Abstract: A nucleoside/tide compound having the structure NUC-L-S-LB/LG is described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nucleoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.

Abstract: A multi-channel capillary electrophoresis apparatus is disclosed. The apparatus includes a capillary array assembly comprising a plurality of capillaries, each capillary having a capillary outlet, and an outlet support for supporting the capillary outlets. The apparatus further includes a cuvette defining a receiving slot, a gap region, and a detection zone, where the receiving slot is adapted to removably receive the outlet support, and wherein when the outlet support is inserted into the receiving slot, the capillary outlets are positioned in the gap region in proximity to the detection zone, and a flow channel is formed by the outlet support and the receiving slot such that the flow channel is in fluid communication with the gap region. In addition, the apparatus includes a front plumbing block in fluid communication with the flow channel for supplying a fluid flow through the gap region sufficient to transport material downstream from the capillary outlets to the detection zone.

Abstract: An electrophoretic method for purifying a nucleic acid sample is disclosed. The method generally comprises the steps of (1) providing a nucleic acid sample comprising a desired nucleic acid and one or more contaminants, (2) providing an electrophoresis matrix having a loading well and a recovery well formed therein, (3) placing the nucleic acid sample into the loading well, (4) performing a first electrophoresis comprising electrophoresing the nucleic acid sample for a first time effective to transport the desired nucleic acid out of the loading well and into the electrophoresis matrix; and (5) performing a second electrophoresis comprising electrophoresing the nucleic acid sample for a second time effective to transport the desired nucleic acid out of the electrophoresis matrix and into the recovery well.

Abstract: A sample handling system in a multi-channel capillary electrophoresis apparatus is disclosed. The sample handling system includes a work surface for supporting a plurality of samples located at a plurality of work surface coordinates and a sample loading assembly comprising a plurality of loading wells. At least one of the loading wells includes a capillary fixedly positioned therein. The system further includes a programmable sample transfer device for automatically transferring a sample from a work surface coordinate to a loading well. The invention further includes methods for using the sample handling system.

Abstract: 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 dibenzorhodarnine compounds, and nucleic acid analysis methods employing the dibenzorhodamine compounds.

Abstract: A method for typing HLA class 1 genes. The method entails first contacting a sample DNA with first and second amplification primers, wherein the first and second primers are each at least partially located in an exonic region. Next, using the first and second primers, a target sequence is amplified by the PCR to form an amplicon of the target sequence. Finally, the amplicon is detected with a sequence-specific detection means, e.g., DNA sequencing. The invention also includes specific amplification primers, specific sequencing primers, and kits especially adapted for use with the above HLA typing method.

Abstract: 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.

Abstract: A nucleoside/tide compound having the structureNUC--L--S--LB/LGis described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure ##STR1## wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nucleoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.

Abstract: A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures ##STR1## wherein R.sub.1 -R.sub.6 are hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrite, lower alkoxy, linking group, 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; R.sub.7 -R.sub.10, R.sub.12 -R.sub.16 and R.sub.18 may be hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrite, lower alkoxy, linking group; R.sub.11 and R.sub.17 may be hydrogen, lower alkyl, lower alkene, lower alkyne, phenyl, aryl, linking group; Y.sub.1 -Y.sub.4 are hydrogen, lower alkyl, or cycloalkyl, or, when taken together, Y.sub.1 and R.sub.2, Y.sub.2 and R.sub.1 Y.sub.3 and R.sub.3, and/or Y.sub.4 and R.sub.4 is propano, ethano, or substituted forms thereof, and X.sub.1 -X.sub.

Abstract: Dibenzorhodamine compounds having the structure ##STR1## are disclosed, including nitogen- and aryl-substituted forms thereof. In addition, intermediates useful for synthesizing such compounds are disclosed, such intermediates having the structure ##STR2## In Formula I, R.sub.1 is H or ##STR3## wherein Y is H, lower alkyl, lower alkene, lower alkyne, aromatic, phenyl, polycyclic aromatic, heterocycle, water-solubilizing group, or linking group, including substituted forms thereof. When R.sub.1 is H, the C-12-bonded nitrogen and the C-12 and C-13 carbons form a first ring structure having from 4 to 7 members, and/or the C-12-bonded nitrogen and the C-11 and C-12 carbons form a second ring structure having from 5 to 7 members. The compounds of Formula I further include aryl- and nitrogen-substituted forms thereof.

Abstract: 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.

Abstract: A data collection method for scanning a scan window comprising one or more channels is described. In the method of the invention an integrated signal (S) is measured across a scan window including one or more channels using an integrating detector. Next, a velocity-normalized integrated signal (Sn) is determined based on the integrated signal (S) and a scan velocity.

Abstract: 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, linking 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, Y.sub.2 and R.sub.1 Y.sub.3 and R.sub.3, or Y.sub.4 and R.sub.4 is propano, ethano, or substituted forms thereof, 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.

Abstract: 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 further 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.

Abstract: A chain-termination type DNA sequencing method is disclosed wherein deoxynucleotide 2'-deoxythymidine-5'-triphosphate is replaced by 2'-deoxyuridine-5'-triphosphate, or analogs thereof Kits for performing the method are also provided.

Abstract: A signal processing method in a processor is provided for performing a multicomponent analysis of a signal resulting from a spectral response of a mixture comprising a plurality of spectrally resolvable molecular species. The method provides both a determination of a concentration estimate and a statistical confidence interval for each species. In the method, a data vector d is received from a multichannel detector, data vector d having a length n.sub.c, n.sub.c being the number of detector channels being monitored. A calibration matrix K having n.sub.c rows and n.sub.p columns is provided wherein n.sub.c is larger than n.sub.p, n.sub.p being the number of spectrally resolvable molecular species. Next, a concentration estimate vector c having length n.sub.p is determined. Finally, a confidence interval CI.sub.i for each of the elements of the concentration estimate vector is determined according to the expressionCI.sub.i =c.sub.i .+-.(varcovar(c.sub.ii)).sup.1/2 Q.sub.

Abstract: A class of aromatic-substituted xanthene compounds useful as fluorescent dyes is disclosed, the compounds having the general structure where Y.sub.1 and Y.sub.2 taken separately are selected from the group consisting of hydroxyl, oxygen, imminium, linking group and amine, or Y.sub.1 taken together with R.sub.2 is cyclic imine, or Y.sub.2 taken together with R.sub.3 is cyclic amine; R.sub.2, R.sub.3, R.sub.5, and R.sub.7 taken separately are selected from the group consisting of hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, imminium, amido, nitrile, lower alkoxy, phenyl, and linking group; R.sub.1 taken separately is selected from the group consisting of phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, linking group and electron-rich heterocycle, or when taken together with R.sub.7 is selected from the group consisting of electron-rich heterocycle and indene; R.sub.

Abstract: 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-sieiving medium.

Abstract: A nucleoside/tide compound having the structureNUC--L--S--LB/LGis described wherein NUC is a nucleoside/tide having a nucleobase portion B, L is a rigid linkage, S is a spacer; and LB/LG is a member of a linkage pair or a label. NUC is attached to L through B such that when B is a purine, L is attached to the 8-position of the purine, when B is 7-deazapurine, L is attached to the 7-position of the 7-deazapurine, and when B is pyrimidine, L is attached to the 5-position of the pyrimidine. In an important aspect of the invention, L has the structure ##STR1## wherein each of n, o and p are integers ranging from 0 to 3, and the sum of n, o and p is at least 2, and each of W, X, Y and Z is selected from the group consisting of carbon and nitrogen. The invention further includes polynucleotide compounds comprising the nuclcoside/tide, and primer extension methods utilizing the nucleoside/tide, particularly when used in combination with certain mutant polymerase enzymes.

Abstract: In a first aspect, the method of the invention includes the steps of annealing a primer to a target nucleic acid; performing a first primer extension reaction using a first primer extension reagent; separating the target-primer hybrid and unreacted first primer extension reagent; performing a second primer extension reaction using a second primer extension reagent, wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto; separating the target-primer hybrid from unreacted second primer extension reagent; measuring a signal produced by the label; treating the label so as to render the label undetectable; and repeating the above steps until the signal is substantially less than a signal detected in a previous cycle.