1-14. (canceled)
15. A method of quantifying a target nucleic acid sequence in a sample, comprising the steps of:
(a) contacting the sample with a first amplification oligonucleotide, specific for a first portion of the target nucleic acid sequence, under conditions allowing hybridization of the first amplification oligonucleotide to the first portion of the target nucleic acid sequence, thereby generating a pre-amplification hybrid that comprises the first amplification oligonucleotide and the target nucleic acid sequence;
(b) isolating the pre-amplification hybrid by target capture onto a solid support followed by washing to remove any of the first amplification oligonucleotide that did not hybridize to the first portion of the target nucleic acid sequence in step (a);
(c) amplifying, in a first phase amplification reaction mixture, at least a portion of the target nucleic acid sequence of the pre-amplification hybrid isolated in step (b) in a first phase, substantially isothermal, transcription-associated amplification reaction under conditions that support linear amplification thereof, but do not support exponential amplification thereof, thereby resulting in a reaction mixture comprising a first amplification product,
wherein the first phase amplification reaction mixture comprises a second amplification oligonucleotide, the second amplification oligonucleotide being complementary to a portion of an extension product of the first amplification oligonucleotide and wherein the second amplification oligonucleotide is not enzymatically extended in the first phase of isothermal transcription-associated amplification reaction, and
wherein the first amplification product is not a template for nucleic acid synthesis during the first phase, substantially isothermal, transcription-associated amplification reaction;
(d) combining the reaction mixture comprising the first amplification product with at least one component that participates in exponential amplification of the first amplification product, but that is lacking from the reaction mixture comprising the first amplification product, to produce a second phase amplification reaction mixture,
wherein the second phase amplification reaction mixture additionally comprises a sequence-specific hybridization probe;
(e) performing, in a second phase, substantially isothermal, transcription-associated amplification reaction in the second phase amplification reaction mixture, an exponential amplification of the first amplification product, thereby synthesizing a second amplification product;
(f) detecting, with the sequence-specific hybridization probe at regular time intervals, synthesis of the second amplification product in the second phase amplification reaction mixture; and
(g) quantifying the target nucleic acid sequence in the sample using results from step (f).
16. The method of claim 15, wherein the first amplification oligonucleotide comprises a 3\u2032 target specific sequence and a 5\u2032 promoter sequence for an RNA polymerase.
17. The method of claim 15, wherein the RNA polymerase is T7 RNA polymerase.
18. The method of claim 15, wherein the solid support comprises an immobilized capture probe.
19. The method of claim 15,
wherein step (a) further comprises contacting the sample with a target capture oligonucleotide that hybridizes to the target nucleic acid sequence, and
wherein the pre-amplification hybrid comprises the target nucleic acid sequence hybridized to each of the target capture oligonucleotide and the first amplification oligonucleotide.
20. The method of claim 15, wherein the solid support comprises magnetically attractable particles.
21. The method of claim 15, wherein each of the first and second phase isothermal transcription-associated amplification reactions comprise an RNA polymerase and a reverse transcriptase.
22. The method of claim 15, wherein the at least one component comprises the first amplification oligonucleotide.
23. The method of claim 15, wherein the first amplification product of step (c) is a cDNA molecule with the same polarity as the target nucleic acid sequence in the sample, and wherein the second amplification product of step (e) is an RNA molecule.
24. The method of claim 15, wherein the sequence-specific hybridization probe in step (d) is a conformation-sensitive probe that produces a detectable signal when hybridized to the second amplification product.
25. The method of claim 15, wherein the sequence-specific hybridization probe in step (d) is a fluorescently labeled sequence-specific hybridization probe.
26. The method of claim 15, wherein step (g) comprises quantifying the target nucleic acid sequence in the sample using a linear calibration curve and results from step (f).
27. The method of claim 15, wherein step (c) comprises amplifying by 10-fold to 10,000-fold, in the first phase amplification reaction mixture.
28. The method of claim 15, wherein the second amplification oligonucleotide comprises a blocked 3\u2032 terminus.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A sigma-delta analog-to-digital converter comprising:
a sigma-delta feedback loop of the sigma-delta analog-to-digital converter;
a variable gain amplifier within the sigma-delta feedback loop; and
an attenuator within the sigma-delta feedback loop.
2. The sigma-delta analog-to-digital converter of claim 1 wherein the sigma-delta feedback loop comprises a loop filter, a quantizer, a loop digital-to-analog converter and a summer, the variable gain amplifier positioned prior to the quantizer and after the summer.
3. (canceled)
4. The sigma-delta analog-to-digital converter of claim 1 wherein the attenuator is operable to attenuate by an attenuation factor and the amplifier is operable to amplify by an amplification factor, the attentuation factor equal to the amplification factor.
5. The sigma-delta analog-to-digital converter of claim 1 further comprising:
an output from the sigma-delta feedback loop;
a processor operable to receive signals on the output and operable to vary a gain of the variable gain amplifier in response to the signals.
6. The sigma-delta analog-to-digital converter of claim 5 wherein the sigma-delta feedback loop comprises a continuous-time sigma-delta loop and wherein the processor is operable to automatically control the gain.
7. The sigma-delta analog-to-digital converter of claim 1 wherein the variable gain amplifier is operable to amplify an output of the sigma-delta analog-to-digital converter, the attenuator operable to attenuate feedback signals for combination with signal input to the sigma-delta analog-to-digital converter prior to amplification by the variable gain amplifier.
8. A signal path with automatic gain control, the signal path comprising:
an analog device;
a sigma-delta analog-to-digital converter coupled with the analog device, the sigma-delta analog-to-digital converter having a sigma-delta feedback loop, an attenuator and a variable gain amplifier within the sigma-delta feedback loop.
9. The signal path of claim 8 wherein the sigma-delta analog-to-digital converter comprises a loop filter, a quantizer, a loop digital-to-analog converter and a summer, the variable gain amplifier positioned prior to the quantizer and after the summers and the attenuator is positioned after the loop digital-to-analog converter and before the summer.
10. The signal path of claim 9 wherein the variable gain amplifier is positioned after the loop filter.
11. (canceled)
12. The signal path of claim 8 wherein the attenuator is operable to attenuate by an attenuation factor and the amplifier is operable to amplify by an amplification factor, the attentuation factor equal to the amplification factor.
13. The signal path of claim 8 further comprising:
an output from the sigma-delta feedback loop;
a processor operable to receive signals on the output and operable to vary a gain of the variable gain amplifier and an attenuation of the attenuator in response to the signals.
14. The signal path of claim 8 wherein the variable gain amplifier is operable to amplify an output of the signal path, the attenuator is operable to attenuate feedback signals for combination with signals input to the signal path prior to amplification by the variable gain amplifier.
15. The signal path of claim 8 further comprising:
at least one of a LNA or an additional variable gain amplifier prior to the sigma-delta analog-to-digital converter, the one operable to partially amplify and the variable gain amplifier operable to partially amplify within the signal path.
16. The signal path of claim 8 wherein the analog device comprises a mixer, further comprising:
a filter between the mixer and the sigma-delta analog-to-digital converter; and
an adjustable gain amplifier between the filter and the sigma-delta analog-to-digital converter.
17. The signal path of claim 8 comprising a mobile telephone receiver.
18. A method for automatically controlling gain with a sigma-delta analog-to-digital converter, the method comprising:
(a) converting analog signals to digital signals with a quantizer of the sigma-delta analog-to-digital converter; and
(b) scaling the digital signals output by the quantizer inside the sigma-delta analog-to-digital converter;
wherein (a) comprises quantizing and summing a sigma-delta feedback signal with input analog signals, and wherein (b) comprises the amplifying and attenuating the sigma-delta feedback signal as a function of the amplification prior to quantizing.
19. The method of claim 18 wherein (b) comprises scaling inside a low-pass or band-pass continuous-time sigma-delta loop.
20. The method of claim 18 wherein (a) comprises quantizing the analog signals, and wherein (b) comprises amplifying the analog signals prior to the quantizing.
21. (canceled)
22. A method for automatically controlling gain with a sigma-delta analog-to-digital converter, the method comprising:
(a) converting analog signals to digital signals with a quantizer of the sigma-delta analogy-to-digital converter;
(b) scaling the digital signals output by the quantizer inside the sigma-delta analog-to-digital converter; and
(c) adjusting the scaling of (b) as a function of the digital signals output by the sigma-delta analog-to-digital converter.
23. The method of claim 22 wherein (b) and (c) comprise automatically controlling gain in a receive path, the receive path including the sigma-delta analog-to-digital converter.
24. The sigma-delta analog-to-digital converter of claim 1 further comprising:
a single digital-to-analog converter in the sigma-delta feedback loop.
25. The sigma-delta analog-to-digital converter of claim 1 further comprising:
a single loop filter in the sigma-delta feedback loop.
26. The signal path of claim 8 wherein the sigma-delta feedback loop includes a single digital-to-analog converter.
27. The signal path of claim 8 wherein the sigma-delta feedback loop includes a single loop filter.
28. The method of claim 18 further comprising:
filtering with a signal loop filter in a sigma-delta feedback loop.
29. The method of claim 18 further comprising:
converting the digital signals with a single digital-to-analog converter.
30. A sigma-delta analog-to-digital converter comprising:
a sigma-delta feedback loop;
a variable gain amplifier within the sigma-delta feedback loop; and
a single digital-to-analog converter in the sigma-delta feedback loop.
31. A sigma-delta analog-to-digital converter comprising:
a sigma-delta feedback loop;
a variable gain amplifier within the sigma-delta feedback loop; and
a single loop filter in the sigma-delta feedback loop.