Abstract: Monomethine dyes that have no or minimal fluorescence in buffer or in the presence of single stranded DNA or RNA, but strongly fluoresce in the presence of double-stranded DNA. In one embodiment, the dye is useful in quantitative RT-PCR.

Abstract: Compounds, compositions, and methods for optical, including fluorescence optical, determinations useful in labeling biomolecules such as protein and deoxyribonucleic acid for their detection and quantitation. The compounds are diastereomeric cyanines with high hydrophilicity and other desirable properties.

Abstract: Monomethine dyes that have no or minimal fluorescence in buffer or in the presence of single stranded DNA or RNA, but strongly fluoresce in the presence of double-stranded DNA. In one embodiment, the dye is useful in quantitative RT-PCR.

Abstract: Compounds, compositions, and methods for optical, including fluorescence optical, determinations useful in labeling biomolecules such as protein and deoxyribonucleic acid for their detection and quantitation. The compounds are diastereomeric cyanines with high hydrophilicity and other desirable properties.

Abstract: The present invention provides a method of synthesizing phosphoramidite linkers that are useful for the production of synthesizing two or more oligonucleotides in tandem. The inventive linker has the following desirable properties: (i) enhanced stability to alkali conditions versus the linkers previously published, (ii) cleaves to produce 5? and 3? ends that are fully biologically compatible, (iii) cleaves completely under conditions that are already used in cleavage/deprotection processes so it is fully compatible with conditions that are common in laboratories and does not require additives that necessitate further purification after cleavage, (iv) integrates easily onto commercially available synthesizers because it is compatible with standard coupling chemistry, and (v) is compatible with DNA, RNA, forward, reverse, and LNA, synthesis chemistries. In addition, the inventive linkers may be coupled to a solid support. Thus, the inventive linkers provide a significant advancement in the state of the art.

Abstract: An assay is provided for nucleic acids that can be post-synthetically labeled, wherein modified nucleoside triphosphates are used that are more efficiently and specifically incorporated during nucleic acid synthesis than labeled nucleoside triphosphates. In a preferred embodiment, nucleoside ?-thiotriphosphates are utilized. Maleimide or iodoacetamide conjugating moieties can be attached post-synthetically. The conjugating moieties may include a reporter group. Also disclosed are new methods for detecting single nucleotide polymorphism.

Abstract: Methods and devices for detecting nucleic acid and protein targets on hydrogel microarrays are disclosed. Fluorophores are incorporated into the targets and detected. A linear correlation between target concentration and signal amplitude is maintained through the elimination of active enzyme amplification.

Abstract: This invention is directed to novel methods of amplifying and detecting DNA. More specifically, the invention applies variations of Rolling Circle Amplification to several detection platforms.

Abstract: [2+2] photo-attachable functional groups were incorporated in polyacrylamide based hydrogels and synthetic oligonucleotide probes. The probes were photochemically attached by covalent bonding to the three dimensional surface of a hydrogel.

Abstract: The present invention provides solid supports (e.g., glass) and polymer hydrogels (particularly polymer hydrogel arrays present on a solid support) comprising one or more reactive sites for the attachment of biomolecules, as well as biomolecules comprising one or more reactive sites for attachment to solid supports and polymer hydrogels. The invention further provides novel compositions and methods for the preparation of biomolecules, solid supports, and polymer hydrogels comprising reactive sites. The invention also provides for preparation of crosslinked solid supports, polymer hydrogels, and hydrogel arrays, wherein one or more biomolecules is attached by means of the reactive sites in a photocycloaddition reaction. Advantageously, according to the invention, crosslinking of the hydrogel and attachment of biomolecules can be done in a single step.

Abstract: An assay is provided for nucleic acids that can be post-synthetically labeled, wherein modified nucleoside triphosphates are used that are more efficiently and specifically incorporated during nucleic acid synthesis than labeled nucleoside triphosphates. In a preferred embodiment, nucleoside &agr;-thiotriphosphates are utilized. Maleimide or iodoacetamide conjugating moieties can be attached post-synthetically. The conjugating moieties may include a reporter group. Also disclosed are new methods for detecting single nucleotide polymorphism.

Abstract: Photoreactive phosphoramidites useful for attaching photoreactive sites to nucleic acids and oligonucleotides are synthesized. The resultant nucleic acid or oligonucleotide probes incorporating the photoreactive sites are then attached to a polymer-coated support by a [2+2] cycloaddition to form a microarray.

Abstract: Methods and devices for detecting nucleic acid and protein targets on hydrogel microarrays are disclosed. Fluorophores are incorporated into the targets and detected. A linear correlation between target concentration and signal amplitude is maintained through the elimination of active enzyme amplification.

Abstract: A chemical compound of the following formula: ##STR1## wherein R.sup.1 is selected from the group consisting of alkyl, aralkyl, and substituted alkyl groups; R.sup.3 is selected from the group consisting of H, PO.sub.3.sup.-2, P.sub.2 O.sub.6.sup.-3 ; P.sub.3 O.sub.9.sup.-4, and .alpha.-thio phoshates (PSO.sub.2.sup.-2 ; P.sub.2 SO.sub.5.sup.-3 ; P.sub.3 O.sub.8.sup.-4); and .alpha.BH.sub.3.sup.- phosphates (P(BH.sub.3)O.sub.2.sup.-2, P.sub.2 (BH.sub.3)O.sub.5.sup.-3, P.sub.3 (BH.sub.3)O.sub.8.sup.-4); R.sup.4 is selected from the group consisting of H, lower alkyl, acyl, (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.3 wherein p is an integer from 0 to 4 and q is an integer from 0 to 4, and 5,6; 6,7; or 7,8-butadienyl; R.sup.5 is selected from the group consisting of H lower alkyl, acyl, (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.

Abstract: A preparation of a labelled nucleotide comprising at least one compound having a Mg.sup.2+ association constant between 1.times.10.sup.-11 to 1.times.10.sup.-2, inclusive. The compound is preferably selected from the group consisting of citrate, isocitrate, phosphate, EGTA, EDTA, and CDTA. The concentration of the compound is preferably at least 5 mM.

Abstract: A chemical compound of the following formula is disclosed: ##STR1## where R is selected from the group consisting of H, trityl, 4-O-monomethoxytrityl, 4,4'-O-dimethoxytrityl, and acyl groups, and whereby R can be used as a protecting group or is an H;R' is a phosphoramidite;R" is selected from the group consisting of H and lower alkyl groups;R'" is selected from the group consisting of H and lower alkyl groups;R.sup.4 is selected from the group consisting of H, lower alkyl, acyl, ##STR2## and (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.3 wherein p is an integer from 0 to 4 and q is an integer from 0 to 4;R.sup.5 is selected from the group consisting of H, lower alkyl, acyl, ##STR3## and (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.3 wherein p is an integer from 0 to 4 and q is an integer from 0 to 4;n is an integer from 0 to 10;m is an integer from 0 to 10;r is 1, 2, or 3; andX.sup.- is a negative ion.

Abstract: Compounds useful to attach a fluorescein label to an oligonucleotide are disclosed. To create these compounds, oxygen groups on the fluorescein moiety are protected (e.g. with acyl groups). One then links a phosphoramidite to the fluorescein moiety via an amide or thiourea linkage to an active site on the fluorescein ring. The resulting compound can then be directly linked to an oligonucleotide as it is being formed in an automated synthesizer and then deprotected using the same deprotection conditions as are used to deprotect the oligonucleotides. Such compounds are, inter alia, useful to create labelled primers for DNA sequencing.

Abstract: Compounds useful to attach a fluorescein label to an oligonucleotide are disclosed. To create these compounds, oxygen groups on the fluorescein moiety are protected (e.g. with acyl groups). One then links a phosphoramidite to the fluorescein moiety via an amide or thiourea linkage to an active site on the fluorescein ring. The resulting compound can then be directly linked to an oligonucleotide as it is being formed in an automated synthesizer and then deprotected using the same deprotection conditions as are used to deprotect the oligonucleotides. Such compounds are, inter alia, useful to create labelled primers for DNA sequencing.

Abstract: A chemical compound of the following formula is disclosed ##STR1## where R is one of H, trityl, 4-0-monomethoxytrityl, 4,4'-O-dimethoxytrityl, or acyl groups and R may be used as a protecting group or is an H; R.sup.1 is a phosphoramidite; R.sup.11 is one of H or lower alkyl groups; R.sup.111 is one of H or lower alkyl groups; R.sup.4 is one of H, lower alkyl, acyl, or (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.3 where p is an integer from 0 to 4 and q is an integer from 0 to 4; R.sup.5 is one of H, lower alkyl, acyl, or (CH.sub.2).sub.p COO(CH.sub.2).sub.q CH.sub.3 where p is an integer from 0 to 4 and q is an integer from 0 to 4; n is an integer from 0 to 10; m is an integer from 0 to 10; and r is 1, 2, or 3.

Abstract: Ether variant lipids bound to phosphoramidites are disclosed. These can be used to create oligonucleotides that are linked to stable lipid-like units. For example, dialkyl glycerols are linked to phosphoramidites.