Abstract: Provided is a method for identifying a functional antisense agent, which method comprises contacting an RNA with an oligonucleotide probe to form a duplex-containing RNA, contacting the duplex-containing RNA with an RNAase to cleave the duplex-containing RNA, and measuring the kinetics of cleavage.

Abstract: The present invention concerns a method for characterizing one or more nucleic acids. This method involves immobilizing double-stranded nucleic acids on a solid phase support and cleaving the immobilized nucleic acids with an endonuclease, such that each cleaved nucleic acid has a double-stranded portion. The cleaved nucleic acids are then denatured to form single-stranded cleaved nucleic acids. One or more oligonucleotide sequences are then hybridized to the resulting single-stranded cleaved nucleic acid. The oligonucleotide sequences used each comprise a pre-determined recognition sequence situated such that it recognizes a sequence which was part of the double-stranded portion of the nucleic acid and a label specific to the recognition sequence. The hybridized oligonucleotide sequences are then extended along the single-stranded portion of the immobilized nucleic acid to form an extended strand which is then denatured from the immobilized strand.

Abstract: The present invention provides a compound having the following formula: N-L-M wherein N comprises one or more nucleic acid bases, L is either a direct bond between N and M or L comprises a linker moiety, and M comprises a mass marker comprising an aryl ether.

Abstract: The present invention provides a method for analyzing a population of nucleic acid fragments each labeled with a mass label, which method comprises: i) ionizing the population; ii) sorting the ionized population in a mass spectrometer according to mass into sub-populations each containing at least one labeled fragment; iii) cleaving each sub-population to release the mass label associated with each labeled fragment; iv) determining the mass of each released mass label by mass spectroscopy; and v) assigning each mass label to its associated fragment.

Abstract: A method for characterizing polypeptides, which comprises: (a) treating a sample comprising a population of one or more polypeptides with a cleavage agent which is known to recognize a specific amino acid residue or sequence in polypeptide chains and to cleave at a cleavage site, whereby the population is cleaved to generate peptide fragments; (b) isolating a population of the peptide fragments which bear at one end a reference terminus comprising either only a C-terminus or only an N-terminus and which bear at the other end the cleavage site proximal to the reference terminus; and c) determining a signature sequence of at least some of the isolated fragments, which signature sequence is the sequence of a predetermined number of amino acid residues running from the cleavage site; wherein the signature sequence and the relative position of the cleavage site to the reference terminus characterize the polypeptide or each polypeptide.