Disclosed are compositions and a method relating to amplifying and detecting nucleic acids.

Photoblocked probes are disclosed including a specific hydrolysis probe having a first nucleic acid sequence complementary to a target having a second nucleic acid sequence, a first and a second interactive labels, a 5′ end and a 3′ end, and one or more photocleavable moieties coupled to one or more nucleotides of the specific hydrolysis probe, wherein the photocleaveable moiety interferes with the hybridization of the specific hydrolysis probe with the region of the amplification product. Also disclosed are PCR methods for the detection of the presence or absence of a target nucleic acid in a sample utilizing the photoblocked probes, as well as kits.

Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li.sup.+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li.sup.+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca.sup.2+. In addition to Li.sup.+, the fluid can contain polyethylenimine (PEI) with or without betaine.

Methods, compositions, kits and apparatuses that include a fluid, the fluid containing a ternary complex and Li.sup.+, wherein the ternary complex includes a primed template nucleic acid, a polymerase, and a nucleotide cognate for the next correct base for the primed template nucleic acid molecule. As an alternative or addition to Li.sup.+, the fluid can contain betaine or a metal ion that inhibits polymerase catalysis such as Ca.sup.2+. In addition to Li.sup.+, the fluid can contain polyethylenimine (PEI) with or without betaine.

A high throughput method for detecting chromosomal aberrations and/or telomere aberrations using a biological sample of 150 μL to 200 μL including preparing a cytogenetic slide from the sample in a microplate, the mitotic index in the cytogenetic slide being 3 times higher on average than the conventional procedure of culturing cells in flasks with 10 to 20 mL of medium, simultaneously labeling the telomeres and centromeres with peptide nucleic acid probes with a hybridisation time from 30 minutes to 1.5 hours, flow image quantifying the fluorescence intensity of telomeres on interphase nuclei using a 10× magnification objective for overall telomere quantification, and automatically capturing the metaphase chromosomes to detect chromosomal aberrations and/or telomere aberrations in each chromosome. Also a high-throughput detection kit for quantifying telomeres and detecting chromosomal aberrations and/or telomere aberrations.

A high throughput method for detecting chromosomal aberrations and/or telomere aberrations using a biological sample of 150 μL to 200 μL including preparing a cytogenetic slide from the sample in a microplate, the mitotic index in the cytogenetic slide being 3 times higher on average than the conventional procedure of culturing cells in flasks with 10 to 20 mL of medium, simultaneously labeling the telomeres and centromeres with peptide nucleic acid probes with a hybridisation time from 30 minutes to 1.5 hours, flow image quantifying the fluorescence intensity of telomeres on interphase nuclei using a 10× magnification objective for overall telomere quantification, and automatically capturing the metaphase chromosomes to detect chromosomal aberrations and/or telomere aberrations in each chromosome. Also a high-throughput detection kit for quantifying telomeres and detecting chromosomal aberrations and/or telomere aberrations.

A high throughput method for detecting chromosomal aberrations and/or telomere aberrations using a biological sample of 150 μL to 200 μL including preparing a cytogenetic slide from the sample in a microplate, the mitotic index in the cytogenetic slide being 3 times higher on average than the conventional procedure of culturing cells in flasks with 10 to 20 mL of medium, simultaneously labeling the telomeres and centromeres with peptide nucleic acid probes with a hybridisation time from 30 minutes to 1.5 hours, flow image quantifying the fluorescence intensity of telomeres on interphase nuclei using a 10× magnification objective for overall telomere quantification, and automatically capturing the metaphase chromosomes to detect chromosomal aberrations and/or telomere aberrations in each chromosome. Also a high-throughput detection kit for quantifying telomeres and detecting chromosomal aberrations and/or telomere aberrations.

Provided for herein is a method for detecting the presence of a nucleic acid target molecule in a biological sample. In certain aspects, the method comprises contacting a test sample that comprises (i) a biological sample comprising a nucleic acid target molecule and (ii) an osmylated single-stranded oligonucleotide probe comprising at least one pyrimidine residue covalently bonded to a substituted or unsubstituted Osmium tetroxide (OsO.sub.4)-2,2′-bypyridine group (OsBp group).

Provided for herein is a method for detecting the presence of a nucleic acid target molecule in a biological sample. In certain aspects, the method comprises contacting a test sample that comprises (i) a biological sample comprising a nucleic acid target molecule and (ii) an osmylated single-stranded oligonucleotide probe comprising at least one pyrimidine residue covalently bonded to a substituted or unsubstituted Osmium tetroxide (OsO.sub.4)-2,2′-bypyridine group (OsBp group).

Provided herein, in some embodiments, are novel compositions and improved methods for nucleic acid manipulation and analysis that can be applied to multiplex nucleic acid sequencing. In certain embodiments, the novel compositions and methods presented herein are more cost effective, more conducive to automation, and faster than traditional approaches. Also provided herein are novel blocking nucleic acids.