60 results about "Immobilized Nucleic Acids" patented technology

Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

Nucleic acids are fixed or immobilized to non-porous solid supports (substrates), and include systems containing such supports and arrays with fixed or immobilized nucleic acids. These compositions are useful for nucleic acid analyses and a host of applications, including, for example, detection, mutational analysis and quantification. The non-porous solid supports can be transparent or translucent, and the surfaces can be treated with agents to fix or immobilize the nucleic acids. Such agents include, for example, amine providing compounds, epoxy compounds and acid solutions. The fixed or immobilized nucleic acids can be unlabeled, or labeled with at least one non-radioactive signaling moiety, such as the case when the nucleic acids are double-stranded.

Provided are methods for sequencing a nucleic acid that include fixing a template to a surface through a template localizing moiety and sequencing the nucleic acid with a sequencing enzyme, e.g. a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid fixed to a surface via a template localizing moiety, and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Compositions for sequencing reactions are provided. Also provided are sequencing systems comprising reaction regions in which or near which template localizing moieties are immobilized.

A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.

In one aspect the present invention provides methods of synthesizing a preparation of nucleic acid molecules, the methods comprising the steps of: (a) utilizing an RNA template to enzymatically synthesize a first DNA molecule that is complementary to at least 50 contiguous bases of the RNA template; (b) utilizing the first DNA molecule as a template to enzymatically synthesize a second DNA molecule, thereby forming a double-stranded DNA molecule wherein the first DNA molecule is hybridized to the second DNA molecule; (c) utilizing the first or second DNA molecule of the double-stranded DNA molecule as a template to enzymatically synthesize a first RNA molecule that is complementary to either the first DNA molecule or to the second DNA molecule; and (d) utilizing the first RNA molecule as a template to enzymatically synthesize a third DNA molecule that is complementary to the first RNA molecule. In another aspect, the present invention provides processed DNA samples prepared by a method of the invention for synthesizing a preparation of nucleic acid molecules. In another aspect, the present invention provides methods for hybridizing a processed DNA sample to a population of immobilized nucleic acid molecules.

A nucleic acid, which is provided in a large amount through a nucleic acid amplification reaction with the use of chimeric oligonucleotide primers, is constructed in a state of containing a modified deoxyribonucleotide for immobilizing the nucleic acid to a solid phase and then immobilized to a solid phase at a high efficiency, thereby giving an immobilized nucleic acid product with excellent qualities.

Particular aspects relate to a method for determining the methylation pattern of a polynucleic acid, comprising: a) preparing a solution comprising a mixture of fragments of the polynucleic acid; b) coupling the fragments with a substance being detectable with a detection method; c) contacting a solution comprising the fragments of b) with a DNA microarray having a plurality of different immobilized oligonucleotides, each comprising at least one methylation site, at respectively assigned different locations thereon, the contacing under conditions affording hybridization of fragments with correlated immobilized oligonucleotides under defined stringency, and wherein the immobilized oligonucleotides have a length of less than 200 bases; d) optionally performing a a washing step; and e) detecting, using the physical detection method, such immobilized nucleic acids to which solution fragments are hybridized and/or to which solution fragments are not hybridized.

The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq.

The invention provides a broad-spectrum nucleic acid aptamer capable of identifying lipopolysaccharides of different Gram-negative bacterium sources. The broad-spectrum nucleic acid aptamer is obtained by directed screening on the basis of the capture-SELEX technology of label-free target molecules and immobilized nucleic acid libraries. A directed screening method of the broad-spectrum nucleic acid aptamer includes: using mouse salmonella typhi lipopolysaccharides as the unique target, using a biotin-avidin effect to fix random oligonucleotide libraries to Fe3O4 magnetic nano particles wrapped by avidin through biotinylated short complementary chains, performing incubation, separation, amplification, digestion single chain preparation, cloning sequencing and the like, adding complete active bacteria of salmonella and escherichia coli to serve as directed molecules to perform directed screening when the libraries are enriched to a certain degree, and one broad-spectrum nucleic acid aptamer capable of identifying four kinds of lipopolysaccharides is obtained through 15 rounds of repeated screening. The nucleic acid aptamer is applicable to the analysis and detection, separation and enriching, toxicity neutralizing and the like of the lipopolysaccharides in aspects of drinking water, food or clinical medicine and the like.

The present invention provides methods of detecting a nucleic acid analyte in a sample. The methods generally involve modifying immobilized nucleic acids from a sample onto an insoluble support in a substantially elongated configuration, where modification generates an identifying feature that identifies the analyte; and detecting the identifying feature(s) using scanning probe microscopy, to detect the analyte. The present invention further provides a method for assigning a profile of a feature to a nucleic acid. The present invention further provides a computer program product for use in a subject method. The present invention further provides a system for detecting a nucleic acid in a sample; and a system for assigning a profile of a feature to a nucleic acid. The present invention further provides a method for immobilizing a nucleic acid onto an insoluble support; and further provides insoluble support having nucleic acid(s) immobilized thereon. The present invention further provides a method of diagnosing a disorder or condition in an individual, where the method involves use of a subject method for detecting a nucleic acid analyte.

The present invention relates to methods of immobilizing nucleic acid aptamers within a sol-gel matrix. The aptamer system remains functionally intact when it is immobilized within a protein and membrane-compatible sol-gel derived from polyol silane precursors or sodium silicate.

Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods.

The present invention provides an RNA detection method detecting, from a reaction system containing a target sample, a target RNA chain originated from the target sample, using a surface having on the surface thereof a polymer substance which contains a first unit having a group derived from a phosphate ester composing the hydrophilic portion of a phospholipid and a second unit having a carboxylic acid derivative group composed of an electron-attractive substitutional group bound to a carbonyl group, while being provided with at least one reaction space, the reaction space having an immobilized nucleic acid primer immobilized therein.

A nucleic acid detection device includes a flow channel through which a solution containing a nucleic acid recognition body flows, probe electrodes having immobilized nucleic acid probes, and a counter electrode used to measure an electrochemical response of the nucleic acid recognition body. The flow channel includes a curved portion and a straight portion continued from and located downstream of the curved portion. The probe electrodes are arranged at intervals along the straight portion, avoiding an upstream end of the straight portion that is located within a distance L from the curved portion. The distance L is given by L=0.065×Re×D, Re=ρuD/μ, and D=4 S/Lp where ρ, u, and μ are a concentration, a flow velocity, and a viscosity of the solution, and S and Lp are a sectional area and a wall peripheral perimeter of the flow channel, respectively.

A superior adsorption method for immobilizing nucleic acid probe on the surface of a solid phase substrate is provided. A nucleic acid immobilization method for immobilizing nucleic acid on a solid phase substrate comprising: bringing the above-mentioned solid phase substrate into contact with a composition comprising a total concentration of 0.1 to 2 mu M of a nucleic acid as a probe and a compound or a salt thereof, the compound being represented by the following formula: HS-L<1>-L<2>-R wherein L<1> is a single bond or a C1-15 alkylene group; L<2> is a single bond, nucleic acid, a polyethylene glycol group, -CO-NH-, or -NH-CO-; R is a hydroxyl group, an amino group, a ferrocenyl group, or a carboxyl group; provided that neither L<1> nor L<2> is a single bond, and incubating the composition in contact with a surface of the solid phase substrate.

The invention discloses a solid-phase nucleic acid probe used to non-marking detection, including solid carrier, on which the scant nucleotide probe, with the fluorescence group, the fluorescence cancellation group and the identification sequence snippet of the peculiar nucleic acid is fixed, and the fluorescence cancellation group can be cancel the fluorescence; after intercrossing the group andthe snippet in the scant nucleotide probe, by the biochemical reaction, separate the two groups in the scant nucleotide probe to make the probe emit the fluorescence.