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

Abstract: Methods are provided for substantially reducing background signals encountered in nucleic acid hybridization assays. The method is premised on the elimination or significant reduction of the phenomenon of nonspecific hybridization, so as to provide a detectable signal which is produced only in the presence the target polynucleotide of interest. In addition, a novel method for the chemical synthesis of isoguanosine or 2'-deoxy-isoguanosine is provided. The invention also has applications in antisense and aptamer therapeutics and drug discovery.

Abstract: 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.

Abstract: Hydroxyl-protecting groups orthogonally removable by reduction with a liquid reducing agent are disclosed. The novel hydroxyl-protecting groups are particularly useful in the chemical synthesis of linear and branched oligonucleotide structures, as they are readily removed from the protected molecule with mild reagents such as dithionite. Examples of such hydroxyl-protecting groups include the 2-methylene-9,10-anthraquinone (Maq) carbonate ester and the p-nitrobenzyl carbonate ester.

Abstract: A method for binding a target polynucleotide in a sample is provided. The method uses an assay reagent which is a substrate noncovalently bound to a hydrophobic moiety which is part of a polynucleotide capture probe. This assay reagent is contacted with the sample under conditions which permit hybridization between said capture probe and said target polynucleotide, thereby binding the target polynucleotide.

Abstract: Methods are provided for substantially reducing background signals encountered in nucleic acid hybridization assays. The method is premised on the elimination or significant reduction of the phenomenon of nonspecific hybridization, so as to provide a detectable signal which is produced only in the presence the target polynucleotide of interest. In addition, a novel method for the chemical synthesis of isoguanosine or 2'-deoxy-isoguanosine is provided. The invention also has applications in antisense and aptamer therapeutics and drug discovery.

Abstract: Linear or branched oligonucleotide multimers useful as amplifiers in biochemical assays which comprise (1) at least one first single-stranded oligonucleotide unit that is complementary to a single-stranded oligonucleotide sequence of interest, and (2) a multiplicity of second single-stranded oligonucleotide units that are complementary to a single-stranded labeled oligonucleotide. Amplified sandwich nucleic acid hybridizations and immunoassays using the multimers are exemplified.

Abstract: Linear or branched oligonucleotide multimers useful as amplifiers in biochemical assays which comprise (1) at least one first single-stranded oligonucleotide unit that is complementary to a single-stranded oligonucleotide sequence of interest, and (2) a multiplicity of second single-stranded oligonucleotide units that are complementary to a single-stranded labeled oligonucleotide. Amplified sandwich nucleic acid hybridizations and immunoassays using the multimers are exemplified.

Abstract: Methods and reagents are provided for synthesizing polynucleotides containing modified deoxyribose residues. Monomeric reagents having the structural formula (I) ##STR1## wherein R.sup.1, R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are as defined herein, are used to create polynucleotides having nonnucleotidic moieties -A-Z-(R.sup.9).sub.n at the 1 position of selected deoxyribose units. The polynucleotides so provided are useful in a variety of hybridization assay formats.

Abstract: Linear or branched oligonucleotide multimers useful as amplifiers in biochemical assays which comprise (1) at least one first single-stranded oligonucleotide unit that is complementary to a single-stranded oligonucleotide sequence of interest, and (2) a multiplicity of second single-stranded oligonucleotide units that are complementary to a single-stranded labeled oligonucleotide. Amplified sandwich nucleic acid hybridizations and immunoassays using the multimers are exemplified.

Abstract: Methods and reagents are provided for synthesizing polynucleotides containing modified deoxyribose residues. Monomeric reagents having the structural formula (I) ##STR1## wherein R.sup.1, R.sup.2, R.sup.3, R.sup.4 and R.sup.5 are as defined herein, are used to create polynucleotides having nonnucleotidic moieties --A--Z--(R.sup.9).sub.n at the 1 position of selected deoxyribose units. The polynucleotides so provided are useful in a variety of hybridization assay formats.

Abstract: 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.

Abstract: 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.

Abstract: Novel reagents useful in a variety of biochemical and chemical contexts, including nucleic hybridization assays and chemical phosphorylation of hydroxyl-containing compounds. The reagents are particularly useful for introducing cleavable sites and/or abasic sites into oligonucleotide or polynucleotide chains.

Abstract: Novel reagents useful in a variety of biochemical and chemical contexts, including nucleic hybridization assays and chemical phosphorylation of hydroxyl-containing compounds. The reagents are particularly useful for introducing cleavable sites and/or abasic sites into oligonucleotide or polynucleotide chains.

Abstract: A polynucleotide which has been modified by a hydrophobic moiety so that the polynucleotide attaches to a substrate by the hydrophobic moiety, rather than by a portion of the polynucleotide, thereby allowing the polynucleotide to be available for hybridization.

Abstract: Novel reagents useful in a variety of biochemical and chemical contexts, including nucleic hybridization assays and chemical phosphorylation of hydroxyl-containing compounds. The reagents are particularly useful for introducing cleavable sites and/or abasic sites into oligonucleotide or polynucleotide chains.

Abstract: Hydroxyl-protecting groups orthogonally removable by reduction with a liquid reducing agent are disclosed. The novel hydroxyl-protecting groups are particularly useful in the chemical synthesis of linear and branched oligonucleotide structures, as they are readily removed from the protected molecule with mild reagents such as dithionite. Examples of such hydroxyl-protecting groups include the 2-methylene-9,10-anthraquinone (Maq) carbonate ester and the p-nitrobenzyl carbonate ester.

Abstract: Polynucleotides containing abasic, cleavable sites are provided. These polynucleotides are useful in a variety of biochemical and chemical contexts, particularly in solid phase nucleic acid hybridization assays because a captured probe can be released from the support. The polynucleotides have the structure ##STR1## where R is selected from the group consisting of 2-nitrobenzyl, 4-penten-1-yl, ##STR2## where R', R.sub.i and R.sub.j are as defined herein.

Abstract: A modified polynucleotide containing at least one cleavable or abasic site as shown below. ##STR1## DNA.sub.1 is a first segment of DNA; DNA.sub.2 is a second segment of DNA; and R.sub.m is C.sub.1 to C.sub.16 alkylene or an oxytheylene oligomer --(CH.sub.2 CH.sub.2 O).sub.z -- where z is an interger in the range of 1 to 16 inclusive, and R.sub.n is selected from the group consisting of ##STR2## Such polynucleotides are useful in solid phase hybridizations because they permit the release of a label from the solid support after the hybridization reaction.