Methods and compositions for nucleic acid amplification

1. A composition comprising:

a TSU promoter oligonucleotide that includes a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to a target sequence contained in a target nucleic acid, wherein the TSU promoter oligonucleotide is a TSU promoter primer that has a 3′ terminus that is capable of being extended by a polymerase, or is a TSU promoter provider oligonucleotide that has a blocked 3′ terminus that is incapable of being extended by a polymerase, directly or indirectly joined to,

a TSU non-promoter primer oligonucleotide made up of a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1,

wherein the TSU promoter oligonucleotide is joined to the TSU non-promoter primer via:

a covalent linkage that is a polynucleotide linker sequence, a non-nucleotide abasic linker compound or a linker containing both nucleotide and non-nucleotide residues;

a hybridization complex between the 5′ promoter sequence and a sequence on the TSU non-promoter primer that is complementary to the 5′ promoter sequence; or

a hybridization complex that includes an S-oligonucleotide that contains a first sequence complementary to a sequence in the TSU promoter oligonucleotide and a second sequence complementary to a sequence in the TSU non-promoter primer oligonucleotide.

2. The composition of claim 1 , wherein the TSU promoter oligonucleotide is directly joined to the TSU non-promoter primer oligonucleotide via the covalent linkage.

3. The composition of claim 1 , further comprising: (i) a target specific capture oligonucleotide that contains a sequence that hybridizes specifically to a sequence in the target nucleic acid at a sequence that is different from the sequence in the target nucleic acid that hybridizes to the TS sequence of the TSU promoter oligonucleotide or the TS sequence of the TSU non-promoter primer, and contains a means for binding the target nucleic acid to a support; (ii) a universal promoter primer made up a 5′ promoter sequence and a 3′ universal sequence that is the same as the universal sequence of the TSU promoter oligonucleotide; (iii) a universal primer made up a universal sequence that is the same as the universal sequence of the TSU non-promoter primer oligonucleotide; (iv) a blocker oligonucleotide that hybridizes specifically to a sequence in a target nucleic acid strand that is different than the sequence that the TS sequence of the TSU promoter oligonucleotide or the TS sequence of the TSU non-promoter primer oligonucleotide binds to in the target nucleic acid strand, wherein the blocker oligonucleotide has a 3′ blocked terminus that is not capable of being extended by a polymerase; (v) a detection probe oligomer; (vi) a molecular torch; (vii) or any combination thereof.

4. The composition claim 1 further comprising at least one universal promoter primer made up of a 5′ promoter sequence and a 3′ U1 sequence and at least one target specific primer (TSP) made up of a sequence that is complementary to a sequence contained in an RNA transcript made from a double stranded DNA that contains a cDNA sequence made from synthetic extension of the 3′ end of the TSU promoter primer oligonucleotide.

5. A method of amplifying a target nucleic acid comprising the steps of:

a. mixing a target nucleic acid with a target specific universal (TSU) primer complex made up of

i. a TSU promoter primer oligonucleotide comprising a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to a target sequence contained in a target nucleic acid, and a 3′ terminus that is capable of being extended by a polymerase, directly or indirectly joined to,

ii. a TSU non-promoter primer oligonucleotide comprising a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1,

iii. wherein the TSU promoter primer oligonucleotide is joined to the TSU non-promoter primer oligonucleotide via:

a covalent linkage that is a polynucleotide linker sequence, a non-nucleotide abasic linker compound or a linker containing both nucleotide and non-nucleotide residues;

a hybridization complex between the 5′ promoter sequence and a sequence on the TSU non-promoter primer that is complementary to the 5′ promoter sequence; or

a hybridization complex that includes an S-oligonucleotide that contains a first sequence complementary to a sequence in the TSU promoter oligonucleotide and a second sequence complementary to a sequence in the TSU non-promoter primer oligonucleotide,

b. hybridizing the TSU promoter primer oligonucleotide of the TSU primer complex to a target sequence in the target nucleic acid via the TS1 sequence in the TSU promoter primer,

c. isolating the target nucleic acid with hybridized TSU complex away from unhybridized TSU primer complexes and other sample components,

d. synthetically extending the 3′ terminus of the TS1 by using a polymerase in vitro nucleic acid synthesis in which the target nucleic acid is a template to make a first cDNA strand,

e. hybridizing the TSU non-promoter primer oligonucleotide of the TSU primer complex to the first cDNA strand by specific hybridization of the TS2 sequence to its target sequence contained in the first cDNA strand,

f. synthetically extending the 3′ terminus of the TS2 sequence hybridized to the first cDNA strand by a polymerase in vitro nucleic acid synthesis to made a second DNA strand, thereby making a substantially double-stranded DNA that contains a functional promoter sequence and the U1 sequence,

g. enzymatically transcribing RNA transcripts from the functional promoter sequence of the substantially double-stranded DNA to make RNA transcripts that contain a 5′ U1 region sequence, a TS1 sequence, a complement of the second target specific sequence (TS2′), and a 3′ universal sequence that is complementary to the U2 sequence (U2′),

h. hybridizing a universal primer oligonucleotide (UP2) that contains a universal sequence U2 to the RNA transcript at the U2′ sequence,

i. synthetically extending the 3′ terminus of the UP2 by enzymatic in vitro nucleic acid synthesis to make a cDNA strand,

j. hybridizing a universal promoter primer oligonucleotide (UP1) that contains a universal sequence U1 to the cDNA made in the previous step at the U1′ sequence,

k. synthetically extending at least the 3′ terminus of the DNA strand made in step i by enzymatic in vitro nucleic acid synthesis to make a functional promoter, and

l. transcribing multiple RNA transcripts from the functional promoter which transcripts are amplification products that may serve as templates for further enzymatic in vitro nucleic acid synthesis.

6. The method of claim 5 , further comprising the step of detecting the amplification products to indicate the presence of an analyte in the mixture from which the target nucleic acid was isolated.

7. A method of amplifying a target nucleic acid comprising the steps of:

a. mixing a target nucleic acid with a target specific universal (TSU) complex made up of

i. a TSU promoter oligonucleotide comprising a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to its target sequence, wherein the TSU promoter oligonucleotide is a TSU promoter provider oligonucleotide that has a blocked 3′ terminus that is incapable of being extended by a polymerase, directly or indirectly joined to,

ii. a TSU non-promoter primer oligonucleotide comprising a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1,

iii. wherein the TSU promoter primer oligonucleotide is joined to the TSU non-promoter primer oligonucleotide via:

a covalent linkage that is a polynucleotide linker sequence, a non-nucleotide abasic linker compound or a linker containing both nucleotide and non-nucleotide residues;

a hybridization complex between the 5′ promoter sequence and a sequence on the TSU non-promoter primer that is complementary to the 5′ promoter sequence; or

a hybridization complex that includes an S-oligonucleotide that contains a first sequence complementary to a sequence in the TSU promoter oligonucleotide and a second sequence complementary to a sequence in the TSU non-promoter primer oligonucleotide,

b. hybridizing the TSU non-promoter primer oligonucleotide of the TSU complex to a target sequence in the target nucleic acid via the TS2 sequence in the TSU non-promoter primer,

c. optionally hybridizing a blocker oligonucleotide to a sequence on the target nucleic acid, wherein said blocker comprises a blocked 3′ terminus to prevent extension of the blocker by a polymerase and wherein the blocker oligomer is hybridized to the target nucleic acid at a position to terminate polymerase extension of the TSU non-promoter primer,

d. isolating the target nucleic acid with hybridized TSU complex away from unhybridized TSU primer complexes and other sample components,

e. synthetically extending the 3′ terminus of the TSU non-promoter primer hybridized to the target nucleic acid by using a polymerase in vitro nucleic acid synthesis in which the target nucleic acid is a template to make a first cDNA strand,

f. hybridizing the TSU promoter provider oligonucleotide of the TSU complex to the first cDNA strand by specific hybridization of the TS1 sequence in the TSU promoter provider oligonucleotide to a target sequence contained in the first cDNA strand,

g. synthetically extending the 3′ terminus of the first cDNA by using the TSU promoter provider as a template to make a substantially double-stranded DNA that contains a functional promoter sequence and the U1 sequence,

h. enzymatically transcribing RNA transcripts from the functional promoter sequence to make RNA transcripts that contain a 5′ U1 region sequence, a TS1 sequence, a complement of the second target specific sequence (TS2′), and a 3′ universal sequence that is complementary to the U2 sequence (U2′),

i. hybridizing a universal primer oligonucleotide (UP2) that contains a universal sequence U2 to the RNA transcript at the U2′ sequence,

j. synthetically extending the 3′ terminus of the UP2 by enzymatic in vitro nucleic acid synthesis to make a cDNA strand,

k. hybridizing to the U1′ sequence a universal promoter oligonucleotide (UP1) that contains a promoter sequence, a universal sequence U1, and a 3′ blocked end to the cDNA made step j,

l. synthetically extending the 3′ terminus of the DNA strand made in step j using the UP1 oligonucleotide as a template to make a functional double-stranded promoter using enzymatic in vitro nucleic acid synthesis, and

m. transcribing multiple RNA transcripts from the functional promoter, which transcripts are amplification products that may serve as templates for further enzymatic in vitro nucleic acid synthesis.

8. The method of claim 7 , further comprising the step of detecting the amplification products to indicate the presence of an analyte in the sample from which the target nucleic acid was isolated.

9. The method of claim 6 , wherein the detection step is performed using a method selected from the group consisting of hybridizing a detection probe oligomer to an amplification product and sequencing an amplification product.

10. The method of claim 9 , wherein the detection probe is present in the reaction of step g.

11. The method of claim 9 , wherein the detection probe is present in the reaction of step d.

12. The method of claim 6 , wherein the detection step is performed using a molecular torch.

13. The method of claim 6 , wherein the detection step is a quantitative detection step to determine the amount of an analyte in the sample from which the target nucleic acid was isolated.

14. The method of claim 8 , wherein the detection step is performed using a method selected from the group consisting of hybridizing a detection probe oligomer to an amplification product or sequencing an amplification product.

15. The method of claim 14 , wherein the detection probe is present in the reaction of step h.

16. The method of claim 14 , wherein the detection probe is present in the reaction of step e.

17. The method of claim 8 , wherein the detection step is performed using a molecular torch.

18. The method of claim 8 , wherein the detection step is a quantitative detection step to determine the amount of an analyte in the sample from which the target nucleic acid was isolated.

19. The composition of claim 1 comprising:

a target specific universal (TSU) complex made up of;

i. a TSU promoter oligonucleotide that includes a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to a target sequence contained in a target nucleic acid, wherein the TSU promoter oligonucleotide is a TSU promoter primer that has a 3′ terminus that is capable of being extended by a polymerase, or is a TSU promoter provider oligonucleotide that has a blocked 3′ terminus that is incapable of being extended by a polymerase, directly or indirectly joined to,

ii. a TSU non-promoter primer oligonucleotide made up of a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1;

iii. wherein the TSU promoter primer oligonucleotide is joined to the TSU non-promoter primer oligonucleotide via:

a covalent linkage that is a polynucleotide linker sequence, a non-nucleotide abasic linker compound or a linker containing both nucleotide and non-nucleotide residues;

a hybridization complex between the 5′ promoter sequence and a sequence on the TSU non-promoter primer that is complementary to the 5′ promoter sequence; or

a hybridization complex that includes an S-oligonucleotide that contains a first sequence complementary to a sequence in the TSU promoter oligonucleotide and a second sequence complementary to a sequence in the TSU non-promoter primer oligonucleotide,

a universal promoter primer oligonucleotide (UP1) comprising a 5′ promoter sequence, a 3′ universal sequence that is the same as the first universal sequence U1 of the TSU promoter oligonucleotide, and optionally a 3′ blocked end; and

a universal primer oligonucleotide (UP2) comprising a universal sequence that is the same as the second universal sequence U2 of the of the TSU non-promoter primer oligonucleotide.

20. The composition of claim 1 , further comprising other reagents suitable for performing in vitro amplification of the target nucleic acid.

21. The composition of claim 1 , wherein the TSU promoter oligonucleotide is directly joined to the TSU non-promoter primer oligonucleotide via the hybridization complex between the 5′ promoter sequence and the sequence on the TSU non-promoter primer that is complementary to the 5′ promoter sequence.

22. The composition of claim 1 , wherein the TSU promoter oligonucleotide and the TSU non-promoter primer oligonucleotide are contained within a target capture reagent mixture.

23. A composition comprising:

a TSU promoter oligonucleotide that includes a 5′ promoter sequence, an internal first universal sequence (U1), and a 3′ first target specific sequence (TS1) that binds specifically to a target sequence contained in a target nucleic acid, wherein the TSU promoter oligonucleotide is a TSU promoter primer that has a 3′ terminus that is capable of being extended by a polymerase, or is a TSU promoter provider oligonucleotide that has a blocked 3′ terminus that is incapable of being extended by a polymerase, directly or indirectly joined to,

a TSU non-promoter primer oligonucleotide made up of a 5′ second universal sequence (U2) and a 3′ second target specific sequence (TS2) which is different from the TS1,

wherein the TSU promoter oligonucleotide is joined to the TSU non-promoter primer via:

a covalent linkage that is a polynucleotide linker sequence, a non-nucleotide abasic linker compound or a linker containing both nucleotide and non-nucleotide residues;

a hybridization complex between a first sequence on the TSU promoter oligonucleotide and a second sequence on the TSU non-promoter primer that is complementary to the first sequence on the TSU promoter oligonucleotide; or

a hybridization complex that includes an S-oligonucleotide that contains a first sequence complementary to a sequence in the TSU promoter oligonucleotide and a second sequence complementary to a sequence in the TSU non-promoter primer oligonucleotide; and

wherein the TSU promoter oligonucleotide and the TSU non-promoter primer oligonucleotide are contained within a target capture reagent mixture.