Abstract: The present invention provides at least one isolated linear composite nucleic acid molecule comprising at least one first tag from at least one first nucleic acid molecule and at least one second tag from at least one second nucleic acid molecule, wherein the first and second nucleic acids interact in a nucleic acid mixture; and wherein the first and second tags are from different nucleic acid molecules. The invention also provides a method of producing at least one isolated linear composite nucleic acid and to a method of detecting and/or identifying nucleic acid interactions.

Abstract: We describe a method of providing an indication of an instance of expression of a gene, the method comprising the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Abstract: A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: The present invention provides at least one isolated linear composite nucleic acid molecule comprising at least one first tag from at least one first nucleic acid molecule and at least one second tag from at least one second nucleic acid molecule, wherein the first and second nucleic acids interact in a nucleic acid mixture; and wherein the first and second tags are from different nucleic acid molecules. The invention also provides a method of producing at least one isolated linear composite nucleic acid and to a method of detecting and/or identifying nucleic acid interactions.

Abstract: A method of identifying at least a nucleic acid molecule fragment to which a protein of interest binds, comprising: (i) preparing at least one nucleic acid molecule fragment to which a protein binds; (ii) isolating the 5? terminus and the 3? terminus of the nucleic acid fragment(s) and linking the 5? terminus and 3? terminus to create the at least one ditag; (iii) sequencing the ditag; and (iv) mapping the ditag sequence(s) to the genome.

Abstract: A method of identifying at least a nucleic acid molecule fragment to which a protein of interest binds, comprising: (i) preparing at least one nucleic acid molecule fragment to which a protein binds; (ii) isolating the 5? terminus and the 3? terminus of the nucleic acid fragment(s) and linking the 5? terminus and 3? terminus to create the at least one ditag; (iii) sequencing the ditag; and (iv) mapping the ditag sequence(s) to the genome.

Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Abstract: A method of providing an indication of an instance of expression of a gene is described herein, the method which may comprise the steps of: (a) providing a complementary deoxyribonucleic acid (cDNA) having a terminus comprising a terminal transcribed sequence of a gene; (b) linking the cDNA to an linker sequence thereby forming a linked nucleic acid, in which the linker sequence comprises a first recognition site for a first nucleic acid cleavage enzyme, preferably a restriction endonuclease, that allows nucleic acid cleavage at a site distant from the first recognition site; and (c) cleaving the linked nucleic acid with the first nucleic acid cleavage enzyme to provide a linked tag, in which the linked tag comprises a nucleotide sequence tag representative of a terminal transcribed sequence of the gene; and (d) detecting the presence or identity of the linked tag or the nucleotide sequence tag to provide an indication of an instance of gene expression.

Abstract: A method of identifying at least a nucleic acid molecule fragment to which a protein of interest binds, comprising: (i) preparing at least one nucleic acid molecule fragment to which a protein binds; (ii) isolating the 5? terminus and the 3? terminus of the nucleic acid fragment(s) and linking the 5? terminus and 3? terminus to create the at least one ditag; (iii) sequencing the ditag; and (iv) mapping the ditag sequence(s) to the genome.

Abstract: An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5?-terminus sequence and the second tag comprises the 3?-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.