The invention relates to methods for the determination and detection of nucleic acids sequences in a sample. The
nucleic acid may be
RNA or
DNA or both. The invention also relates to methods for the determination of the presence and species of various microorganisms in a sample. We have also identified a set of
oligonucleotide nucleic acid sequences within the rRNAs of
Gram-negative organisms that facilitates both the broad identification of
Gram-negative organisms as a class when used as a
pool, or in combination, for example in a hybridization
assay. This set of oligonucleotides may detect sequences that are indicative of the presence of organisms of the broad class of
Gram-negative organisms while exhibiting little or no false identification of Gram-positive organisms, and fungi, or other microorganisms. The
assay includes concurrent incubation with at least one
nucleotide sequence of interest, at least one
nucleic acid probe, a
fluorosurfactant, and a
nuclease. The
assay may further be employed to detect the presence of
bacteria, fungi, or other microorganisms by use of additional specific probes, or to detect and / or identify target nucleic acid sequences in a sample. Further, the invention also relates to methods of reducing non-specific binding and facilitating
complex formation in a binding assay. The binding assay may be, but is not limited to, a nucleic acid hybridization assay or an
immunoassay. The invention also relates to methods of detection that employ at least one target of interest, which may be a
nucleotide sequence, at least one probe, which may be a nucleic acid probe and a
nuclease.