Abstract: Artificial nucleosides including 2-methyl-nucleobase-substituted butane-1,3-diol nucleosides are disclosed. Four different stereoisomers of such nucleosides are possible. Oligonucleotides made up of the artificial nucleosides form homoduplexes of greater stability than DNA duplexes and have a reduced ability to hybridize to DNA or RNA.

Abstract: 3-alkynyl inosine analogs and their uses as universal bases are provided. The inosine analogues can be incorporated into nucleic acid primers and probes. They do not significantly destabilize nucleic acid duplexes. As a result, the novel nucleic acid primers and probes incorporating the inosine analogues can be used in a variety of methods. The analogs function unexpectedly well as universal bases. Not only do they stabilize duplexes substantially more than hypoxanthine opposite A, C, T, and G but they are also recognized in primers by polymerases, allowing efficient amplification.

Abstract: Minor groove binder phosphoramidites having the formula M-L-PA, wherein M is a minor groove binder comprising a protected heteroaromatic amine, L is a linker, and PA is a phosphoramidite group, have been synthesized. Preferred methods of synthesis include synthesizing a minor groove binder intermediate containing a transiently protected hydroxyl group, protecting heteroaromatic amines of the corresponding minor groove binder intermediate as carbamate intermediates, reacting the carbamate intermediate to remove the transient protecting group to yield carbamate-protected minor groove binder agent as an intermediate with a free hydroxyl group, and converting the intermediate with a free hydroxyl group to the desired minor groove binder phosphoramidite. These minor groove binder phosphoramidites are useful in the preparation of oligonucleotide conjugates, particularly those for use as probes and primers.

Abstract: 3-alkynyl inosine analogs and their uses as universal bases are provided. The inosine analogs can be incorporated into nucleic acid primers and probes. They do not significantly destabilize nucleic acid duplexes. As a result, the novel nucleic acid primers and probes incorporating the inosine analogs can be used in a variety of methods. The analogs function unexpectedly well as universal bases. Not only do they stabilize duplexes substantially more than hypoxanthine opposite A, C, T, and G but they are also recognized in primers by polymerases, allowing efficient amplification.

Abstract: Artificial nucleosides including 2-methyl-nucleobase-substituted butane-1,3-diol nucleosides are disclosed. Four different stereoisomers of such nucleosides are possible. Oligonucleotides made up of the artificial nucleosides form homoduplexes of greater stability than DNA duplexes and have a reduced ability to hybridize to DNA or RNA.

Abstract: Compounds useful in labeling biological materials are provided along with methods for their use.

Abstract: 3-alkynyl inosine analogs and their uses as universal bases are provided. The inosine analogues can be incorporated into nucleic acid primers and probes. They do not significantly destabilize nucleic acid duplexes. As a result, the novel nucleic acid primers and probes incorporating the inosine analogues can be used in a variety of methods. The analogs function unexpectedly well as universal bases. Not only do they stabilize duplexes substantially more than hypoxanthine opposite A, C, T, and G but they are also recognized in primers by polymerases, allowing efficient amplification.

Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.

Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.

Abstract: Minor groove binder phosphoramidites having unique structures have been synthesized according to particular methods. These minor groove binder phosphoramidites are useful in the preparation of oligonucleotide conjugates, particularly those for use as probes and primers.

Abstract: 3-alkynyl inosine analogs and their uses as universal bases are provided. The inosine analogues can be incorporated into nucleic acid primers and probes. They do not significantly destabilize nucleic acid duplexes. As a result, the novel nucleic acid primers and probes incorporating the inosine analogues can be used in a variety of methods. The analogs function unexpectedly well as universal bases. Not only do they stabilize duplexes substantially more than hypoxanthine opposite A, C, T, and G but they are also recognized in primers by polymerases, allowing efficient amplification.

Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.

Abstract: The invention provides methods to identify pRNA- and pDNA oligomer affinity pairs. Affinity pairs comprised of nucleic acid oligomers which demonstrate no cross-reactivity (“orthogonal”) are designed using software and empirically verified by thermodynamic study and lateral flow testing. The design software uses a semi-random algorithm to build such sequences of nucleic acid oligomers based on user-input parameters for affinity strength and orthogonal stringency. These pairs can be applied for use in multi-analyte solid support and lateral flow diagnostic tests.

Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.

Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.

Abstract: The present invention relates to a hyperthermostable endonuclease IV substrate probe to be used in nucleic acid assay methods which can be carried out using hyperthermostable enzymes, including detection of target nucleic acids, and detection of nucleic acid polymorphism.

Abstract: The present invention provides a negatively charged minor groove binding compound, oligonucleotide conjugates comprising the same, and methods for using the same. The negatively charged minor groove binding compounds of the present invention comprises an acidic moiety that is capable of being ionized under physiological conditions. In particular, the negatively charged minor groove binding compound of the present invention comprises a binding moiety that binds preferentially into a minor groove of a double, triple or higher stranded DNA, RNA, PNA or hybrids thereof. The binding moiety comprises at least one aryl moiety and an acidic moiety which is covalently attached to a phenyl portion of the aryl moiety or to a heteroatom of a heteroaryl portion of the aryl moiety.

Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.

Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.

Abstract: Reagents are provided for the introduction of phosphonate groups into fluorescent dyes. Methods are also provided for preparing dye conjugates.