Method for detecting the presence of nucleases in a sample, characterized in that it comprises the steps of: —incubating the sample to be tested for the presence of nucleases with at least one oligonucleotide linker constituting the substrate for the nuclease to be detected, for a sufficient time to cause degradation of said oligonucleotide linker by the nuclease possibly present in the sample, —adding to the sample, upon incubation, colloidal gold nanoparticles comprising gold nanoparticles functionalized with a first probe oligonucleotide and gold nanoparticles functionalized with a respective second probe oligonucleotide, said first and second probe oligonucleotides being complementary to a respective portion of the nucleotide sequence of the oligonucleotide linker, and—examining the possible colour change of the sample as a result of the addition of said nanoparticles, a colour change of the sample to the colour assumed by the colloidal gold particles when aggregated at a distance less than their size being indicative of the absence of the tested nuclease from the sample.

Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.

Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.

A method of cleaving DNA molecules into smaller fragments by the creation of “cleavage trigger sites” followed by enzymatic processing. In some embodiments the “cleavage trigger sites” are created by the incorporation of nucleotides having uracil bases into a DNA molecule and processing with uracil DNA glycosylase, endonuclease IV and T7 endonuclease I.

A method of cleaving DNA molecules into smaller fragments by the creation of “cleavage trigger sites” followed by enzymatic processing. In some embodiments the “cleavage trigger sites” are created by the incorporation of nucleotides having uracil bases into a DNA molecule and processing with uracil DNA glycosylase, endonuclease IV and T7 endonuclease I.

Provided herein is a polymerase-free enzyme mix (FRAG) for fragmenting double-stranded DNA. In some embodiments the enzyme mix may comprise a double-stranded DNA nickase and at least one of a DNA ligase capable of sealing a nick within a DNA, and a single-strand specific DNA nuclease. Methods for fragmenting double-stranded DNA are also provided.

Provided herein is a polymerase-free enzyme mix (FRAG) for fragmenting double-stranded DNA. In some embodiments the enzyme mix may comprise a double-stranded DNA nickase and at least one of a DNA ligase capable of sealing a nick within a DNA, and a single-strand specific DNA nuclease. Methods for fragmenting double-stranded DNA are also provided.

The present invention provides a method of detecting and a method of quantifying oligonucleotides with more excellent specificity and quantitativity as compared to conventional signal amplification (PALSAR) measurement methods.

In the present invention, the problem is solved by hybridizing a target oligonucleotide to be measured with a complementary nucleic acid probe (3′-complementary sequence of target sequence-5′), or hybridizing the target oligonucleotide to be measured having given bases such as poly(A) added thereto with a complementary nucleic acid probe (3′-complementary sequence of target oligonucleotide+complementary sequence of given bases-5′), decomposing and removing an incomplete hybridization product by using a single-strand-specific nuclease such as Si nuclease, and measuring the nucleic acid probe contained in a remaining complete hybridization product by a PALSAR method.

The present invention provides a method of detecting and a method of quantifying oligonucleotides with more excellent specificity and quantitativity as compared to conventional signal amplification (PALSAR) measurement methods.

In the present invention, the problem is solved by hybridizing a target oligonucleotide to be measured with a complementary nucleic acid probe (3′-complementary sequence of target sequence-5′), or hybridizing the target oligonucleotide to be measured having given bases such as poly(A) added thereto with a complementary nucleic acid probe (3′-complementary sequence of target oligonucleotide+complementary sequence of given bases-5′), decomposing and removing an incomplete hybridization product by using a single-strand-specific nuclease such as Si nuclease, and measuring the nucleic acid probe contained in a remaining complete hybridization product by a PALSAR method.

Methods are provided for tagging, characterizing and sorting double-stranded biomolecules while maintaining the integrity of the biomolecules.