Methods and apparatuses are described for nucleic acid analysis of environmental water samples and biological samples without the need for purification.

The present disclosure provides, among other things, systems, methods, and kits include internal amplification controls. Provided internal amplification controls are or include non-target sequences that are amplified during nucleic acid amplification. Provided internal amplification controls are linearly amplified. Provided internal amplification controls are useful for systems, methods and kits for nucleic acid amplification.

The present disclosure provides, among other things, systems, methods, and kits include internal amplification controls. Provided internal amplification controls are or include non-target sequences that are amplified during nucleic acid amplification. Provided internal amplification controls are linearly amplified. Provided internal amplification controls are useful for systems, methods and kits for nucleic acid amplification.

The invention features methods, systems, and cartridges for amplification of target nucleic acids in complex samples, for example, whole blood. The invention also features diagnostic and therapeutic methods based on amplification of target nucleic acids characteristic of pathogens present in complex samples containing cells and/or cell debris, for example, whole blood.

The invention features methods, systems, and cartridges for amplification of target nucleic acids in complex samples, for example, whole blood. The invention also features diagnostic and therapeutic methods based on amplification of target nucleic acids characteristic of pathogens present in complex samples containing cells and/or cell debris, for example, whole blood.

Methods of assaying cells of a cellular sample for the presence of a target nucleic acid are provided. Aspects of the methods include evaluating a cellular sample that has been contacted with a nuclease inhibitor for the presence of a target nucleic acid. Also provided are devices and kits that find use in practicing the methods described herein.

Methods of assaying cells of a cellular sample for the presence of a target nucleic acid are provided. Aspects of the methods include evaluating a cellular sample that has been contacted with a nuclease inhibitor for the presence of a target nucleic acid. Also provided are devices and kits that find use in practicing the methods described herein.

A method of detecting a nucleic acid including mixing a fluid including a target nucleic acid with a detection reagent including a first enzyme for cleaving a first nucleic acid having a first flap and a second enzyme for cleaving a second nucleic acid such that the target nucleic acid, the first nucleic acid and the second nucleic acid form a complex as a first invasive structure, conducting a first reaction which causes the first enzyme to cleave the first flap of the first invasive structure and produces a third nucleic acid that forms a complex, as a second invasive structure, with a fourth nucleic acid having a second flap, and conducting a second reaction which causes the second enzyme to cleave the second flap of the second invasive structure and produces a cleaved product.

A method of detecting a nucleic acid including mixing a fluid including a target nucleic acid with a detection reagent including a first enzyme for cleaving a first nucleic acid having a first flap and a second enzyme for cleaving a second nucleic acid such that the target nucleic acid, the first nucleic acid and the second nucleic acid form a complex as a first invasive structure, conducting a first reaction which causes the first enzyme to cleave the first flap of the first invasive structure and produces a third nucleic acid that forms a complex, as a second invasive structure, with a fourth nucleic acid having a second flap, and conducting a second reaction which causes the second enzyme to cleave the second flap of the second invasive structure and produces a cleaved product.

Reaction condition compositions for detecting a genomic variation from a small sample amount from 5 nano grams (ng) to 1 microgram (ug) includes DNA ligase, DNA polymerase, at least one COP, a DNA polymerase buffer, NAD+, at least two primers, and deoxynucleotide triphosphates (dNTPs). Detection of the genomic variation utilizes COPs with increased ligation efficiency and RCA with fluorescence detection due to simultaneous ligation of COPs to CPs and replication of the genomic variation. The reaction condition composition eliminates the need to perform background reduction of un-hybridized or un-ligated COPs.