Abstract: The invention provides molecules and methods for nucleic acid synthesis reactions useful in sequencing-by-synthesis processes.

Abstract: The invention provides methods for correcting misincorporation of a nucleotide in a primer during a sequencing-by-synthesis reaction by using both a polymerase substantially lacking in exonuclease activity and an enzyme, preferably a polymerase, having exonuclease activity.

Abstract: In one aspect the invention relates to an apparatus for analyzing the presence of a single molecule using total internal reflection. In one embodiment an apparatus for single molecule analysis includes a support having a sample located thereon; two sources of light at distinct wavelengths, a collimator for directing the light onto the sample through a total internal reflection objective; a receiver for receiving a fluorescent emission produced by a single molecule in the sample in response to the light; and a detector for detecting each of the wavelengths in the fluorescent emission. In another embodiment the apparatus further comprises a focusing laser for maintaining focus of the objective on the sample.

Abstract: In one aspect the invention relates to an apparatus for analyzing the presence of a single molecule using total internal reflection. In one embodiment an apparatus for single molecule analysis includes a support having a sample located thereon; two sources of light at distinct wavelengths, a collimator for directing the light onto the sample through a total internal reflection objective; a receiver for receiving a fluorescent emission produced by a single molecule in the sample in response to the light; and a detector for detecting each of the wavelengths in the fluorescent emission. In another embodiment the apparatus further comprises a focusing laser for maintaining focus of the objective on the sample.

Abstract: The invention provides methods for sequencing a nucleic acid comprising stabilizing a primer/target nucleic acid duplex on a substrate. Methods of the invention generally contemplate the use of a dual-anchored primer/target nucleic acid duplex, or a stabilizing molecule in a single molecule sequencing reaction.

Abstract: The instant inventon provides methods and devices for detecting, enumerating and/or identifying small RNA molecules using single molecule sequencing techniques.

Abstract: Described herein is a mutant polymerase, specifically the Klenow exo? polymerase in which the proline at amino acid position 680 is replaced by a glycine (P680G), and its use in sequencing a single polynucleotide template using single molecule sequencing.

Abstract: In one aspect, the invention relates to an optical apparatus for producing light of a predetermined intensity from light sources of less than the predetermined intensity. In one embodiment the apparatus includes a first light source; a second light source; a double dove anti-Gaussian generator in optical communication with the first light source; and a compensator in optical communication with the second light source. Light from the first light source passes through the double dove anti-Gaussian generator and light from the second light source passes through the compensator, and are combined to produce a flattened Gaussian intensity distribution. In another aspect, the invention relates to a method and apparatus for separating an image into subunits and reading the separate subimages out of the detectors in parallel.

Abstract: In one aspect, the invention relates to an optical apparatus for producing light of a predetermined intensity from light sources of less than the predetermined intensity. In one embodiment the apparatus includes a first light source; a second light source; a double dove anti-Gaussian generator in optical communication with the first light source; and a compensator in optical communication with the second light source. Light from the first light source passes through the double dove anti-Gaussian generator and light from the second light source passes through the compensator, and are combined to produce a flattened Gaussian intensity distribution. In another aspect, the invention relates to a method and apparatus for separating an image into subunits and reading the separate subimages out of the detectors in parallel.

Abstract: The invention provides methods for improving the accuracy of a sequencing-by-synthesis reaction by sequencing at least a portion of a template and at least a portion of template complementary sequence.

Abstract: A hydrocarbyldithiomethyl-modified compound of the Formula: R1—O—CH2—S—S—R2 or a salt thereof wherein R1 is an organic molecule and R2 is a hydrocarbyl is useful for protecting and/or blocking hydroxyl groups in organic molecules such as nucleotides. The hydrocarbyldithiomethyl-modified compounds can also be used for chemically synthesizing oligonucleotides and for sequencing nucleic acid compounds.

Abstract: The present invention relates to apparatus, systems, and methods for analyzing biological samples. The apparatus, systems, and methods can involve using a vacuum source to pull microfluidic volumes through analytical equipment, such as flow cells and the like. Additionally, the invention involves using optical equipment in conjunction with the analytical equipment to analyze samples and control the operation thereof.

Abstract: A method of increasing the spatial uniformity of the detected intensity of a beam of light from a laser in a system including the laser and a light detector. In one embodiment the method includes the steps of generating a beam of light with the laser; and moving the beam of light and the light detector relative to each other, such that the detector averages the spatial intensity of the beam of light over time. In another embodiment the invention relates to a system for increasing the detected spatial uniformity of the intensity of a beam of light.

Abstract: Images with closely spaced objects can be processed using a deblending procedure that includes the calculation of some moments and centroids of intensity data. Methods and apparatus for performing this processing are well-suited for use in DNA sequencing, where the locations of fluorescing nucleotides appearing in images must be compared across several images and can be very close to one another in any single image. The increased accuracy and resolution provided by embodiments of the invention reveals previously undetected or misdetected fluorescing nucleotides, thereby facilitating the sequencing process. Embodiments of the invention can be used in other applications where, for example, defects in testing apparatus and/or limitations on image resolution frustrate subsequent analyses.

Abstract: The invention provides methods for sequencing a nucleic acid comprising stabilizing a primer/target nucleic acid duplex on a substrate. Methods of the invention generally contemplate the use of a dual-anchored primer/target nucleic acid duplex, or a stabilizing molecule in a single molecule sequencing reaction.

Abstract: In one aspect the invention relates to an apparatus for analyzing the presence of a single molecule using total internal reflection. In one embodiment an apparatus for single molecule analysis includes a support having a sample located thereon; two sources of light at distinct wavelengths, a collimator for directing the light onto the sample through a total internal reflection objective; a receiver for receiving a fluorescent emission produced by a single molecule in the sample in response to the light; and a detector for detecting each of the wavelengths in the fluorescent emission. In another embodiment the apparatus further comprises a focusing laser for maintaining focus of the objective on the sample.

Abstract: The invention relates to compositions and methods for a temporal signal pattern or signature representative of a characteristic of a nucleic acid template. The signature is created by monitoring the real time sequential pattern of signal emissions generated during nucleic acid template-dependent polymerization reactions.

Abstract: The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.

Abstract: Sensors, including ultrasonic components, within a robotic system facilitate the overall operation and efficiency of the robotic system through the detection of objects and surfaces, including the levels of liquids, without contacting the objects or surfaces. The sensors are well-suited for use in connection with microfluidic volumes and biological materials.

Abstract: A target nucleic acid sequence information obtained from a biological sample can be compared against a collection of reference nucleic acid sequences. The target nucleic acid sequence is aligned or matched against the reference sequences, wherein some of the target sequences have one or more polymorphisms. Different collections of reference sequences are created and used depending on what one is trying to determine about the target. For example, reference sequences associated with a particular disease may be stored in one or more databases and subsequently compared with a target sequence to determine whether a patient from which the sample sequence was obtained has that disease.