Abstract: A method of detecting a nucleic acid sequence in a genomic sample, includes: providing the genomic sample containing a target nucleic acid sequence of a duplex nucleic acid; providing, a probe containing a probe nucleic acid sequence; providing a hybridization mixture containing the genomic sample, the probe, a hybridization promoting agent and labels; incubating the hybridization mixture; irradiating the incubated mixture with radiation effective to stimulate at least some of the labels to emit energy; and detecting from a fluorescent signal whether the probe perfectly matches the target nucleic acid sequence, wherein the detecting is completed within sixty minutes of the hybridization mixture providing, and the method is conducted without denaturing and without PCR amplifying the duplex nucleic acid. A kit for practicing the method includes the probe, the hybridization promoting agent, and labels.

Abstract: A method of detecting a nucleic acid sequence in a genomic sample, includes: providing the genomic sample containing a target nucleic acid sequence of a duplex nucleic acid; providing, a probe containing a probe nucleic acid sequence; providing a hybridization mixture containing the genomic sample, the probe, a hybridization promoting agent and labels; incubating the hybridization mixture; irradiating the incubated mixture with radiation effective to stimulate at least some of the labels to emit energy; and detecting from a fluorescent signal whether the probe perfectly matches the target nucleic acid sequence, wherein the detecting is completed within sixty minutes of the hybridization mixture providing, and the method is conducted without denaturing and without PCR amplifying the duplex nucleic acid. A kit for practicing the method includes the probe, the hybridization promoting agent, and labels.

Abstract: A complex includes: (1) a probe containing a heteropolymeric probe sequence of nucleic acids or nucleic acid analogues; and (2) a target containing a heteropolymeric target sequence of nucleic acids or nucleic acid analogues, wherein: (a) at least one of the probe and the target is purified or synthetic; and (b) the heteropolymeric probe sequence is bonded to the heteropolymeric target sequence by Watson-Crick complementary base interaction or by homologous base interaction, provided that when the complex is a duplex and the heteropolymeric probe sequence is antiparallel to the heteropolymeric target sequence, the heteropolymeric probe sequence is bonded to the heteropolymeric target sequence by homologous base interaction, and provided that when the complex is a triplex, the complex is free of recombination proteins. A method for assaying a target includes detecting formation of the complex.

Abstract: A method for homogeneously assaying biopolymer bonding includes obtaining signals from a test sample before, during and/or after the application of stimulus to the test sample and correlating the signals. The signals, whose magnitude correlate with binding affinity, can be, for example, electrical conductance and/or fluorescent intensity. The stimulus can be, for example, electric voltage and/or laser radiation. Preferably, different types of signals are measured and compared so as to enhance the reliability of the assay.

Abstract: A purification method includes bonding a probe to a target in a sample to form a complex, and separating the sample from the complex to separate in a sequence specific manner the target from the sample. The complex, which is immobilized on a support, is a duplex, triplex or quadruplex formed by Watson-Crick complementary base interaction or by homologous base interaction, provided that when the complex is a duplex and the heteropolymeric probe sequence is antiparallel to the heteropolymeric target sequence, the heteropolymeric probe sequence is bonded to the heteropolymeric target sequence by homologous base interaction, and provided that when the complex is a triplex, the complex is free of recombination proteins. A kit for performing the method includes the support and the probe.

Abstract: An apparatus for assaying specific binding of a probe to a target, includes: a sample support; a light source; an optical train; a light detector; an electricity source; an electrical property detector; and a data analysis device adapted to: (a) compare an optical determination of binding with an electrical determination of binding, or (b) compare a pre-electrification determination of binding with a post-electrification determination of binding.

Abstract: Heteropolymeric triplexes and quadruplexes and methods for making them; the use of accelerator agents such as cations to create them; the use of fluorescent intercalators and fluorescent probe-bound non-intercalators to detect them.

Abstract: An improved method of forming a specific complex between a probe containing probe nucleobases and a target containing target nucleobases, includes mixing the probe and the target under hybridizing conditions, wherein the probe and/or the target is conjugated to a blocking agent, which enhances the avidity and/or specificity of hybridization, whether by Watson-Crick motif or by homologous binding motif. The blocking agent contains at least one nucleobase and can be, e.g., a free nucleobase, a nucleoside or a nucleotide.

Abstract: An assay includes catalytic hybridization of targets and cleavable probes to form triplexes and quadruplexes based on Watson-Crick bonding rules. The probes contain scissile linkages that are cleaved by enzymes when hybridized to a target, yielding detectable probe fragments free of the target. The target is recycled to help catalyze the cleavage of additional intact probes to form additional detectable probe fragments, thus amplifying the signal.

Abstract: A multiplex structure, such as a nucleic acid quadruplex, includes: a first strand containing a first sequence of nucleobases; a second strand containing a second sequence of nucleobases, wherein the second strand is associated with the first strand by Watson-Crick bonding; a third strand containing a third sequence of nucleobases; and a fourth strand containing a fourth sequence of nucleobases, wherein the fourth strand is associated with the second strand and the third strand by Watson-Crick bonding. Formation of the multiplex structure is promoted by monovalent cations (e.g., sodium and potassium), divalent cations, multivalent cations, intercalating agents and/or molecules known to bind within the minor grooves of nucleic acids. The multiplex structure and the process of forming it have diagnostic, therapeutic, prophylactic and nanoengineering applications.

Abstract: Triplex complexes contain a single-stranded probe bound to a double-stranded nucleic acid target, in which the probe includes a heteropolymeric nucleic acid or a heteropolymeric nucleic acid analog. All base triplets of the complex are members selected from the group consisting of A-T-A, T-A-T, U-A-T, T-A-U, A-U-A, U-A-U, G-C-G and C-G-C. A cation-facilitated assay includes detecting the presence of such triplex complexes to determine the degree of complementarity between the probe and target sequence. The assay preferably detects a change in fluorescent intensity of a label as a function of binding affinity between the probe and target. The label can be covalently tethered to the probe or to the target, or can be an intercalating fluorophore in the reaction medium.

Abstract: An aptamer contains at least two parallel or antiparallel heteropolymeric nucleobase-containing sequences bonded together by Watson-Crick complementary base interaction or by homologous base interaction, provided that: (a) when the aptamer is single-stranded, the at least two sequences are bonded together by homologous base interaction; and (b) when the aptamer is a duplex and the at least two sequences are antiparallel to each other, the at least two sequences are bonded together by homologous base interaction. The aptamer can be used to bind ligands or to catalyze reactions when functioning as an aptazyme.

Abstract: A method for assaying a nucleobase-containing target with a nucleobase-containing probe, wherein: (a) the target is pre-incubated with at least one target incubation agent prior to being mixed with the probe; and/or (b) the probe is pre-incubated with at least one probe incubation agent prior to being mixed with the target to form the hybridization mixture. The pre-incubation enhances the signal to noise ratio of the assay. The pre-incubation medium and/or the hybridization medium can be pretreated with electric voltage. A kit for performing the method includes the probe, a label adapted to emit the signal, and at least one target incubation agent and/or probe incubation agent.

Abstract: A kit for capturing a target includes a probe and a capture primer adapted to bond to the probe to form a primed probe complex pursuant to a Watson-Crick complementary base interaction or a homologous base interaction binding motif, wherein the primed probe complex is adapted to capture the target by binding the probe to the target pursuant to the binding motif of the primed probe complex. A corresponding method for capturing a target is also disclosed.

Abstract: A complex includes: (1) a probe containing a heteropolymeric probe sequence of nucleic acids or nucleic acid analogues; and (2) a target containing a heteropolymeric target sequence of nucleic acids or nucleic acid analogues, wherein: (a) at least one of the probe and the target is purified or synthetic; and (b) the heteropolymeric probe sequence is bonded to the heteropolymeric target sequence by Watson-Crick complementary base interaction or by homologous base interaction, provided that when the complex is a duplex and the heteropolymeric probe sequence is antiparallel to the heteropolymeric target sequence, the heteropolymeric probe sequence is bonded to the heteropolymeric target sequence by homologous base interaction, and provided that when the complex is a triplex, the complex is free of recombination proteins. A method for assaying a target includes detecting formation of the complex.

Abstract: A method for assaying specific binding between a fluorophore-labeled probe and an unlabeled target is provided. The method includes detecting a quenching effect on fluorescence emitted by the fluorophore-labeled probe resulting from binding. The method is conducted without separating complexes of the target and probe from the free target and free probe prior to quenching effect detecting, and without providing a signal quenching agent to quench fluorescent light. Preferably, the probe and target are amino acid-containing compounds, such as proteins. The method can be used for a variety of applications, including screening for drug candidates having optimum binding properties, and quantifying and classifying the binding characteristics between peptide-containing compounds. The method is more sensitive than conventional assays, enabling the analysis of minute samples and low affinity binding interactions between receptors and ligands that are below the detection limits of conventional technology.

Abstract: A method for determining an affinity of a first nucleobase-containing sequence for a second nucleobase-containing sequence includes providing a test medium containing the first nucleobase-containing sequence and the second nucleobase-containing sequence, applying a voltage across the test medium, measuring a test electric current through the test medium; and determining the affinity by evaluating whether the test electric current is equivalent to a reference electric current of a reference medium containing a longer of the first nucleobase-containing sequence and the second nucleobase-containing sequence. A complex in an electrically-stimulated phase contains at least two nucleobase-containing sequences in a medium, wherein the electrical conductivity of the medium increases linearly without a plateau as the temperature of the medium approaches and exceeds a Tm of the complex.

Abstract: A method for modifying transcription and/or translation in an organism (e.g.

Abstract: A method for influencing binding of a first biopolymer to a second biopolymer includes applying an electric charge to a binding medium in which the first and second biopolymers are to be bonded together, wherein the electric charge is applied sufficiently to enhance or diminish a binding characteristic of the binding to thereby enhance the binding desired, provided that the binding characteristic is not denaturation of the first and second biopolymers from each other or from another biopolymer.

Abstract: A method for determining an affinity of a first nucleobase-containing sequence for a second nucleobase-containing sequence includes providing a test medium containing the first nucleobase-containing sequence and the second nucleobase-containing sequence, applying a voltage across the test medium, measuring a test electric current through the test medium; and determining the affinity by evaluating whether the test electric current is equivalent to a reference electric current of a reference medium containing a longer of the first nucleobase-containing sequence and the second nucleobase-containing sequence. A complex in an electrically-stimulated phase contains at least two nucleobase-containing sequences in a medium, wherein the electrical conductivity of the medium increases linearly without a plateau as the temperature of the medium approaches and exceeds a Tm of the complex.