 306 is positioned about midway between two rows of sample wells along the X direction; in contrast, in microplate 200, reference fiducial 206 is positioned about in line with a row of sample wells along the X direction.
  • reference fiducials are positioned in approximately the same position in each microplate, but the center line of one row of sample wells in microplate 200 because the center line between two rows of sample wells in microplate 300 as the density of wells is quadrupled.
  • Sample wells 304 in microplate 300 are similar to sample wells 204 in microplate 200.
  • Sample wells 304 may be characterized by a top diameter D ⁇ > 384, a bottom diameter D Bj384 , a height H 384 , and a cone angle ⁇ 38 .
  • the preferred values of D B 384 and ⁇ 384 for microplate 300 are substantially similar to the preferred values of D B>96 and ⁇ 96 for microplate 200.
  • the preferred value for D ⁇ >384 which is about 4.7 mm, is smaller than the preferred value for D T 384 , which is about 6.7 mm.
  • microplate 300 the upper diameter must be smaller than the upper diameter of the sample wells in microplate 200, because the sample wells are close packed, leaving no more interwell spacing than necessary for moldability.
  • the preferred value for H 384 is about 4.7 mm, so that the wells are elevated by about 7.3 mm.
  • Sample well 304 has a total volume of about 25 ⁇ L, and a smallest practical working volume of about 1-12 ⁇ L.
  • Reference fiducial 306 in microplate 300 may be essentially identical to reference fiducial 206 in microplate 200.
  • FIGS 31-35 are views of a 1536-well microplate 350 constructed in accordance with aspects of the invention.
  • Microplate 350 is similar in many respects to microplates 200 and 300, and includes a frame 352 and a plurality of sample wells 354 disposed in the frame.
  • the pitch in microplate 350 is about 2.25 mm, or about one-half the pitch in microplate 300 and about one-fourth the pitch in microplate 200. This pitch corresponds to a density of wells of about sixteen wells per 81 mm 2 .
  • Sample wells 354 may be exclusively frusto-conical, like sample wells 204 in microplate 200 and sample wells 304 in microplate 300. However, due to spatial constraints, the volume of such wells would have to be small, about 1-2 ⁇ L. Alternatively, sample wells 354 may have a frusto-conical lower portion 306 coupled to a cylindrical upper portion 308. The volume of such wells may be larger, for example, about 7-8 ⁇ L. The larger wells permit use of smaller or larger sample volumes. Larger sample volumes may be useful if the microplate is used in conjunction with standard fluid dispensing equipment, or if reagents are to be added to the well from stock solutions, such as 100X DMSO or DMF stock solutions.
  • Reference fiducials in microplate 350 may be essentially identical to reference fiducials 206 in microplate 200 and reference fiducials 306 in microplate 300.
  • the invention also may provide additional new microplate designs that are useful for high-efficiency sample analysis in luminescence polarization assays. These designs include:
  • the wells are organized in a density of at least about 4 wells per 81 mm 2 .
  • Each well has a bottom wall that is elevated at least about 7 millimeters above a plane defined by a bottom edge of the frame,
  • a preferred small- volume well design has a volume capacity of 1-20 microliters.
  • a microplate having an array of wells in the top portion, where each well has a maximum volume capacity of less than about 55 microliters and a well bottom that is elevated at least about 7 millimeters above a plane defined by a bottom edge of the frame.
  • a microplate having an array of conical wells characterized by a cone angle ⁇ , where ⁇ 2arcsin (NA/n) and NA is equal to or greater than about 0.07.
  • a microplate having an array of wells organized in a density of at least about 16 wells per 81 mm , where each well has a frusto-conical bottom portion and a substantially cylindrical upper portion.
  • a microplate comprising a frame and a plurality of frusto-conical sample wells disposed in the frame, where the sample wells are characterized by a cone angle of at least about 8°.
  • the microplate further may include a reference fiducial that provides information to facilitate sample analysis. 8. Application of Sensed Volumes
  • Microplates are a preferred sample holder in luminescence assays.
  • sample wells in standard microplates and other luminescence sample holders may have regions that are optically inaccessible, from which luminescence can be neither excited nor detected. Sample in such regions effectively is wasted because it does not contribute to the analysis. Wasted sample can translate into significant extra cost, particularly for assays that are performed in large numbers, that use expensive reagents, and/or that are inhomogeneous, requiring washing.
  • Sample wells also may have walls or other regions that are themselves detectable optically, increasing background if such regions luminesce.
  • an optical device capable of detecting light substantially exclusively from a sensed volume
  • a sample holder configured to support a sample so that the shape of the sample conforms to the shape of at least a portion of the sensed volume.
  • the sample holder may be a sample well in a microplate and may have a conical or frusto-conical shape, so that the sample conforms to a portion of an hourglass-shaped sensed volume.
  • Figure 36 is an enlarged cross-sectional view of a standard cylindrical or square microplate well 400, showing air 402 above the sample well, a sample 404 within the sample well, and a light beam 406 passing through the sample well.
  • the interface between air 402 and sample 404 is termed a meniscus 408 and may be convex, plan, or concave.
  • Light beam 406 is created by an optical device, such as luminescence apparatus 90 described above.
  • the optical device focuses the light so that the light beam has an hourglass shape along a cone or optical axis Z.
  • Light beam 406 is narrowest at its "waist" 410, which has a diameter W and which is located in a focal plane FP of the optical device.
  • Light beam 406 increases in width monotonically above and below waist 410, having a total included angle ⁇ .
  • Angle ⁇ is the cone angle of the "maximum cone” defined by the "marginal rays" of the optical device, and is twice the angle between the marginal rays and the optical axis Z.
  • the marginal rays trace the path of the most outlying light rays normally detectable by the system.
  • the maximum cone defines the outer boundary of the hourglass-shaped light beam and is the volume into which light may be delivered and from which light may be transmitted by the optical device.
  • Angle ⁇ also is the angle subtended at focal plane FP by the light-gathering components (e.g., the objective lens) of the optical device.
  • W and ⁇ depend on components and properties of the optical device and may be varied by varying these components.
  • NA the numerical aperture of the optical device
  • NA the index of refraction of the medium adjacent the optical device.
  • NA the numerical aperture of the optical device
  • NA the numerical aperture
  • NA 0.22 is a good compromise, creating a sensed volume that fits into sample wells in a 384-well microplate without hitting walls, and creating a sensed volume that can read to the bottom of microplates conforming to Society of Biomolecular Screening size standards.
  • the preferred numerical aperture and preferred index of refraction correspond to a cone angle of about 25.4°.
  • the portion of the hourglass to which light may be delivered and from which light may be transmitted further may be limited by one or more confocal optics elements within the optical device.
  • confocal optics elements may include apertures placed in image planes of the optical device, conjugate to focal plane FP.
  • the maximum cone and the confocal optics elements combine to create a sensed volume 412.
  • the shape of sensed volume 412 may differ in directions parallel and pe ⁇ endicular to the optical axis Z. Parallel to optical axis Z, the shape may be a Lorentzian, among others. Pe ⁇ endicular to optical axis Z, the shape may be a Gaussian, or it may be a rounded pulse function, among others. A laser beam might give rise to a Gaussian, whereas a fiber optic bundle might give rise to a rounded pulse function. Generally, lower numerical apertures will create sensed volumes shaped more like cylinders, whereas higher numerical apertures will create sensed volumes shaped more like hourglasses.
  • the shape and volume of the sample holder may be chosen or designed to conform to the shape and volume of the sensed volume.
  • FIG 37 is a partially schematic cross-sectional view of a sample holder 450 constructed in accordance with the invention.
  • Sample holder 450 supports a sample 452 illuminated by a light beam 454 forming a sensed volume 456.
  • Sensed volume 456 is shaped substantially like an hourglass, having a waist 458 with diameter W and conical margins 460 characterized by a cone angle ⁇ ' and a cone or optical axis Z'.
  • Sample holder 450 is configured to support sample 452 so that the shape of the sample conforms to the shape of at least a portion of sensed volume 456.
  • Light is delivered to a sensed volume of the sample from a light source, and transmitted from a sensed volume to a detector.
  • sample holder 450 has a frusto-conical shape configured to conform to substantially one-half of the hourglass shape of sensed volume 456.
  • sample holder 450 has conical wall portions 462 that substantially conform to conical margins 460 of sensed volume 456, and a planar bottom portion 464 that substantially conforms to waist 458 of sensed volume 456.
  • the cone angle associated with conical margins 462 substantially equals cone angle ⁇ ' of sensed volume 456.
  • the sample holder may have a purely conical shape or an hourglass shape, so that it conforms to a larger portion of the sensed volume.
  • the sample holder may have yet other shapes, to conform to alternatively shape sensed volumes. Optically inaccessible regions within sample holder 450 are reduced, so that most of the sample contributes to the analysis, reducing sample waste.
  • Figure 38 is a partially schematic cross-sectional view of an alternative sample holder 500 constructed in accordance with the invention.
  • Sample holder 500 is configured to match substantially half of an hourglass-shaped sensed volume 502.
  • Sample holder 500 is dimensioned so that the waist 504 of the sensed volume may be aligned with the bottom 506a of the sample holder, with the top 508 of the sensed volume substantially aligned with the top 506b of the sample holder.
  • This embodiment may be especially useful for very small sample volumes, such as may be used in 1536-well microplates, because it may increase the sample volume to an amount that may be handled and dispensed more easily.
  • Figure 39 is a partially schematic cross-sectional view of another alternative sample holder 550 constructed in accordance with the invention.
  • Sample holder 550 is configured to match substantially all of an hourglass- shaped sensed volume 552.
  • Sample holder 550 is dimensioned so that the bottom and top 554a,b of the sensed volume may be aligned with the bottom and top 556a,b of the sample holder, with the waist 558 of the sensed volume substantially in between. This embodiment also may be especially useful for very small sample volumes.
  • Preferred sample wells are chosen to optimize lower detection limit, signal-to-noise ratio, and signal-to-background ratio, and to minimize sample volume, for a given sensed volume.
  • Lower detection limit is the lowest concentration of sample that can be measured.
  • Signal-to-noise ratio is the signal from the sample divided by variations in the signal due to noise.
  • Signal- to-background ratio is the signal from the sample divided by the signal from contaminants in the sample, the sample holder, and components of the optical system.
  • the cone angle of the sample holder substantially conforms to the approximately 25° cone angle of the sensed volume of the ANALYST optical device. For frusto-conical wells, optimal cone angles and well bottom diameters will depend on the cone angle and waist diameter of the sensed volume.
  • Cone angles may range from about 8° for a low (0.07) NA optical system, on up. Such cone angles significantly exceed the slight 1-2° angle introduced into molded cylindrical sample holders to permit removal of the sample holder from the molding tool. Bottom diameters may range from about 1 ⁇ m for a high NA optical system, on up, though typical values might be 1 mm or 1.5 mm.
  • the smallest practical working volume for frusto-conical and other sample holders is the volume for which there still is sufficient sample volume to enclose the portion of the sensed volume contained within the sample well, or at least to enclose a sufficient portion of the sensed volume to yield acceptable signal-to-noise and signal-to-background ratios.
  • the shape and volume of the sensed volume produced by the apparatus may be adapted like a probe to match the shape and volume of the sample holder. In this way, the sensed volume may be expanded for maximum signal in a large sample holder, and contracted to avoid nearby walls in a small sample holder.
  • the shape and volume of the sensed volume may be held constant, and the position of the sensed volume varied to match the sample holder and/or assay.
  • the sensed volume will report on equal volumes of each composition analyzed, so that the apparatus effectively reports "intensive" quantities.
  • Intensive quantities do not depend on the amount of composition in a sample holder; in contrast, extensive quantities do depend on the amount of composition in the sample holder.
  • This approach can be used to facilitate comparison of results obtained from different-sized sample wells. This approach also can be used to facilitate comparison of results obtained from like-sized sample wells containing different volumes of solution.
  • Figure 40 shows how the sensed volume can be directed to different regions of a standard microplate well, and how directing the sensed volume affects signal-to-noise and signal-to-background ratios.
  • microplate wells having a frusto-conically- shaped portion may be particularly advantageous.
  • the conical shape of the well tends to focus cells into a smaller area defined by the substantially flat bottom wall.
  • the conical shape of the well and the selected confocal optics allow substantially all of the cells at the bottom of the well to be detected in the sensed volume, thus maximizing signal sensitivity and reagent utilization regardless of whether the cells are uniformly distributed across the bottom of the well.
  • the conical geometry of the wells also makes it possible to perform cell-based assays from the top without requiring transmission of light through the bottom wall of the well.
  • the geometry is also useful for performing luminescence polarization assays that may be based on receptor/ligand binding to the bottom of the well.
  • the shape and position of the sensed volume within the well may be affected by (l) the meniscus and (2) the geometry of the sample well, among other factors.
  • Figure 41 shows how the meniscus affects the shape and position of the sensed volume within a sample well.
  • the meniscus affects the sensed volume because light is refracted as it crosses the meniscus boundary between the air and the composition. Specifically, light passing from air (with its lower index of refraction) into the sample (with its higher index of refraction) bends toward the normal, as described by Snell's law.
  • the normal is the direction pe ⁇ endicular to the surface of the meniscus at a given point. If there is no fluid and hence no meniscus, the beam has a nominal undistorted shape (Panel A).
  • Sample wells can be configured to account for these changes in the shape and position of the sensed volume created as excitation and emission light passes through the meniscus.
  • the invention includes shaping the sample well to account for changes in the shape and position of the sensed volume, and shaping and treating the sample well to alter the shape of the meniscus, as appropriate.
  • Figures 42 and 43 show how the geometry of the sample well affects the position of the sensed volume.
  • the well is sufficiently narrow relative to the diameter of the beam, or if the well is sufficiently deep relative to the angle made by the beam, then the light beam may impinge upon the top walls of the well.
  • setting the Z-height too low can reduce sensitivity (1) by decreasing the desired signal because less light enters the well, and (2) by increasing the background because the light beam illuminates the tops of wells.
  • Many microplates are made from materials that are fluorescent or otherwise photoluminescent, and the instrument will detect this photoluminescence from materials at the tops of wells.
  • Z height must be appropriately maintained; Z height should be kept above a critical focal height, Hz , c r i t
  • the height at which the beam first impinges on the walls of the well is the critical focal height, Hz , cri t .
  • Figure 43 shows how Hz.
  • C ri t depends on the well height H and well diameter Dw, for a beam of diameter 1.5 millimeters (mm) and a beam angle 25.4°.
  • Table 1 shows how Hz , crit depends on well height and well diameter for four commercially available microplates.
  • H Zcrit shows that for a microplate having a standard height and XY area, as the aspect ratio (length/diameter) and density of wells increases, the ability of a confocal optic system to read small volumes in standard straight-walled wells decreases. This may require reading through the bottom of the well for cell-based assays, which is not always convenient or practical.
  • Z-height can be optimized for a particular microplate and assay by (1) preparing a test microplate with representative assay (e.g., blanks, positive and negative controls, dilution series), (2) and reading the microplate multiple times at different Z-heights to determine the Z-height that gives the best signal- to-background data.
  • representative assay e.g., blanks, positive and negative controls, dilution series
  • Optical spectroscopic assays are subject to artifacts that alter the apparent luminescence of the analyte and thus the accuracy, repeatability, and reliability of the assay.
  • Some artifacts increase the apparent luminescence of the analyte, causing intensity-based assays to overreport the amount of light emitted by the analyte.
  • Such artifacts include background.
  • Other artifacts decrease the apparent luminescence of the analyte, causing intensity-based assays to underreport the amount of light emitted by the analyte.
  • Such artifacts include scattering and abso ⁇ tion.
  • Such artifacts also include changes in the composition that change the optical transfer function (photons collected / photons injected), including changes in index of refraction and surface tension.
  • Optical spectroscopic assays also are subject to artifacts that alter the apparent polarization of the analyte. Such artifacts also include background, scattering, and abso ⁇ tion, among others, and can increase or decrease the apparent polarization.
  • Background refers to light and other signals that do not arise from the analyte, but that can be confused with light that does arise from the analyte. Background may arise from non-analyte luminescent components of the sample (e.g., library compounds, target molecules, etc.). Background also may arise from luminescent components of the sample container and detection system (e.g., microplates, optics, fiber optics, etc.). Background also may arise from scattered excitation light that leaks through the optical filters, which is equivalent to luminescence with a zero lifetime, and from room light.
  • non-analyte luminescent components of the sample e.g., library compounds, target molecules, etc.
  • Background also may arise from luminescent components of the sample container and detection system (e.g., microplates, optics, fiber optics, etc.). Background also may arise from scattered excitation light that leaks through the optical filters, which is equivalent to luminescence with a zero lifetime, and from room light.
  • background may be at least partially discriminated using appropriate optical filters, which pass light emitted by the analyte but block background. If the analyte and background have overlapping spectra, background may be at least partially discriminated in two ways. First, background may be discriminated using a blank. In this method, data such as intensity data are collected for the sample and for a blank that lacks analyte but otherwise resembles the sample. Background is at least partially discriminated by subtracting the data obtained from the blank from the data obtained from the sample. Second, background may be discriminated by gating.
  • compositions containing biological molecules there is no way to eliminate every source of scattering and abso ⁇ tion. This is especially true in compositions containing biological molecules, because biological molecules such as nucleic acids and proteins may absorb light having wavelengths commonly used in luminescence assays.
  • the invention provides methods and apparatus for improving signal resolution in hybridization assays. These improvements may be obtained without using information from a blank, and/or without requiring a determination of the lifetime or intensity of the background. These improvements also may be obtained irrespective of whether a significant amount of the background is being detected by the detector at the same time that light emitted by the analyte is being detected. Consequently, the invention permits discrimination between analyte and background and/or other non- analyte emitters in measurements performed in a single sample container. The invention also permits light to be detected and analyzed continuously, so that signal is not wasted and data collection is not slowed.
  • background can be represented as a combination of (1) a relatively constant background luminescence (from well to well in microplate experiments) having a relatively constant anisotropy and (2) random fluctuations in both the luminescence level and its anisotropy caused by luminescent contamination ("hot wells" in microplate experiments).
  • This background can be reduced or subtracted using various methods, including:
  • the latter methods may involve converting detected light to a signal, and discriminating between a first portion of the signal that is attributable to light emitted by the luminophore and a second portion of the signal that is attributable to a background.
  • the discriminating step may be performed using a processor.
  • the processor may discriminate between the first and second portions of the signal without requiring a determination of the lifetime or intensity of the background, or without requiring the use of information obtained from a blank (irrespective of whether a significant amount of the background is being detected by a detector at the same time that light emitted by the analyte is being detected).
  • the processor also may discriminate between the first and second portions in the frequency domain without requiring a determination of the intensity of the background, or without requiring the use of information obtained from a blank.
  • intensity-based method may be used to analyze polarization results:
  • step 5 is carried out using the following relation between intensity and polarization:
  • and _L subscripts indicate the
  • Anisotropy-based method A novel alternative anisotropy-based procedure also may be used to analyze polarization results.
  • a basic difference between the intensity-based and anisotropy-based procedures is how the background is subtracted: in the intensity-based procedure, intensities are subtracted, whereas in the anisotropy-based procedure, anisotropies are subtracted.
  • the anisotropy-based procedure may provide the following benefits: (1) a more robust method for background subtraction, and (2) insight into how hot wells affect polarization measurements, and a mechanism to address them.
  • anisotropy-based method Derivation of anisotropy-based method. To simplify the math, the anisotropy-based method is derived in terms of anisotropy rather than polarization, with the understanding that we can readily convert between anisotropy and polarization.
  • the underlying assumption for this analysis is that the assay system can be decomposed into two components: (1) the label of interest, and (2) everything else, which is lumped together as background. This typically would include autoluminescence from the microplate or other substrate and from the optical elements of the light detection device. (The same assumption is used in the intensity-based background-subtraction analysis.)
  • the average anisotropy for the system is then given by the following expression:
  • the preceding equation indicates that background can be subtracted by manipulating anisotropies rather than intensities.
  • the anisotropy of the label (R L ) can be estimated from the total anisotropy (R ⁇ ) if the background anisotropy (Ro) and background relative intensity (f 0 ) are known.
  • R depends on the label of interest; for free fluorescein in PBS, it is about 0.02 (27 mP), and for the antibody-bound tracer in the TKXTM assay kit marketed by LJL BioSystems, it is about 0.1 (140 mP).
  • Ro can range from about 0.400 (500 mP) for PBS in black plates to less than about 0.015 (22 mP) for white plates.
  • f 0 has an absolute range of 0.0 to 1.0, but will be small in most applications. For instance, in the TKX assay, the average background intensity is typically about 0.006. In the fluorescein dilution series used to test the light detection device presented above, the buffer wells are roughly the same brightness as 6 pM fluorescein, so that f 0 is about 0.06 when compared with our performance specification of 100 pM.
  • a potential advantage of the anisotropy-based procedure is that it may be more robust than the intensity-based procedure. If intensities vary for some reason, such as a change in lamp power or alignment, the intensity-based background-subtraction procedure may give erroneous results. However, the anisotropy-based background-subtraction procedure will still give correct results because the background anisotropy and relative background intensity should remain unchanged.
  • AR L ⁇ AR 1 ) 2 + f 0 2 ( 0 ) 2 + ⁇ R, - R 0 ) 2 ( ⁇ 0 ) 2 (11)
  • Errors in R ⁇ translate directly into errors in R L .
  • Errors in the background anisotropy have only a small effect on our determination of R L ; for instance, if f 0 is 0.01 and ⁇ Ro is 0.1 (150 mP), the effect on R L is O.001 (1.5 mP).
  • AR L (2 7 . Y + (AR 0 Y + (R ⁇ - R 0 f (4 ⁇ / 0 ) 2 (12)
  • LDL lower-detection limit
  • treated plates for control of hot wells in polarization Assume that we can fabricate or treat microplates in such a way that their background anisotropy is controllable. For instance, we could add some titanium dioxide to a black plate to cause scattering, which would reduce background polarization.
  • TKX assay we look for a decrease in anisotropy from a nominal value of 0.100 (140 mP) to some lower value. The plate is designed with a background anisotropy of about 0.100 (140 mP) so that it provides a background that matches the assay.
  • the background polarization of the of the black plates is very high (about 500 mP). 2.
  • the background polarization of the of the black plates is consistent from plate to plate. 3.
  • the background polarization of the white plate is very low.
  • FLAMe method Another method to remove unwanted fluorescence background is to employ the fluorescence lifetime anisotropy method (FLAMe). This method can eliminate the effect of background fluorescence in a polarization assay if the background has an average lifetime distinct from the analyte lifetime.
  • FLAMe fluorescence lifetime anisotropy method
  • FLAMe uses the time-resolved fluorescence anisotropy measured in the frequency domain to distinguish the long and short lifetime components. The measurement is then manipulated to establish the ratio of bound probe molecules to the sum of the bound and free molecules (the fraction of bound molecules). The goal of the method is to establish a way to measure the fraction of bound molecules (or free ones) without interference from other fluorescing compounds.
  • the lifetime discriminated intensity may be used for the rejection of short lifetime background when a long lifetime analyte is used (also the reverse is possible).
  • the LDI can be substituted anywhere a conventional intensity would be used.
  • the LDI of the parallel intensity and the LDI of the perpendicular intensity can replace the parallel and pe ⁇ endicular intensity values used to calculate the polarization (or anisotropy).
  • Figure 37 shows using experimental results that short-lifetime background with low polarization does not significantly affect performance of FLAMe methods.
  • the apparatus and methods provided by the invention can be used to discriminate between analyte and background in intensity assays.
  • Background- corrected intensities derived from such intensity assays can be used directly, as intensities, or they can be used indirectly to determine quantities such as polarization and luminescence lifetime.
  • the invention permits determination of background-corrected intensities for systems having one or more analytes and one or more background components.
  • LDM lifetime-discriminated intensity
  • I(t) is the time-dependent luminescence intensity
  • « is a preexponential factor
  • r is the luminescence lifetime of the ith component.
  • the fraction of the steady-state luminescence intensity contributed by each component may be found by integrating Equation 14 over time.
  • fj is the fractional intensity of the ith component.
  • the phase and modulation phasor of a complex luminophore or a mixture of luminophores is a vector sum of the phase and modulation of the individual components, weighted by the individual components' fractional contributions to the total intensity.
  • Figure 38 shows phase and modulation for a system containing two luminophores, such as an analyte and background.
  • the phase and modulation of the system can be expressed in terms of X and Y components of the phasor.
  • V denotes system
  • 'y' denote X and Y components.
  • the X and Y components for the system can be expressed in terms of X and Y components for the analyte and background alone.
  • Equations 18 and 19 can be rearranged to solve for the fractional intensities of the analyte and background.
  • the fractional intensity f a of the analyte is
  • M s corresponding to the system
  • M a i corresponding to analyte alone
  • M o l corresponding to background alone.
  • M s i is determined for each sample, by making a measurement on each sample.
  • M a i is determined for each analyte, not for each sample, either (1) by measuring the modulation phasor using a blank containing the analyte "without" background (possibly at high concentration), or (2) by calculating the modulation phasor using Equations 4-5 and the analyte lifetime as measured above without background.
  • M b l may be estimated for each sample by making a measurement on a blank for each sample.
  • M D l typically varies from sample to sample, because the background includes contribution from the composition.
  • An alternative method leading to larger errors in HTS would be to measure an average background using a single blank Mi, ,) and to apply this background to each sample.
  • Equation 20 can be rewritten as a power series of ⁇ D or 1/ ⁇ j, (assuming that the background follows a single exponential decay).
  • the motivation for the power series is that the power series can be conveniently truncated if the background has a short lifetime ( ⁇ b «l) or if the background has a long lifetime ( ⁇ l ⁇ b « ⁇ ). If the background has a short lifetime, the analyte fractional intensity is
  • Equations 21 and 22 discriminate between light emitted by the analyte and short- or long-lifetime background, based on differences in lifetime, without requiring the lifetime or intensity of the background. If the value of the background lifetime is only known to be short (as compared to the frequency), we employ the limiting case of Eq. 21. Likewise, if the background lifetime is only known to be long, we employ the limiting case of Eq. 22. When the background lifetime is better known (yet, still short or long), higher order terms in Eq. 21 and 22 may be calculated and used to yield a better approximation. Although both the X and Y versions of Eq.
  • phase-based approach has a potential advantage. If only the phase is desired, a device could be optimized to measure just the high- frequency (AC) intensity or phase without measuring the average (DC) intensity. With the elimination of DC electronics, the device is likely to be more stable electronically and to provide a more precise measurement. This increased precision may allow the frequency to be reduced so that the neglected terms in the phase approach (Eq. 23) become comparable to those in the modulation phasor approach (Eq. 21). This increase in precision may even make the phase approach preferable to the modulation phasor approach. Variations in the excitation intensity and lifetime of the background do not affect the determination of f a , to the extent that the background lifetime remains small or large, as appropriate. This is true even if the background includes multiple components, as long as the lifetime of each component is short (Equations 21 and 23) or long (Equation 22). In these cases, the average or effective lifetime of the background may be used in Equations 21-23 as needed.
  • Eq. 21 and 22 can be formulated by creating a power series in ⁇ b / ⁇ a (for short-lifetime background) or ⁇ a / ⁇ b (for long-lifetime background) from Eq. 20.
  • the short-lifetime expansion is
  • the contribution of each component to the total intensity can be determined using the intensity, phase, and modulation of the system, measured at two angular modulation frequencies ( ⁇ j, ⁇ 2 ).
  • the fractional intensity of the analyte is , - 1 j/ , -
  • the methods to reduce background luminescence outlined above have all determined the fractional intensity of the analyte.
  • the quantity of interest is not the analyte fractional intensity but the analyte intensity, which is the total intensity times the fractional intensity.
  • Eq. 20-23a single-frequency, two-component
  • LRI lifetime discriminated intensity
  • LRI lifetime-resolved intensity
  • Figure 39 shows simulation results demonstrating the ability of the invention to discriminate between an analyte and a background. Results are shown for three zeroth-order embodiments of the invention, as described in Equations 21 (LDI, M x -based), 23 (LDI, ⁇ -based), and 24 (LR1).
  • the error is determined by the choice of frequency and analyte lifetime. When the lifetimes of the analyte and background differ by more than a factor of ten for the equations based on the X components of the modulation, the error is low enough ( ⁇ 2%) for HTS applications.
  • the choice of frequency also is important for small systematic errors.
  • the frequency In the lifetime-discriminated case (Equation 21), the frequency must be chosen so that the measured quantity (M s x ) is useable.
  • the errors in M s>x must not translate into a large uncertainty in the derived fractional intensity. If the fraction of analyte is large, any frequency appropriate for measuring the analyte will suffice. For example, if the analyte has a lifetime of 100 nanoseconds, any frequency in the range of 300 kHz to 8 MHz is appropriate (from 1/5 to 5 x the inverse lifetime).
  • Equation 25 the choice of frequencies is more difficult. Roughly, one frequency is needed to discriminate between the long and intermediate lifetimes, and one frequency is needed to discriminate between the intermediate and short lifetimes. Each frequency may be chosen as for a two-component system. However, using an optimization program to choose the frequencies may be more reliable and robust. The program optimizes the frequencies to minimize systematic error due to finite lifetimes of the short and long components, while also minimizing the error due to changes in analyte lifetime.
  • the luminescence intensity due to the analyte can be found by multiplying the total intensity by the calculated fractional intensity, using Equations 20 (LDI), 22 (LDI), or Equation 23 (LRI), among others. Total intensity is obtained from the steady-state value of the luminescence emission, without performing a separate experiment.
  • LRI Equation 23
  • the analyte was [Ru(bpy) 3 ]Cl 2 (ruthenium tris-2,2'-bipyridyl chloride), which has a long lifetime in buffer (measured at 330 nanoseconds at a temperature of 26-28 °C in 20 millimolar PBS, pH 7.4).
  • the background was from the sample container and/or added R-phycoerythrin.
  • R-phycoerythrin was used as an intentional background contaminant because its excitation and emission spectra overlap those of Ru(bpy)3 and because it has a short lifetime in buffer (measured at 2.9 nanoseconds in 20 millimolar PBS, pH 7.4). All samples were prepared with 20 mM PBS, pH 7.4, and all data were collected with a 400 millosecond integration time in COSTAR-brand flat-black 96-well microplates.
  • Ruthenium is a good long-lifetime probe for several reasons.
  • ruthenium is an atomic luminophore, so that it is not subject to the common problem of photobleaching.
  • the ruthenium complex has a convenient excitation spectrum (460 nanometer peak) and a large (140 nanometer) Stokes' shift. (The Stokes' shift is the separation between maxima in excitation and emission spectra.)
  • Typical dispensing errors, concentration errors, and instrument drift can combine to give an error of several percent. Considering these other errors, it is practical to use data with a 10% CV for quantitative work, which may be considered the limit for precise data. These confidence and precision limits allow quantitatively comparison of data from background-subtracted intensity, lifetime-discriminated intensity, and lifetime-resolved intensity measurements.
  • Figure 40 shows experimental results demonstrating sensitivity to background, determined by adding increasing concentrations of R- phycoerythrin to a constant concentration of Ru(bpy) 3 . The result was a series of solutions with increasing total intensity but constant analyte intensity. All solutions were prepared in duplicate, and errors in the average were compared with expected values.
  • Figure 40 shows three curves.
  • LDI corresponds to Equation 21, evaluated at 2.85 MHz.
  • BSI corresponds to the background-subtracted intensity, computed using a blank. The ability of a method to discriminate analyte and background is given by the analyte fractional intensity at which measurement error exceeds the confidence limit.
  • the background-subtraction method can discriminate between analyte and background only if the analyte fractional intensity exceeds 17%, whereas LDI and LRI can discriminate between analyte and background if the analyte fractional intensity exceeds 2% and ⁇ 0.8%, respectively. Therefore, both methods are less than one-tenth as responsive to background luminescence as background subtraction. This reduced responsivity is achieved while reducing experimental complexity. Under the proper conditions, LDI and LRI do not require any measurement of the background luminescence, including its lifetime and intensity. The contribution of background to the measured intensity is removed simply because of its short lifetime.
  • Figure 41 shows experimental results demonstrating sensitivity to analyte, determined by adding increasing concentrations of Ru(bpy) 3 to a constant (1 nanomolar) concentration of R-phycoerythrin. The result was a series of solutions with increasing total intensity but constant background intensity. This setup permits a determination of the minimum resolvable fraction of analyte in the presence of background. All solutions were prepared in duplicate, and errors in the average were compared with expected values. We measured the LDI was measured at 2.85 MHz, and LRI was measured at 0.35 and 2.85 MHz. The difference between methods is again substantial. Background subtraction quickly fails to resolve the analyte (at a fractional intensity of 13% or 100 micromolar of ruthenium complex).
  • LDI reports the correct analyte intensity down to a fractional intensity of 1% (10 ⁇ M), while LRI reports the correct intensity down to less than 0.1% (5 micromolar). This is a greater than tenfold increase in the sensitivity to the analyte for either method.
  • the invention is robust, simple, and fast, making it ideal for high- throughput screening.
  • LDI is able accurately to distinguish short- and long- lifetime components using phase and modulation at only a single frequency.
  • LRI is able accurately to separate three lifetime components using phase and modulation at two frequencies. Extension to even more components also is possible. Knowledge of the lifetime of one component is used to determine the intensity of each component, without requiring a determination of the lifetime or intensity of the other component.
  • the apparatus and methods provided by the invention also can be used to discriminate between analyte and background in polarization assays.
  • the invention permits determination of background-corrected polarizations for systems having one or more analytes and one or more background components.
  • Background-corrected steady-state polarizations may be determined using Equation 1, where l ⁇ and L may be determined using appropriate combinations of parallel and pe ⁇ endicular excitation and emission polarizers, and the apparatus and methods described above for computing background-corrected intensities. Such corrections are important, because steady-state anisotropies are intensity -weighted averages of the anisotropies of all components present, so that background affects the measured anisotropies directly.
  • Background-corrected time-resolved polarizations may be determined using time-domain or frequency-domain techniques.
  • background-corrected polarizations may be determined using Equation 1, where 1 ⁇ and L are replaced by I
  • background-corrected polarizations may be determined using appropriate combinations of parallel and pe ⁇ endicular phase ⁇ p and parallel and pe ⁇ endicular modulation M p .
  • ⁇ p and M p denotes parallel or pe ⁇ endicular, corresponding to parallel and pe ⁇ endicular components.
  • ⁇ p and M p are determined using the same apparatus and methods as ⁇ and M, with the addition of parallel and pe ⁇ endicular polarizers, as appropriate.
  • ⁇ p and M p may be rewritten in terms of ⁇ and I(t).
  • Experimental results may be inte ⁇ reted using a differential phase angle A ⁇ and a ratio ⁇ ⁇ of the parallel and pe ⁇ endicular AC components of the polarized emission.
  • ⁇ ⁇ may be used to define a frequency-dependent quantity r ⁇ , called the modulated anisotropy.
  • a + 2 J r ⁇ tends to the fundamental anisotropy r 0 at high frequency and to the steady- state anisotropy r ss at low frequency.
  • Frequency-domain time-resolved polarization may be used to investigate the motional properties of biological molecules in more detail than steady-state polarization.
  • a biophysical model may be used to generate functional forms of / ( (t) and I (t) , using parameters such as lifetimes and rotational correlation times. This model can be used to predict A ⁇ and A ⁇ . Experiments then can be done to measure A ⁇ and A ⁇ , at one or more modulation frequencies. Experimental results may be fitted to the model by adjusting the parameters to give the best fit between predicted and observed values of A ⁇ and A ⁇ or r ⁇ , for example, by using nonlinear least-squares optimization algorithms.
  • Figure 42 shows how A ⁇ (Panel A) and r ⁇ (Panel B) depend on ⁇ for a simple binding system in the absence of background.
  • Figure 42 shows results for 0%, 25%, 50%, 75%, and 100% binding.
  • the extent of binding of the labeled molecule can be determined quickly and sensitively by measuring A ⁇ and r ⁇ at a single suitable frequency (e.g., -20 MHz for A ⁇ , and ⁇ 10 MHz for r ⁇ ), and then reading off the extent of binding from an empirical calibration curve.
  • binding could be determined using LDI and LRI, among others, if the binding is associated with a change in analyte lifetime.
  • Figure 43 shows how A ⁇ (Panel A) and r ⁇ (Panel B) depend on ⁇ for a simple binding system in the presence of 50% background.
  • r o 0.3
  • r rot l nanosecond
  • r rot 0.1 nanosecond.
  • the psi function is a ratio of the parallel and pe ⁇ endicular AC intensities, weighted by the sines of the parallel and pe ⁇ endicular phases, respectively.
  • Figure 44 shows how ⁇ ⁇ depends on ⁇ for the system of Figures 42 and 43, in the presence of 0% (Panel A) and 50%) (Panel B) background.
  • the lower the frequency the less ⁇ ⁇ is affected by the (short- lifetime) background.
  • ⁇ ⁇ is much less affected by background than A ⁇ and r ⁇ .
  • ⁇ p also becomes small, and measurement of the sine becomes imprecise.
  • the optimum modulation frequency will be determined by a balance of these factors, among others.
  • N ⁇ a , ⁇ a l ⁇ ,[L( ⁇ l ) - r 0l ⁇ L( ⁇ l )] ⁇ (41)
  • L(x) x/(l+x 2 ).
  • L(x) reaches a maximum value of/2 at x l.
  • the rotational correlation time enters the system only through
  • ⁇ ⁇ gives small weight to signals from short-lived species ( ⁇ , or ⁇ , « ⁇ ), in comparison to signals for which ⁇ t or ⁇ , ⁇ l.
  • ⁇ ⁇ also gives small weight to the anisotropy contributions of long-lived components that have extremely short rotational correlation times (i.e., ⁇ t « 1 , r l l ⁇ l « 1).
  • Kappa function The kappa function, or K ⁇ , is a ratio involving the parallel and pe ⁇ endicular AC intensities, weighted in part by the cosines of the parallel and pe ⁇ endicular phases, respectively.
  • ⁇ I
  • K ⁇ may be shown to be a ratio involving lifetime-discriminated intensities, as defined above, in associated parallel and pe ⁇ endicular measurements.
  • Figure 45 shows how K ffl depends on ⁇ for the system of Figures 42 and 43, in the presence of 0% (solid lines) and 90% (dashed lines) background.
  • Results for K ⁇ are similar to results for ⁇ ⁇ , except that K ⁇ may be less sensitive than ⁇ ⁇ to frequency for low frequencies, and to binding for high binding.
  • Neither the kappa nor the psi function depends on properties of the background, so neither function requires use of a blank or a determination of the lifetime or intensity of the background.
  • the invention provides additional new methods for discriminating between analyte and background in intensity (and thus indirectly in polarization) assays. Generally, these methods permit determination of background-corrected intensities for systems having one or more analytes and one or more background components.
  • the remainder of this section is divided into three sections, which describe different methods provided by the invention: (A) "exact” algorithms for analyzing FLAReTM data, (B) correction of lifetime measurements for short-lived background, and (C) third-order FLDI (fluorescence lifetime discriminated intensity) algorithm for analyzing FLAReTM data.
  • a sample in a fluorometric assay may contain multiple fluorescent components. Some are present intentionally, and the characteristics of their emissions form the basis of the assay. Others constitute background and interfere with the inte ⁇ retation of the assay. Sources of background include the optical components of the detection instrument, contaminants in the sample container, and various components of the assay solution. Where the background is the same in every sample being assayed (e.g., a predictable emission from the sample container), a separate measurement coupled with background subtraction can sometimes improve performance. However, a particular problem occurs during high- throughput screening for new pharmaceuticals, where the library compound being assayed is fluorescent. Background subtraction would necessitate doubling the number of assays performed (true measurement and background measurement for each compound), and background subtraction is in any event of limited utility.
  • N f 1 ⁇ /[l+( ⁇ 1 ) 2 ]+ f 2 ⁇ 2 /[l+( ⁇ 2 ) 2 ]+... f n ⁇ n /[l+( ⁇ n ) 2 ] (46)
  • Estimates of the intensity and lifetime parameters can be extracted from phase and modulation measurements by, e.g., nonlinear least-squares fitting of predicted to observed data.
  • the number of unknowns must in general not exceed the number of independent data points. There are at most 2n-l unknowns (fractional intensities and lifetimes, reduced by one because the fractions must sum to unity). If reference measurements have already determined the values of parameters for individual components or subsets of components, this number can be reduced.
  • the number of independent data points can be increased by making measurements at multiple modulation frequencies. For example, using two modulation frequencies generates four data points ( ⁇ and M each at two values of ⁇ ).
  • the fluorescence signal is produced by a single fluorophore exhibiting a single-exponential decay, these two equations yield the same value of the lifetime, the time constant for the decay.
  • the two equations typically give different values of ⁇ . Relating the measurement to the underlying molecular processes is more complicated and in general requires measurements at multiple wavelengths or modulation frequencies that are inte ⁇ reted by fitting to some model. For example, when there are two fluorophores with distinct lifetimes, the measured values of phase and modulation are weighted averages of the phase and modulation results that would be obtained in experiments on the separate components. Moreover, the weighting is different for phase and modulation. Two separate FD measurements at appropriately chosen modulation frequencies are required to resolve the lifetimes and relative contributions to the FLINT of the two components.
  • M A , ⁇ A , M B , and ⁇ B are those that would obtain if the A and B components were present separately.
  • Equation 52 [Y s /(1-Xs)] [(1-XA)/XA] (54)
  • Figure 46 shows the performance that can be expected of the algorithm, obtained using a simulation of FD experiments on a two-component system containing analyte (fluorescent label) and a fluorescent background in varying proportions.
  • the FLDL algorithm demonstrates its superiority to the application of Equations 50 or 51 in that the lifetime of the analyte calculated with FLDL is much closer to the true value than the lifetime calculated with Equation (4) or (5) when there is appreciable background fluorescence.
  • the present invention truncates the expansion before the fourth-order term and thus is good to third order in ⁇ B . This improves the ability of the method to determine analyte intensity in the presence of background fluorescence. In contrast to previous work, however, ⁇ B now appears in the formulas and must be measured explicitly or implicitly.
  • the apparatus, methods, and compositions of matter provided by the invention also can be used to correct for modifications in analyte signal from scattering, abso ⁇ tion, and other modulators, including background, through use of a reference compound. These modifications may affect intensity and polarization, among others.
  • the compositions of matter provided by the invention may include first and second luminophores having emission spectra that overlap significantly, but luminescence emissions that may be resolved using lifetime-resolved methods.
  • the first and second luminophores may include an analyte and a reference compound.
  • the analyte may be designed to participate in an assay
  • the reference compound may be designed to participate in an assay
  • the reference compound may be designed to be inert and constant from assay to assay.
  • the apparatus provided by the invention may include a stage, light source, detector, processor, and first and second optical relay structures. These components are substantially as described above, especially in supporting and inducing an emission from a composition, and in detecting and converting the emission to a signal.
  • the emission may include fluorescence or phosphorescence.
  • the processor may use information in the signal to determine the intensity of the light emitted by the analyte and the intensity of the light emitted by the reference compound.
  • the analyte and reference compound have luminescence lifetimes that are resolvable by lifetime-resolved methods, so that the intensities of the analyte and reference compound may be determined using lifetime-resolved methods. These methods may include frequency-domain methods, such as those described above for distinguishing analyte and background.
  • a signal modulator such as scattering or abso ⁇ tion
  • the apparent intensity I c ' of light detected from a composition will equal the product of a transmission factor T and the true intensity I c of the light emitted from the composition.
  • the transmission factor may include contributions from changes in the excitation light and changes in the emission light.
  • the transmission factor typically (but not always) will range from zero to one.
  • the apparent intensity of the composition will equal the product of the transmission factor and the sum of the true intensity I A of the analyte and the true intensity I R of the reference compound.
  • V T - . + I r ) (65)
  • the apparent intensity I a ' of the analyte will equal the apparent intensity of the composition minus the apparent intensity of the reference compound.
  • the apparent intensity I r ' of the reference compound will equal the apparent intensity of the composition minus the apparent intensity of the analyte.
  • intensities may be computed using LDI or LRI methods, among others.
  • a typical experiment may include a short-lifetime analyte and a long-lifetime reference compound, although other combinations also may be used.
  • the apparent intensity of the analyte may be calculated using Equation 22, where the reference compound effectively is treated as long-lifetime background.
  • the processor also uses information in the signal to calculate a quantity that expresses the intensity of the analyte as a function of the intensity of the reference compound. This quantity may be a ratio of the intensity of the analyte to the intensity of the reference compound, among others.
  • the processor also is capable of discriminating between the light emitted by the analyte, the light emitted by a reference compound, and a background, if all three have different lifetimes, using the dual-frequency lifetime-resolved methods described above (e.g., Equation 25).
  • the methods provided by the invention may include various steps, including (1) providing a composition that includes the analyte and a reference compound, (2) illuminating the composition, so that light is emitted by the analyte and reference compound, (3) detecting the light emitted by the analyte and reference compound and converting it to a signal, (4) processing the signal to determine the intensity of the light emitted by the analyte and the intensity of the light emitted by the reference compound, and (5) calculating a quantity that expresses the intensity of the analyte as a function of the intensity of the light emitted by the reference compound.
  • the methods also may include additional or alternative steps. The methods may be practiced using the apparatus described above.
  • the invention may handle a variety of analytes, reference compounds, and backgrounds.
  • the excitation and emission spectra of the reference compound should be the same as the excitation and emission spectra of the analyte, so that the intensity of the reference compound will be modulated by the same amount as the intensity of the analyte.
  • the lifetime of the reference compound should be significantly larger or significantly smaller than the lifetime of the analyte, and the lifetimes of the reference compound and analyte should be greater than the lifetime of the background.
  • the specific lifetime of the background should be confined to a range. These conditions apply for most assays of commercial interest; for example, in most high-throughput assays, the background from the microplate and assay components is under 10 nanoseconds. These are preferred conditions; because the lifetime-resolved methods described above are so sensitive, the composition actually need include only a small amount of the reference compound (roughly 2% of the total intensity), and the lifetimes of analyte, reference compound, and background can be reasonably similar.
  • the reference compound may be associated with the composition using a variety of mechanisms.
  • the reference compound may be associated with the composition directly, for example, by dissolving or suspending (e.g., as a micelle) the reference compound in the composition.
  • the reference compound also may be associated with the composition indirectly, for example, by inco ⁇ orating the reference compound into or onto beads, other carriers, or sample containers associated with the composition.
  • the carriers may be suspended in the composition or allowed to sink to the bottom of the sample container holding the composition.
  • the carriers also may be attached to the walls or bottom of the sample container, for example, by chemical linkages such as biotin-streptavadin.
  • the carriers also may be rendered magnetic, so that they may be pulled to one part of the sample container (e.g., a side or bottom) to permit the composition to be analyzed with and without the reference compound.
  • Associating the reference compound with the sample container also has a number of advantages.
  • the reference compound may be layered onto the surface of the sample container, or formed into the plastic or other material used to form the sample container.
  • Such approaches eliminate the need to add the reference compound to the composition, and they may prevent the reference compound from interacting with components of the composition and affecting the associated assay.

Abstract

L'invention concerne des procédés et un dispositif servant à détecter une hybridation de polynucléotides dans des techniques à luminescence. Les procédés peuvent comprendre (1) une hybridation spécifique d'allèle utilisant une détection par luminescence, (2) une ligature d'oligonucléotides spécifique d'allèle utilisant une ligature d'oligonucléotides marqués à l'aide d'un colorant avec détection de transfert d'énergie de résonance de luminescence (FRET), et (3) une incorporation de nucléotides spécifique d'allèle utilisant une extension d'amorce avec détection de polarisation de luminescence (FP). Plus spécifiquement, les procédés peuvent comporter les étapes consistant à : (1) placer un échantillon contenant un matériel d'acides nucléiques sur un site d'examen, (2) éclairer l'échantillon, (3) détecter la lumière émise par l'échantillon, et (4) déterminer la présence, l'absence, et/ou l'identité d'une acide nucléique voulu dans l'échantillon au moyen de la lumière émise par l'échantillon.
PCT/US2000/006841 1997-09-20 2000-03-15 Procedes et dispositif servant a detecter des polymorphismes d'acides nucleiques WO2000055372A1 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU37488/00A AU3748800A (en) 1999-03-16 2000-03-15 Methods and apparatus for detecting nucleic acid polymorphisms
US09/770,720 US20010046673A1 (en) 1999-03-16 2001-01-25 Methods and apparatus for detecting nucleic acid polymorphisms
US10/445,292 US6992761B2 (en) 1997-09-20 2003-05-22 Broad range light detection system

Applications Claiming Priority (18)

Application Number Priority Date Filing Date Title
US12468699P 1999-03-16 1999-03-16
US60/124,686 1999-03-16
US12534699P 1999-03-19 1999-03-19
US60/125,346 1999-03-19
PCT/US1999/008410 WO1999054711A1 (fr) 1998-04-17 1999-04-16 Dispositifs de maintien d'echantillons et systemes
USPCT/US99/08410 1999-04-16
US13528499P 1999-05-21 1999-05-21
US60/135,284 1999-05-21
US34973399A 1999-07-08 1999-07-08
US09/349,733 1999-07-08
PCT/US2000/000895 WO2000042209A1 (fr) 1999-01-15 2000-01-14 Procede et dispositif de detection de l'hybridation de polynucleotides
USPCT/US00/00895 2000-01-14
US09/494,407 US6297018B1 (en) 1998-04-17 2000-01-28 Methods and apparatus for detecting nucleic acid polymorphisms
US09/494,407 2000-01-28
US18471900P 2000-02-24 2000-02-24
US60/184,719 2000-02-24
US18492400P 2000-02-25 2000-02-25
US60/184,924 2000-02-25

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WO2003083447A1 (fr) * 2002-03-22 2003-10-09 Diversa Corporation Procede d'intensification de la detection optique d'echantillons contenus en solution dans des puits traversants d'un plateau de reception
EP2012125A1 (fr) 2000-04-28 2009-01-07 MDS Analytical Technologies (US) Inc. Analyses de modification moléculaire
EP2270205A3 (fr) * 2003-10-20 2011-03-02 Isis Innovation Ltd Procédé de séquençage d'acide nucléique
US8669056B2 (en) 2002-12-31 2014-03-11 Cargill Incorporated Compositions, methods, and systems for inferring bovine breed
WO2016120494A1 (fr) * 2015-01-30 2016-08-04 Norwegian University Of Life Sciences Procédé et produit de prévention des faux positifs dans des procédés utilisant des ddntp
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EP2012125A1 (fr) 2000-04-28 2009-01-07 MDS Analytical Technologies (US) Inc. Analyses de modification moléculaire
EP1291625A1 (fr) * 2001-09-07 2003-03-12 Wallac Oy Dispositif perfectionné pour la mesure optique d'échantillons
US6822741B2 (en) 2001-09-07 2004-11-23 Wallac Oy Optical instrument and process for measurement of samples
WO2003083447A1 (fr) * 2002-03-22 2003-10-09 Diversa Corporation Procede d'intensification de la detection optique d'echantillons contenus en solution dans des puits traversants d'un plateau de reception
US9206478B2 (en) 2002-12-31 2015-12-08 Branhaven LLC Methods and systems for inferring bovine traits
US8669056B2 (en) 2002-12-31 2014-03-11 Cargill Incorporated Compositions, methods, and systems for inferring bovine breed
US9982311B2 (en) 2002-12-31 2018-05-29 Branhaven LLC Compositions, methods, and systems for inferring bovine breed
US10190167B2 (en) 2002-12-31 2019-01-29 Branhaven LLC Methods and systems for inferring bovine traits
US11053547B2 (en) 2002-12-31 2021-07-06 Branhaven LLC Methods and systems for inferring bovine traits
EP2270205A3 (fr) * 2003-10-20 2011-03-02 Isis Innovation Ltd Procédé de séquençage d'acide nucléique
WO2016120494A1 (fr) * 2015-01-30 2016-08-04 Norwegian University Of Life Sciences Procédé et produit de prévention des faux positifs dans des procédés utilisant des ddntp
CN111492223A (zh) * 2017-12-29 2020-08-04 豪夫迈·罗氏有限公司 组织样品制备系统
CN111492223B (zh) * 2017-12-29 2023-07-25 豪夫迈·罗氏有限公司 组织样品制备系统

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