A molecular zipper () contains a generic, dsDNA sequence (38 bp) with a quencher moiety at the 5′ end of one strand (positive) and a fluorophore moiety at the 3′ end of the other strand (negative). The positive strand of the molecular zipper also contains an additional sequence (24 nt) at its 3′ end, which is identical to a portion of the C-probe and serves as a reverse primer for the RAM reaction. In its double-stranded form, the fluorophore of the negative strand is held close to the quencher of the positive strand, therefore, no fluorescence is emitted. However, when the two strands are separated from each other, for example, by increasing temperature, the quencher is separated from fluorophore and light is emitted. shows a typical denaturation curve (or unzipping) of a molecular zipper. At temperatures below 70°C, low background fluorescence was noticed, indicating that both strands were bound together, thereby efficiently quenching the fluorophore. However, there was a sharp increase of fluorescence above 72°C (the Tm of the molecular zipper is ~77°C) that reached plateau at 81°C, indicating a rapid unzipping of the molecular zipper. There was a decrease of fluorescence above 82°C. This is probably due to random interactions of the fluorophores with the quenchers in solution. Another explanation is that increasing of temperature induces the decreasing in pH of Tris buffer, which causes the decreasing in fluorescence of pH-sensitive fluorophore (i.e. fluorescein in this study).
In a RAM reaction, a forward primer bound to the C-probe is extended along the DNA circle by the large fragment of Bst
DNA polymerase that has high processivity and displacement activity (12
). The DNA polymerase displaces the initiating forward primer from the C-probe and continues copying around the circle, generating a long ssDNA with multiple repeats of the C-probe sequence (). Multiple molecular zippers bind to the growing ssDNA under isothermal conditions (2
) and are extended simultaneously by the DNA polymerases. The polymerases displace upstream molecular zippers and their associated sequences from the growing ssDNA when they encounter the molecular zippers, generating ssDNAs identical to the sequence of the original C-probe. To these ‘second-round products,’ multiple forward primers bind and are likewise extended by the polymerases. When the polymerases encounter the molecular zippers, they displace the negative strands of the molecular zippers (containing the fluorophores) from the positive strands, thereby separating fluorophore and quencher pairs and resulting in an increase of fluorescence ().
To determine the actual performance of the molecular zipper in RAM reaction, we carried out two reactions, both containing target DNA, C-probe and molecular zipper. One reaction included Taq
DNA ligase and the other contained no ligase (Methods). In the presence of the ligase, two ends of C-Probe were linked to form a DNA circle, while the C-probe remained linear in the absence of DNA ligase. As expected, the DNA circles formed in the presence of DNA ligase were utilized as templates in RAM reactions, and fluorescence was increasing as the RAM reaction proceeds (). The change in fluorescence in the RAM reaction was similar to that observed in conventional real-time exponential amplification (i.e. PCR), confirming the exponential nature of the RAM reaction (12
). In the other reaction, no circle was formed in the absence of the DNA ligase, thus, no fluorescence was detected even after a long period of incubation (), indicating a circle-dependent amplification in RAM reaction. Our results also indicate that the presence of dsDNA sequence in the molecular zipper does not interfere with the RAM reaction.
Figure 3 Characterization of molecular zipper in RAM reaction. (A) Molecules (1 × 107) of the C-probe were hybridized to 1 × 1010 molecules of the DNA target in a 20 μl reaction at 65°C for 15 min in the presence or absence of DNA (more ...)
After completion of the RAM reaction, we further measured the fluorescence change by denaturing the RAM products (). Our results showed that the denaturation curve of the RAM products initiated with unligated C-probe was the same as that of the molecular zipper alone (compare with ), indicating that the molecular zipper was intact during the incubation. In contrast, the fluorescence intensity of the RAM products derived from the ligated C-probe increased only mildly (25%) as compared with that derived from unligated C-probe, indicating that the majority of the molecular zippers were in an unzipped state. These results indicate that the positive strand of the molecular zipper was incorporated into the RAM products and the negative strand was displaced from the positive strand (i.e. unzipped).
To test the ability of the molecular zipper to quantify the copy number of C-probes present in a RAM reaction, we initiated the RAM reaction with known concentrations of ligated C-probes. presented real-time observation of triplicates for each concentration of C-probe (from 108 to 10 molecules), demonstrating a reasonably high reproducibility of RAM reactions monitored by molecular zipper. Most importantly, the figure showed that the time at which fluorescence raised above the baseline (response time, or Rt) correlated with the number of C-probes initially present. The greater the number of the C-probes, the earlier the response time occurred. A linear relationship (R2 = 0.985) existed between the threshold times (Rt values) and initial number of the C-probe (), demonstrating the ability of the molecular zipper for the real-time quantitative analysis in RAM reactions. Our results also demonstrated that RAM, in combination with the molecular zipper, detected a large dynamic range of C-probe (101–108 molecules) with an excellent analytical sensitivity.
Because of its sensitivity (i.e. exponential amplification), specificity (i.e. ligation-dependent discrimination of single nucleotide difference) and isothermal nature, the RAM technology becomes an important tool in research and clinical diagnosis (12
). However, its applications can be further broadened if the RAM products can be monitored in a real-time fashion as in real-time PCR. Several FRET-based DNA probes, such as molecular beacons (19
), Taqman probe (22
) and Scorpion probe (23
), have been described. However, the use of these FRET probes in RAM reactions is problematic and challenging. Owing to the lack of exonuclease activity of the DNA polymerase that is required for the displacement in RAM reaction (20
), Taqman cannot be used in RAM reaction. The use of molecular beacons in RCA also encountered some difficulties because of the interaction of neighboring beacons, which resulted in insufficient fluorescent signal (14
). Our attempts to directly use molecular beacons in RAM reactions also were discouraged because of the high background and low signal-to-noise ratios (data not shown), most likely due to the poor accessibility of molecular beacons to dsDNA product under isothermal conditions. On the other hand, a FRET probe linked to a primer, such as a molecular beacon (21
) and a Q-PNA (5
), has been used successfully in real-time monitoring of isothermal DNA amplification. The molecular beacon (21
), in this case, was designed to have a specific sequence to restrict enzyme recognition and digestion. This digestion, similar to the case of a stem–loop Scorpion (23
), separates the fluorophore from the quencher for maximum fluorescence release.
A molecular zipper, either a dsDNA as described in this study or a PNA/DNA hybrid as in previous study (5
) can be used and the release of fluorescence was achieved by displacement of the quencher in RAM. No specific sequence of molecular zipper is required for additional enzymatic digestion for real-time monitoring. The workability of molecular zipper was demonstrated in real-time RAM for genotyping detections with a Q-PNA (5
). Our DNA molecular zipper further demonstrated its utility for quantitative determination of targeted DNA in a real-time fashion. Furthermore, molecular zipper offers several advantages over Taqman and molecular beacons for real-time detection of amplification products. First, the long double-stranded region of the molecular zipper is more stable. Therefore, the background signal is much lower as compared with molecular beacons in which the short-stem region is less stable (19
). Second, the generic sequence of the molecular zipper allows it to be used universally for different targets. Third, the fluorophore and quencher are attached to two separate strands and the positions of fluorophore and quencher can be exchanged between the two strands. For example, in multiplex RAM reactions the quencher can be attached to the negative strand that can be used as a common strand (generic quencher) for different positive strands, each with a different fluorophore. This makes the synthesis of the FRET probe less costly and permits the convenient design of different probes with different fluorophores, thus increasing the capability for multiplexing. Finally, the molecular zipper can be used in other DNA amplification technologies that involve strand separation, such as PCR (24
), transcription-mediated amplification (NASBA) (26
), loop-mediated DNA amplification (27
) and strand displacement amplification (28