Chiron Corporation

Cetus Corporation

Siemens Healthcare Diagnostics Gmbh

Applied Biosystems, LLC

Johnson & Johnson Clinical Diagnostics, Inc.

Chu-an Chang

Michael S Urdea

Thomas Horn

Brian David Warner

Fred T Oakes

Corey H Levenson

Timothy J Fultz

Patrick J Sheridan

Joyce A Running

John Bruce Findlay

Shiaw-Min Chen

Minxue Zheng

Marlene M King

Ming Wu

David Ahle

Janice M Mayer

The invention provides a set of highly orthogonal six-code universal sequences for use in bDNA singleplex and multiplex nucleic acid hybridization assays. The six-code orthogonal sequences do not cross-hybridize and thus, minimize or eliminate the 3-mer cross-hybridization inherent in the second and third generation bDNA assays. The highly orthogonal universal sequences may be used in singleplex or multiplex bDNA assays quantitatively and qualitatively to determine mRNA levels in a sample; to screen for and genotype targets, such as viruses, that are present in low volumes in a sample; to screen for and genotype SNPs; and to measure changes in the amount of a gene in a sample such as when gene amplifications or deletions occur. The highly orthogonal universal sequences may also be used as universal capture probes to selectively bind assay components in a way that facilitates their further analysis.

Highly orthogonal universal sequences for use in nucleic acid assays

A method of generating a single-stranded nucleic acid molecule comprising (a) combining in a mixture under conditions suitable for a polymerase extension reaction, (i) a polymerase, (ii) an initial polynucleotide comprising a 5' portion and a 3&#x2032; portion, wherein the polynucleotide forms the nucleic acid molecule 5&#x2032; end; and (iii) a plurality of overlapping template oligonucleotides each having a 5&#x2032; template portion and a 3&#x2032; portion. The method further comprises (b) hybridizing the initial polynucleotide or the extension polynucleotide and one of the template oligonucleotides; (c) incubating the mixture for sufficient time to allow an extension polynucleotide to be synthesized; (d) adding a competimer that competes with the template oligonucleotide in step (b); (e) denaturing the extension polynucleotide and template oligonucleotide; and (f) repeating steps (b), (c), (d), and (e) to generate the single-stranded nucleic acid molecule, wherein the number of repeated cycles equals the number of different template oligonucleotides.

Method of generating long nucleic acid molecules of defined sequence

Comb-type branched polynucleotides are used as amplification multimers in nucleic acid hybridization assays.

Nucleic acid hybridization assays employing large comb-type branched

Nucleic acid probes are immobilized on polystyrene surfaces such as the wells of microtiter plates for use in solution phase nucleic acid sandwich hybridization assays, particularly those using large branched DNA amplification multimers, by: (a) cleansing the surface by washing it sequentially with a strong acid, a strong base, and water, (b) passively adsorbing a polypeptide having primary amino groups onto the cleansed surface, and (c) covalently bonding the probe to the adsorbed polypeptide via a base-stable bifunctional crosslinking agent, and (d) subjecting the surface to conditions that simulate the hybridization conditions used in the assay.

Nucleic acid probes immobilized on polystyrene surfaces

Process for immobilizing nucleic acid probes on polystyrene surfaces

Large comb-type branched polynucleotides useful as amplifier molecules in nucleic acid hybridization assays are provided, the polynucleotides comprising: a polynucleotide backbone having at least about 15 multifunctional nucleotides, each of which defines a sidechain site and a first single-stranded oligonucleotide unit that is capable of binding specifically to a first single-stranded polynucleotide sequence of interest; and pendant polynucleotide sidechains extending from said multifunctional nucleotides each comprising iterations of a second single-stranded oligonucleotide unit that is capable of binding specifically to a second single-stranded polynucleotide sequence of interest, the total number of iterations in all sidechains being at least 20. Methods of making these polynucleotides are also provided.

Large comb type branched polynucleotides

Novel oligonucleotide probes are provided having the structure ##STR1## wherein: R.sup.2 is lower alkyl; R.sup.3 is C.sub.1 -C.sub.12 alkylene containing 0 to 6 linkages selected from the group consisting of --O--, --S-- and --NR.sup.12 -- wherein R.sup.12 is hydrogen or lower alkyl; R.sup.5 is hydrogen or lower alkyl; R.sup.6 is selected from the group consisting of hydrogen, methyl, bromo and iodo; R.sup.7 is C.sub.1 -C.sub.12 alkylene containing 0 to 6 linkages selected from the group consisting of --O--, --S-- and --NR.sup.12 --, and bound to R.sup.8 through an --O--, --S-- or --NR.sup.12 -- moiety; and R.sup.8 is a protecting group that can be removed and replaced, without affecting the remainder of the compound, by reduction with a reducing agent. Methods for using the probes are provided as well.

N-4 modified pyrimidine deoxynucleotides and oligonucleotide probes

Novel N-4 modified pyrimidine analogs are provided having the structure (I) or (II) ##STR1## wherein: R.sup.1 is selected from the group consisting of hydrogen, acid-sensitive, base-stable blocking groups and acyl capping groups; R.sup.2 is lower alkyl; R.sup.3 is C.sub.1 -C.sub.12 alkylene containing 0 to 6 linkages selected from the group consisting of --0--, --S-- and --NH--; R.sup.4 is ##STR2## in which R.sup.9 is hydrogen or an optionally substituted aliphatic group; R.sup.10 and R.sup.11 are hydrocarbyl or together form a mono- or polyheterocyclic ring; R.sup.5 is hydrogen or lower alkyl; R.sup.6 is selected from the group consisting of hydrogen, methyl, bromo and iodo; R.sup.7 is C.sub.1 -C.sub.12 alkylene containing 0 to 6 linkages selected from the group consisting of --O--, --S-- and --NR.sup.12 -- wherein R.sup.12 is hydrogen or lower alkyl; and R.sup.8 is a protecting group that can be removed and replaced by reduction. Synthetic methods for preparing the compounds are provided as well, as are methods for making and using polynucleotide probes containing the novel pyrimidine analogs.

A nucleic acid test article can be used to detect a targeted nucleic acid found in a specimen. The test article includes a substrate having two opposing surfaces and a water-insoluble nucleic acid probe attached in a distinct zone of one of the surfaces. The probe is prepared from a water-insoluble particle to which is covalently attached an oligonucleotide which is complementary to the targeted nucleic acid. Substantially none of the probe is embedded within the surface of the substrate. Particularly useful test articles have a multiplicity of water-insoluble probes located in distinct zones on one of the substrate surfaces. These probes are useful for the detection of a multiplicity of targeted nucleic acids, particularly after amplification by polymerase chain reaction.

Nucleic acid test article and its use to detect a predetermined nucleic

Oligonucleotides derivatized to incorporate horseradish peroxidase (HRP) are useful in diagnostic methods and provide significant advantage over radioactively labeled oligonucleotide probes. The HRP-derivatized oligonucleotides can be easily and efficiently prepared by reacting a sulfhydryl containing oligonucleotide with a conjugate of a mal-sac-HNSA ester and HRP under mild and easily controlled reaction conditions.

Covalent oligonucleotide-horseradish peroxidase conjugate

Oligonucleotide functionalizing reagents are disclosed which are useful in introducing sulfhydryl, amino and additional hydroxyl groups into oligonucleotides. The reagents are substantially linear in structure, at one end provided with a phosphoramidite moiety, at an opposing end provided with a sulfhydryl, amino or hydroxyl moiety, the two ends linked through a hydrophilic spacer chain. Methods of using and synthesizing the novel reagents are disclosed as well.

Growing community of inventors

Piedmont, CA, United States of America

Chu-an Chang