u2032 terminus as used herein a nucleic acid sequence even if internal to a larger oligonucleotide or polynucleotide also can be said to have 5 u2032 and 3 u2032 ends for example a gene sequence located within a larger chromosome sequence can still be said to have a 5 u2032 and 3 u2032 end as used herein the 3 u2032 terminal region of the nucleic acid probe refers to the region of the probe including nucleotides within about 10 residues from the 3 u2032 terminal position in either a linear or circular dna molecule discrete elements are referred to as being u201c upstream u201d or u201c 5 u2032 u201d relative to an element if they are bonded or would be bonded to the 5 u2032 end of that element similarly discrete elements are u201c downstream u201d or u201c 3 u2032 u201d relative to an element if they are or would be bonded to the 3 u2032 end of that element transcription proceeds in a 5 u2032 to 3 u2032 manner along the dna strand this means that rna is made by the sequential addition of ribonucleotide 5 u2032 triphosphates to the 3 u2032 terminus of the growing chain with the elimination of pyrophosphate as used herein the term u201c target nucleic acid u201d or u201c nucleic acid target u201d refers to a particular nucleic acid sequence of interest thus the u201c target u201d can exist in the presence of other nucleic acid molecules or within a larger nucleic acid molecule as used herein the term u201c nucleic acid probe u201d refers.