Abstract: Energy transfer dye pairs including a donor dye covalently attached to an acceptor dye through a linker, uses of the energy transfer dye pairs, for example, in conjugates of an energy transfer dye pair covalently attached to a quencher and an analyte (e.g., an oligonucleotide), for biological applications including, for example, amplification assays such as quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR).

Abstract: A system (1000) comprising first and second excitation sources (101a, 101b) with respective excitation wavelengths for exciting first second and third dyes in a sample (110) and further comprising a detector (115), first and second emission spectral elements (121a, 121b) for transmitting respective first and second emission wavelengths as well as a processor (130) for automatically operating the elements of the system. The first dye comprises a first absorption spectrum comprising a first maximum absorption wavelength and the second dye comprises a second absorption spectrum comprising a second maximum absorption wavelength that is equal to or substantially equal to the first maximum absorption wavelength. The second dye comprises a second emission spectrum comprising a second maximum emission wavelength and the third dye comprises a third emission spectrum comprising a third maximum emission wavelength that is equal to or substantially equal to the second maximum emission wavelength.

Abstract: Disclosed is a probe for use in biological assays. The probe includes a fluorescent dye bound to a quencher compound through an oligonucleotide linker. Also disclosed are methods of using the probe, such as for a polymerase chain reaction (PCR), such as in a quantitative PCR reaction (qPCR), as well as kits including the probe.

Abstract: Disclosed is a probe for use in biological assays. The probe includes a fluorescent dye bound to a quencher compound through an oligonucleotide linker. Also disclosed are methods of using the probe, such as for a polymerase chain reaction (PCR), such as in a quantitative PCR reaction (qPCR), as well as kits including the probe.

Abstract: Disclosed is a probe for use in biological assays. The probe includes a fluorescent dye bound to a quencher compound through an oligonucleotide linker. Also disclosed are methods of using the probe, such as for a polymerase chain reaction (PCR), such as in a quantitative PCR reaction (qPCR), as well as kits including the probe.

Abstract: 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? portion, wherein the polynucleotide forms the nucleic acid molecule 5? end; and (iii) a plurality of overlapping template oligonucleotides each having a 5? template portion and a 3? portion.

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

Abstract: 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.

Abstract: 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.

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: 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: 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.

Abstract: Apparatus for immunoassay of multiple samples of biological fluids (e.g., AIDS antibodies), the apparatus being capable of mounting for rocking during incubation. A frame receives plural test vessels so that the vessels are interconnected for circulation through all the vessels of buffers, de-ionized water and air and for discharge of waste. Each vessel is transparent and contains nitrocellulose test paper impregnated with antigens to the antibodies. Valved ports in each vessel accept sequential insertion of the biological fluids, an enzyme conjugate and color developer. Color changes in the individual test papers are observed through the transparent vessels and identify presence of antibodies in the samples.