Patents Represented by Attorney, Agent or Law Firm Paul D. Grossman
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Patent number: 5942609Abstract: The present invention concerns methods of assembly of a polynucleotide on a solid-support by performing steps of annealing, ligation, and extension. The steps may be repeated in a cyclical manner to assemble immobilized double- or single-stranded polynucleotides with functional gene properties. The immobilized polynucleotides may be amplified by the polymerase chain reaction, and detected and quantitated by an exonuclease assay with a self-quenching, fluorescent probe. The polynucleotide may be cleaved from the solid-support by chemical or enzymatic cleavage.Type: GrantFiled: November 12, 1998Date of Patent: August 24, 1999Assignee: The Porkin-Elmer CorporationInventors: Michael W. Hunkapiller, Andrew C. Hiatt
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Patent number: 5936087Abstract: Dibenzorhodamine compounds having the structure ##STR1## are disclosed, including nitogen- and aryl-substituted forms thereof. In addition, two intermediates useful for synthesizing such compounds are disclosed, a first intermediate having the structure ##STR2## including nitrogen- and aryl-substituted forms thereof, and a second intermediate having the structure ##STR3## including nitrogen- and aryl-substituted forms thereof, wherein substituents at positions C-14 to C18 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl, carboxylic acid, sulfonic acid, --CH.sub.2 OH, alkoxy, phenoxy, linking group, and substituted forms thereof. The invention further includes energy transfer dyes comprising the dibenzorhodamine compounds, nucleosides labeled with the dibenzorhodamine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.Type: GrantFiled: November 25, 1997Date of Patent: August 10, 1999Assignee: The Perkin-Elmer CorporationInventors: Scott C. Benson, Joe Y. L. Lam, Steven Michael Menchen
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Patent number: 5916426Abstract: The invention provides uncharged water-soluble silica-adsorbing polymers for suppressing electroendoosmotic flow and to reduce analyte-wall interactions in capillary electrophoresis. In one aspect of the invention, one or more of such polymers are employed as components of a separation medium for the separation of biomolecules, such as polynucleotides, polysaccharides, proteins, and the like, by capillary electrophoresis. Generally, such polymers are characterized by (i) water solubility over the temperature range between about 20.degree. C. to about 50.degree. C., (ii) concentration in a separation medium in the range between about 0.001% to about 10% (weight/volume), (iii) molecular weight in the range of about 5.times.10.sup.3 to about 1.times.10.sup.6 daltons, and (iv) absence of charged groups in an aqueous medium having pH in the range of about 6 to about 9.Type: GrantFiled: August 19, 1997Date of Patent: June 29, 1999Assignee: The Perkin-Elmer CorporationInventors: Ramakrishna S. Madabhushi, Steven M. Menchen, J. William Efcavitch, Paul D. Grossman
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Patent number: 5891313Abstract: A capillary electrophoresis system and method of electrokinetically loading a capillary electrophoresis sample into a separation medium in a capillary tube in which an entangled polymer matrix is formed having the sample embedded therein. The matrix has a mesh size effective to retard movement of macromolecules such as DNA sequencing templates through the matrix when an electric field is applied across the matrix. The entangled polymer matrix is formed by a linear polymer having a molecular weight of at least 20K Daltons. Furthermore, the invention includes stable denaturants useful for the electrophoresis of nucleic acids.Type: GrantFiled: November 8, 1995Date of Patent: April 6, 1999Assignee: The Perkin-Elmer Corp.Inventors: Ben F. Johnson, Steven M. Menchen, Will Bloch
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Patent number: 5873052Abstract: Methods for assigning a quantitative score to the relatedness of aligned polymorphic biopolymer sequences such that small differences between otherwise identical sequences are highlighted are disclosed, including computer systems and program storage devices for carrying out the methods on a computer. Specifically, the methods of the invention comprise the steps of providing a test sequence and a basis set of sequences such that the test sequence and the basis set of sequences are aligned; determining the identity of a monomer unit at a position m in the test sequence; assigning a value of 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence matches any members of the basis set at position m, or, assigning a value of between 0 and 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence does not match any members of the basis set at position m.Type: GrantFiled: November 6, 1996Date of Patent: February 16, 1999Assignee: The Perkin-Elmer CorporationInventor: Muhammad A. Sharaf
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Patent number: 5866429Abstract: Solvents for salt-gradient anion-exchange separation of nucleic acids, especially double-stranded DNA and especially by liquid chromatography, are improved by replacing NaCl as the eluting salt with any of a wide range of alkyl ammonium salts and can be used to elute nucleic acids in strict order of increasing length, with reduced sensitivity to elution temperature and salt concentration. Anion-exchange chromatography with these solvents is well suited for identification of DNA fragments on the basis of size, with greater accuracy, precision, and resolvable size range than often is possible with gel electrophoresis.Type: GrantFiled: August 16, 1995Date of Patent: February 2, 1999Inventor: Will Bloch
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Patent number: 5856192Abstract: Solvents for salt-gradient anion-exchange separation of nucleic acids, especially double-stranded DNA and especially by liquid chromatography, are improved by replacing NaCl as the eluting salt with any of a wide range of alkyl ammonium salts and can be used to elute nucleic acids in strict order of increasing length, with reduced sensitivity to elution temperature and salt concentration. Anion-exchange chromatography with these solvents is well suited for identification of DNA fragments on the basis of size, with greater accuracy, precision, and resolvable size range than often is possible with gel electrophoresis.Type: GrantFiled: January 23, 1996Date of Patent: January 5, 1999Assignee: The Perkin-Elmer CorporationInventor: Will Bloch
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Patent number: 5847162Abstract: A class of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structure ##STR1## wherein R.sub.1 -R.sub.6 are hydrogen, fluorine, chlorine, lower alkyl lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, lining group, or combinations thereof or, when taken together, R.sub.1 and R.sub.6 is benzo, or, when taken together, R.sub.4 and R.sub.5 is benzo; Y.sub.1 -Y.sub.4 are hydrogen or lower alkyl or, when taken together, Y.sub.1 and R.sub.2 is propano and Y.sub.2 and R.sub.1 is propano, or, when taken together, Y.sub.3 and R.sub.3 is propano and Y.sub.4 and R.sub.4 is propano; and X.sub.1 -X.sub.3 taken separately are selected from the group consisting of hydrogen, chlorine, fluorine, lower alkyl carboxylate, sulfonic acid, --CH.sub.2 OH, and linking group. In another aspect, the invention includes reagents labeled with the 4,7-dichlororhodamine dye compounds, including deoxynucleotides, dideoxynucleotides, and polynucleotides.Type: GrantFiled: June 27, 1996Date of Patent: December 8, 1998Assignee: The Perkin Elmer CorporationInventors: Linda Lee, Scott C. Benson, Barnett B. Rosenblum, Sandra L. Spurgeon
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Patent number: 5843656Abstract: Cloning systems useful for the isolation of recombinant nucleic acid are disclosed in which the recombination of cloning-system nucleic acid and foreign nucleic acid is linked to the expression of a moiety on the surface of a host organism, the moiety being a first member of a binding pair. When recombination occurs between the nucleic acid and the foreign nucleic acid, the moiety is expressed on the surface of the host organism. The isolation of recombinant nucleic acid is then performed by attaching a second member of the binding pair to a solid support and contacting the host organism with the support. When the first member of the binding pair is expressed on the surface of the host organism, the host organism binds to the second member of the binding pair attached to the solid support, thereby selectively isolating those organisms.Type: GrantFiled: August 7, 1995Date of Patent: December 1, 1998Assignee: The Perkin-Elmer CorporationInventors: John A. Bridgham, John Brandis, John Leong, Paul D. Hoeprich, Jr.
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Patent number: 5840999Abstract: A class of asymmetric monobenzoxanthene compounds useful as fluorescent dyes are disclosed having the structure ##STR1## wherein Y.sub.1, and Y.sub.2 are individually hydroxyl, amino, imminium, or oxygen, R.sub.1 -R.sub.8 are hydrogen, fluorine, chlorine, alkyl alkene, alkyne, sulfonate, amino, amido, nitrile, alkoxy, linking group, and combinations thereof, and R.sub.9 is acetylene, alkane, alkene, cyano, substituted phenyl and combinations thereof The invention ftrther includes novel intermediate compounds useful for the synthesis of asymmetric benzoxanthene compounds having the general structure ##STR2## where substituents R.sub.3 -R.sub.7 correspond to like-referenced substituents in the structure of described above, and Y.sub.2 is hydroxyl or amine. In another aspect, the invention includes methods for synthesizing the above dye compounds and intermediates.Type: GrantFiled: March 26, 1997Date of Patent: November 24, 1998Assignee: The Perkin-Elmer CorporationInventors: Scott C. Benson, Steven M. Menchen, Peter D. Theisen, Kevin M. Hennessey, Vergine C. Furniss, Joan Hauser
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Patent number: 5833826Abstract: An electrophoresis system including means for reducing the distortion of a sample zone eluting from a capillary electrophoresis separation capillary is disclosed. The system includes one or more separation capillaries, each separation capillary having an inlet end and an outlet end; a first electrode in electrical communication with the inlet ends of the separation capillaries; a second electrode in electrical communication with the outlet ends of the separation capillaries; and one or more focusing electrodes in electrical communication with the outlet ends of the separation capillaries. In operation, the voltage of each of the electrodes is adjusted such that (i) the sample zone is transported from the inlet end to the outlet end of the separation capillaries and (ii) the distortion of the sample zone eluting from the separation capillaries is reduced.Type: GrantFiled: December 13, 1996Date of Patent: November 10, 1998Assignee: The Perkin-Elmer CorporationInventor: Eric S. Nordman
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Patent number: 5821356Abstract: Propargylethoxyamino nucleosides are disclosed having the structure ##STR1## wherein R.sub.1 and R.sub.2 are --H, lower alkyl, or label; B is a 7-deazapurine, purine, or pyrimidine nucleoside base; W.sub.1 is --H or --OH; W.sub.2 is --OH or a moiety which renders the nucleoside incapable of forming a phosphodiester bond at the 3'-position; and W.sub.3 is --PO.sub.4, --P.sub.2 O.sub.7, --P.sub.3 O.sub.10, phosphate analog, or --OH. Additionaly, a primer extension method is provided employing the above propargylethoxyamino nucleosides.Type: GrantFiled: August 13, 1996Date of Patent: October 13, 1998Assignee: The Perkin Elmer CorporationInventors: Shaheer H. Khan, Steven M. Menchen, Barnett B. Rosenblum
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Patent number: 5798032Abstract: Methods and apparatus are disclosed for improved mapping and sequencing of carbohydrate polymers. In one aspect, the improvement includes a means for coupling two capillary electrophoresis (CE) tubes in such a way so as to (i) efficiently transfer a selected sample component from a first CE capillary to a second CE capillary or, (ii) introduce a supplementary reagent into the separation path between the two capillaries, e.g., an internal standard, binding agent, enzyme, and the like. In an additional aspect, the invention includes improved apparatus and methods for electrophoresis of labeled carbohydrates in which a sample carbohydrate labeled with a first label is separated by CE and its migration behavior is compared with an internal standard labeled with one or more second labels which are distinguishable from the first label.Type: GrantFiled: November 13, 1995Date of Patent: August 25, 1998Assignee: The Perkin-Elmer CorporationInventors: Shaheer H. Khan, Roger A. O'Neill, Louis B. Hoff
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Patent number: 5750346Abstract: Cloning systems useful for the isolation of recombinant nucleic acid are disclosed in which the recombination of cloning-system nucleic acid and foreign nucleic acid is linked to the expression of a moiety on the surface of a host organism, the moiety being a first member of a binding pair. When recombination occurs between the nucleic acid and the foreign nucleic acid, the moiety is expressed on the surface of the host organism. The isolation of recombinant nucleic acid is then performed by attaching a second member of the binding pair to a solid support and contacting the host organism with the support. When the first member of the binding pair is expressed on the surface of the host organism, the host organism binds to the second member of the binding pair attached to the solid support, thereby selectively isolating those organisms. Other aspects of the invention include devices for the isolation of individual cells that differentially express binding moieties on their surface.Type: GrantFiled: August 7, 1996Date of Patent: May 12, 1998Assignee: The Perkin-Elmer CorporationInventors: John A. Bridgham, John Brandis, John Leong, Paul D. Hoeprich, Jr., Charles L. Sloan, Roger A. O'Neill, Charles Andre
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Patent number: 5748491Abstract: An improved signal processing method in a signal processor for performing the deconvolution of a signal resulting from an analytical separation process is disclosed. In a first aspect, a signal representing a plurality of partially separated sample zones is measured, a point-spread-function of the signal is determined, and the Fourier transform of the signal and the point-spread-function is taken. Next, a noise component n of the signal is determined and the value of a result signal A(f) is calculated using the following filter ##EQU1## where D(f) is the Fourier transform of the signal, P(f) is the Fourier transform of the point-spread-function, and P*(f) is the complex conjugate of P(i). Finally, the inverse Fourier transform of the result A(f) is taken and reported as A(t). Preferably, the point-spread function is a Gaussian function having a standard deviation .sigma., where .sigma. is determined using either an .alpha..beta. tracker or the function .sigma.=(a+bt.sup.2).sup.Type: GrantFiled: December 20, 1995Date of Patent: May 5, 1998Assignee: The Perkin-Elmer CorporationInventors: Daniel B. Allison, James O. Bowlby, Jr.
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Patent number: 5736626Abstract: The compounds of the invention are exemplified by the class of diglycolate synthesis supports particularly useful as support reagents for the direct synthesis of 3'-labeled polynucleotides. Generally, the compounds of the invention have the structure ##STR1## where T is an acid-cleavable hydroxyl protecting group, e.g., 4,4'-dimethoxytrityl; L.sub.1 is a linker for connecting a 3'-terminal nitrogen to carbon; L.sub.2 and L.sub.3 are linkers for connecting oxygen and carbon; W is a solid support, e.g., CPG or polystyrene; L.sub.4 is a linker for connecting the solid support to nitrogen; R.sub.1 and R.sub.2 are nitrogen substituents, e.g., hydrogen, lower alkyl, nitrogen protecting group, or label; and R.sub.3 through R.sub.7 are carbon substituents, e.g., hydrogen or lower alkyl. In a first particularly preferred embodiment, the synthesis supports of the invention are exemplified by compounds having the structure ##STR2## where DMT is 4,4'-dimethoxytrityl and W is polystyrene.Type: GrantFiled: January 29, 1996Date of Patent: April 7, 1998Assignee: The Perkin-Elmer CorporationInventors: Khairuzzaman Bashar Mullah, William A. Andrus
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Patent number: 5691146Abstract: An oligonucleotide probe is disclosed, the probe including an oligonucleotide, a fluorescer molecule attached to a first end of the oligonucleotide and a quencher molecule attached to the opposite end of the oligonucleotide. The probe is rendered impervious to digestion by the 5'.fwdarw.3' exonuclease activity of a polymerase and the 3'.fwdarw.5' extension of by a polymerase. The invention also includes methods for performing combined PCR amplification and hybridization probing, one such method including the steps of contacting a target nucleic acid sequence with PCR reagents and an oligonucleotide probe as described above, and subjecting these reagents to thermal cycling. One preferred refinement of the above method further includes the addition of a strand displacer to facilitate amplification. Additional similar combined PCR hybridization methods are disclosed, such methods not requiring probes having their 5' ends protected, wherein (i) the polymerase lacks 5'.fwdarw.3' exonuclease activity, (ii) a 5'.Type: GrantFiled: September 11, 1996Date of Patent: November 25, 1997Assignee: The Perkin Elmer CorporationInventor: Paul E. Mayrand
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Patent number: 5656034Abstract: A syringe pump particularly adapted for delivery of small volumes at a high pressure in an accurate and reproducible manner. The syringe pump includes a frame, a motor attached to the frame, and a lead screw drivably connected to the motor. A cover seal is mounted to the front end of the lead screw, the cover seal having grooves formed therein to facilitate mounting and demounting of the cover seal. The pump further includes a cylindrical barrel within which the cover seal reciprocates, the barrel being made of a ceramic material, wherein the barrel is fixedly attached to the frame at the front end and floatably mounted to the frame at the back end. A barrel head is mounted to the front end of the barrel for closing off that end of the barrel, the barrel head including an outlet port for allowing fluid to enter and exit the barrel. In addition, the present invention includes a multi-syringe gradient syringe pump, a liquid chromatography system, a cover seal, and a mixer for mixing multiple flow streams.Type: GrantFiled: March 31, 1995Date of Patent: August 12, 1997Inventors: Michael L. Kochersperger, Reid B. Kowallis, Andrew A. Pham
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Patent number: 5653259Abstract: A manifold block and valving system using the manifold block are provided, which are used for conducting chemical reagents, solvents, and other fluids. The manifold block includes a "straight-through" common passage in fluid connection with several entry ports, including also a number of projections in the common passage in the vicinity of the entry ports. These projections partially obstruct the fluid flow, causing a turbulence that provides a washing action in those port regions. The manifold may be constructed of a photosensitive glass ceramic such as Fotoceram.TM. which consists of a number of layers which have been processed to form the manifold block, or of other suitable materials such as silicon.Type: GrantFiled: October 6, 1995Date of Patent: August 5, 1997Assignee: Applied Biosystems, Inc.Inventor: Paul O. Ramstad
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Patent number: 5624800Abstract: Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieving medium.Type: GrantFiled: May 19, 1995Date of Patent: April 29, 1997Assignee: The Perkin-Elmer CorporationInventors: Paul D. Grossman, Steven Fung, Steven M. Menchen, Sam L. Woo, Emily S. Winn-Deen