Methods and apparatus for analyzing polynucleotide sequences

Abstract

Methods for high speed, high throughput analysis of polynucleotide sequences, and apparatuses with which to carry out the methods are provided in the invention.

1 . A method of obtaining nucleotide sequence information for a target nucleic acid molecule having a plurality of nucleotide bases, said method comprising: 
 providing a single complex of a nucleic acid polymerizing enzyme and the target nucleic acid molecule oriented with respect to each other in a position suitable to add a nucleotide analog at an active site complementary to the target nucleic acid, wherein the complex is immobilized to a solid support;    providing a plurality of types of nucleotide analogs proximate to the active site, each type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid and having a different detectable moiety, and polymerizing a nucleotide analog without a blocking substituent at the active site, wherein the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid, leaving the added nucleotide analog ready for subsequent addition of nucleotide analogs;    identifying the nucleotide analog added at the active site as a result of said polymerizing by detecting its detectable label, wherein said identifying is carried out by directing activating radiation to a region corresponding to the active site and detecting the detectable label from the nucleotide analog added to the active site by a technique which reduces background noise resulting from free unpolymerized nucleotide analogs; and    repeating, with the complex immobilized to the solid support, said providing a plurality of types of nucleotide analogs, said polymerizing, and said identifying, so that nucleotide analogs added at downstream active sites are identified and, as a result, nucleotide sequence information for the target nucleic acid is determined.    
     
     
         2 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is selected from the group consisting of a DNA polymerase, an RNA polymerase, reverse transcriptase, and mixtures thereof.  
     
     
         3 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is a thermostable polymerase.  
     
     
         4 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is a thermodegradable polymerase.  
     
     
         5 . A method according to  claim 1 , wherein the target nucleic acid molecule is selected from the group consisting of double-stranded DNA, single-stranded DNA, single stranded DNA hairpins, DNA/RNA hybrids, RNA with a recognition site for binding of the polymerase, and RNA hairpins.  
     
     
         6 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is bound to the target nucleic acid molecule complex at an origin of replication, a nick or gap in a double-stranded target nucleic acid, a secondary structure in a single-stranded target nucleic acid, a binding site created by an accessory protein, or a primed single stranded nucleic acid.  
     
     
         7 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is provided with one or more accessory proteins to modify its activity.  
     
     
         8 . A method according to  claim 7 , wherein the accessory protein is selected from the group consisting of a single-stranded binding protein, a primase, and helicase.  
     
     
         9 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is processive.  
     
     
         10 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme is non-processive.  
     
     
         11 . A method according to  claim 1 , wherein the nucleotide analogs are selected from the group consisting of a ribonucleotide, a deoxyribonucleotide, a modified ribonucleotide, and a modified deoxyribonucleotide.  
     
     
         12 . A method according to  claim 1  further comprising: 
 hybridizing an oligonucleotide primer to the target nucleic acid molecule prior to or during said providing a plurality of nucleotide analogs.    
     
     
         13 . A method according to  claim 12 , wherein the oligonucleotide primer comprises nucleotides selected from the group consisting of ribonucleotides, deoxyribonucleotides, modified ribonucleotides, and modified deoxyribonucleotides.  
     
     
         14 . (canceled)  
     
     
         15 . A method according to  claim 1 , wherein the label is selected from the group consisting of chromophores, fluorescent moieties, enzymes, antigens, heavy metals, dyes, phosphorescent groups, chemiluminescent moieties, scattering or fluorescent nanoparticles, and Raman signal generating moieties.  
     
     
         16 . A method according to  claim 1 , wherein the label is attached to the nucleotide analog at its gamma phosphate.  
     
     
         17 . A method according to  claim 1 , wherein the label is attached to the nucleotide analog with a linker.  
     
     
         18 . A method according to  claim 1 , wherein the label is attached to the nucleotide analog without a linker.  
     
     
         19 - 22 . (canceled)  
     
     
         23 . A method according to  claim 1 , wherein the detectable labels are enzymatically cleaved from the nucleotide analogs.  
     
     
         24 - 25 . (canceled)  
     
     
         26 . A method according to  claim 1 , wherein the labels for the different types of nucleotide analogs are distinguished by different properties due to the presence of base fluorophores, quenched fluorophores, or fluorogenic nucleotide analogs.  
     
     
         27 . A method according to  claim 1 , wherein the nucleic acid polymerizing enzyme carries a label and said identifying is carried out by detecting interaction between the label and the nucleotide analog.  
     
     
         28 . A method according to  claim 27 , wherein the label is a fluorescence resonance energy transfer donor or acceptor.  
     
     
         29 . (canceled)  
     
     
         30 . A method according to  claim 1 , wherein said identifying is carried out by optical procedures selected from the group consisting of far-field microspectroscopy, near-field microspectroscopy, evanescent wave or wave guided illumination, nanostructure enhancement, and combinations thereof.  
     
     
         31 . A method according to  claim 1 , wherein said identifying is carried out by utilizing single and/or multiphoton excitation, fluorescence resonance energy transfer, or photoconversion.  
     
     
         32 . A method according to  claim 1 , wherein said identifying is achieved by spectral wavelength discrimination, measurement and separation of fluorescence lifetimes, fluorophore identification and/or background suppression.  
     
     
         33 . A method according to  claim 32 , wherein fluorophore identification and/or background suppression utilizes switching between excitation modes and illumination sources, and combinations thereof  
     
     
         34 . A method according to  claim 1 , wherein said providing a complex comprises: 
 positioning either (1) an oligonucleotide primer or (2) the target nucleic acid molecule on the solid support;    hybridizing either (1) the target nucleic acid molecule to the positioned oligonucleotide primer or (2) an oligonucleotide primer to the positioned target nucleic acid molecule, to form a primed target nucleic acid molecule complex; and    providing the nucleic acid polymerizing enzyme on the primed target nucleic acid molecule complex in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site.    
     
     
         35 . (canceled)  
     
     
         36 . A method according to  claim 34 , wherein the solid support and either 1) the oligonucleotide primer or 2) the target nucleic acid molecule are bound reversibly or irreversibly with corresponding components of a covalent or noncovalent binding pair selected from the group consisting of an antigen-antibody binding pair, a streptavidin-biotin binding pair, photoactivated coupling molecules, and a pair of complementary nucleic acids.  
     
     
         37 . A method according to  claim 34 , wherein the oligonucleotide primer is positioned on the solid support and the target nucleic acid molecule is hybridized to the positioned oligonucleotide primer.  
     
     
         38 . A method according to  claim 34 , wherein the target nucleic acid molecule is positioned on the solid support and the oligonucleotide primer is hybridized to the positioned target nucleic acid molecule.  
     
     
         39 . A method according to  claim 1 , wherein said providing a complex comprises: 
 positioning, on the solid support, a double stranded nucleic acid molecule comprising the target nucleic acid and having a recognition site proximate the active site, and    providing the nucleic acid polymerizing enzyme on the target nucleic acid molecule in a position suitable to move along the target nucleic acid molecule.    
     
     
         40 . A method according to  claim 1 , wherein said providing a complex comprises: 
 positioning a nucleic acid polymerizing enzyme on the solid support in a position suitable for the target nucleic acid to move relative to the nucleic acid polymerizing enzyme.    
     
     
         41 . A method according to  claim 40 , wherein the solid support and the nucleic acid polymerizing enzyme are bound to each other reversibly or irreversibly with corresponding components of a covalent or non-covalent binding pair selected from the group consisting of an antigen-antibody binding pair, a streptavidin-biotin binding pair, photoactivated coupling molecules, and a pair of complementary nucleic acids.  
     
     
         42 . (canceled)  
     
     
         43 . A method according to  claim 1 , wherein the solid support on which the nucleic acid polymerizing enzyme or the target nucleic acid is positioned is a gel with pores.  
     
     
         44 - 48 . (canceled)  
     
     
         49 . A method according to  claim 1 , wherein said identifying is carried out in a nanostructure.  
     
     
         50 . A method according to  claim 49 , wherein the nanostructure is a punctuate, acicular, or resonant nanostructure which enhances said detecting.  
     
     
         51 . A method according to  claim 1 , wherein the confined region is defined by a microstructure.  
     
     
         52 . A method according to  claim 51 , wherein the microstructure comprises: 
 a plurality of channels to direct different nucleotide analogs to the confined region and    a discharge channel to permit materials to be removed from the confined region, and the nanostructure comprises:    a housing defining the confined region and constructed to facilitate said identifying.    
     
     
         53 . A method according to  claim 62 , wherein the technique which reduces background noise resulting from free unpolymerized nucleotide analogs comprises: 
 enhancing electromagnetic radiation proximate to a metal tip with a radius of curvature and which extends toward the complex at the active site.    
     
     
         54 . A method according to  claim 62 , wherein the technique which reduces background noise resulting from free unpolymerized nucleotide analogs comprises: 
 positioning the primed target nucleic acid molecule in near-field illumination of cavities.    
     
     
         55 . A method according to  claim 62 , wherein the technique which reduces background noise resulting from free unpolymerized nucleotide analogs comprises: 
 placing optical fibers proximate to the complex.    
     
     
         56 . A method according to  claim 62 , wherein the technique which reduces background noise resulting from free unpolymerized nucleotide analogs comprises: 
 utilizing time-gated delay of photon detection.    
     
     
         57 . A method according to  claim 1 , wherein said method is carried out by sequencing different target nucleic acid molecules at a plurality of different locations on an array.  
     
     
         58 . A method according to  claim 1 , wherein said method is carried out by simultaneously or sequentially sequencing the same target nucleic acid and combining output from such sequencing.  
     
     
         59 - 61 . (canceled)  
     
     
         62 . A method according to  claim 1 , wherein the technique which reduces background noise resulting from free unpolymerized nucleotide analogs is selected from the group consisting of: (1) electromagnetic field enhancement with electromagnetic radiation being enhanced proximate to a metal tip with a radius of curvature and which extends toward the complex at the active site; (2) near-field illumination of cavities in which the primed target nucleic acid molecule is positioned; (3) optical fibers proximate to the complex; and (4) time-gated delay of photon detection.  
     
     
         63 . A method according to  claim 1 , wherein nucleotide sequence information is simultaneously and independently determined for different target nucleic acid molecules in separate confined regions.  
     
     
         64 . A method according to  claim 1  wherein the label is attached to the nucleotide analog at its beta phosphate.