A method for monitoring of polynucleotide amplification of a set of one or more target nucleic acid sequences, comprising: (a) providing a mixture comprising a sample containing the target nucleic acid sequences, one or more than one oligonucleotide primers substantially complementary to a portion of the target nucleic acid sequences, a polymerizing enzyme, nucleotide substrates, and a detectable nucleic acid oligomer probe of between 5 and 100 bases, wherein said detectable nucleic acid oligomer probe has a backbone component selected from the group consisting of a sugar phosphate backbone, a modified sugar phosphate backbone, a locked nucleic acid backbone, a peptidic backbone, or a variant thereof, wherein said nucleic acid oligomer probe has a sequence substantially complementary to a probe region of at least one of the target nucleic acid sequences, wherein at least one of said oligonucleotide primers has a sequence complementary to an adjacent or overlapping portion of the probe region of the target nucleic acid sequences, and wherein said nucleic acid oligomer probe has at least one nucleic acid base substituted with a 3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4 -one analogue; wherein the 3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4 -one analogue comprises Formula III or Formula IV: wherein: R 1 is H; R 1' is H; L is a sugar or sugar/phosphate backbone analogue, including but not limited to a backbone of DNA, RNA, PNA, locked nucleic acid, modified DNA, modified PNA, modified RNA, or any combination thereof, and n is 1 to 5; and (b) incubating the mixture under conditions favorable for polymerization with a polymerase. (a) providing a mixture comprising a sample containing the target nucleic acid sequences, one or more than one oligonucleotide primers substantially complementary to a portion of the target nucleic acid sequences, a polymerizing enzyme, nucleotide substrates, and a detectable nucleic acid oligomer probe of between 5 and 100 bases, wherein said detectable nucleic acid oligomer probe has a backbone component selected from the group consisting of a sugar phosphate backbone, a modified sugar phosphate backbone, a locked nucleic acid backbone, a peptidic backbone, or a variant thereof, wherein said nucleic acid oligomer probe has a sequence substantially complementary to a probe region of at least one of the target nucleic acid sequences, wherein at least one of said oligonucleotide primers has a sequence complementary to an adjacent or overlapping portion of the probe region of the target nucleic acid sequences, and wherein said nucleic acid oligomer probe has at least one nucleic acid base substituted with a 3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4 -one analogue; wherein the 3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4 -one analogue comprises Formula III or Formula IV: wherein: R 1 is H; R 1' is H; L is a sugar or sugar/phosphate backbone analogue, including but not limited to a backbone of DNA, RNA, PNA, locked nucleic acid, modified DNA, modified PNA, modified RNA, or any combination thereof, and n is 1 to 5; and R 1 is H; R 1' is H; L is a sugar or sugar/phosphate backbone analogue, including but not limited to a backbone of DNA, RNA, PNA, locked nucleic acid, modified DNA, modified PNA, modified RNA, or any combination thereof, and n is 1 to 5; and (b) incubating the mixture under conditions favorable for polymerization with a polymerase.