Cooperative primers, probes, and applications thereof

1. A cooperative nucleic acid molecule comprising:

a. a first nucleic acid sequence, wherein the first nucleic acid sequence is complementary to a first region of a target nucleic acid, and wherein the first nucleic acid sequence is extendable on the 3′ end;

b. a second nucleic acid sequence, wherein the second nucleic acid sequence is complementary to a second region of the target nucleic acid, such that in the presence of the target nucleic acid it hybridizes to the target nucleic acid downstream from the 3′ end of the first nucleic acid sequence;

c. a linker connecting said first and second nucleic acid sequences, the linker configured to allow both the said first nucleic acid sequence and the said second nucleic acid sequences to hybridize to the target at the same time, wherein the linker comprises at least one non-nucleic acid chemical group.

2. The cooperative nucleic acid molecule of claim 1 wherein the first nucleic acid molecule will not hybridize to the target without the second nucleic acid molecule hybridizing to the target.

3. The cooperative nucleic acid molecule of claim 1 wherein the second nucleic acid molecule will not hybridize to the target without the first nucleic acid molecule hybridizing to the target.

4. The cooperative nucleic acid molecule of claim 1 wherein neither the first nor the second nucleic acid molecule will hybridize to the target without the other hybridizing to the target.

5. The cooperative nucleic acid molecule of claim 1 wherein the effective melting temperature (Tm) of the first nucleic acid molecule is increased by at least 1° C. as compared to the isolated Tm of the first nucleic acid sequence without the second nucleic acid sequence attached to it.

6. The cooperative nucleic acid molecule of claim 1 wherein the cooperative nucleic acid molecule comprises a label.

7. The cooperative nucleic acid molecule of claim 6 , wherein the second nucleic acid sequence comprises a label.