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“Our work, in part, involves development of high sensitivity tests for mutations present in only a small fraction of cells under test. This requires high specificity also and it has proven to be the case that the TriLink CleanAmp™ Primers provided the specificity needed to capitalize on qPCR’s inherent high sensitivity. Using your primers we can routinely identify the presence of mutation fractions as low as 0.001%.”
John Owen M.D.
Wake Forest University
“We designed a quadruplex PCR assay to simultaneously amplify four herpesviruses, including herpes simplex virus (HSV), cytomegalovirus (CMV), Epstein-Barr virus (EBV) and varicella zoster virus (VZV). We found that the use of CleanAmp™ Turbo Primers enhanced amplification efficacies in the quadruplex herpesvirus PCR assay where normal multiplex techniques previously failed.”
Yi-Wei Tang
University of Vanderbilt |
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A Hot Start Assay for Less
 CleanAmp™ Primers are similar to CleanAmp™ dNTPs in that they contain a thermolabile chemical modification that allows Hot Start activation in PCR. This novel modification also serves to prevent primer extension at the lower temperatures of PCR setup and manipulation. A Hot Start thermal activation step removes the modification generating the corresponding unmodified primer, which supports amplification of the desired target. CleanAmp™ Primers specifically amplify the target by eliminating formation of primer dimer (Figure 1A) and mis-priming (Figure 1B) events. Furthermore, CleanAmp™ Primers eliminate the need for Hot Start DNA polymerases because they are compatible with a number of standard DNA polymerases, such as Taq.
CleanAmp™ Primers are a key choice for diagnostic kits and other established assays. In these assays CleanAmp™ Primers can be as little as $0.03 per reaction at our standard starting scale. TriLink guarantees at least 10 ODs per primer synthesis, which is enough material for approximately 6,250 reactions. TriLink offers two types of CleanAmp™ Primers that vary in the rate of thermal activation: Turbo and Precision. The different rates of release of CleanAmp™ Turbo and Precision Primer modifications can be exploited for improved results in advanced applications, such as multiplex PCR (Figure 2), reverse-transcription PCR, low copy number detection (Figure 4) and fast PCR. The performance of CleanAmp™ Primers can be applied to critical applications such as molecular diagnostics, forensics, detection of infectious agents and gene expression validation.
Maximize Your Multiplex
If you are seeking a Hot Start solution for a problematic multiplex system, CleanAmp™ Primers may be your answer. Like CleanAmp™ dNTPs, CleanAmp™ Primers will improve yield and specificity in multiplex systems. However, CleanAmp™ Primers offer higher specificity with a greater number of targets. In the systems shown in Figure 2, CleanAmp™ Turbo Primers greatly improve formation of the desired products in multiplex PCR for seven and nine targets from genomic DNA sources. The development of a robust multiplex PCR assay typically requires an iterative design process to discover primer pairs that are both specific for the targets of interest and exhibit a low level of off-target amplicon formation. With CleanAmp™ Primers minimal design optimization is required.
The reduction or elimination of nonspecific amplifications achieved with the use of CleanAmp™ Primers makes them a powerful solution for improved one-step reverse-transcription (RT) PCR performance (Figure 3). By introducing CleanAmp™ Primers only the RT Primer can elongate during the reverse transcription step of the protocol, resulting in specific amplification in a one tube, single step protocol.
Reaching New Limits of Detection
CleanAmp™ Primers also offer an advantage over CleanAmp™ dNTPs in systems hindered by low template concentrations. A 10-100 fold increase in correct amplicon formation is seen when standard primers are replaced with CleanAmp™ Precision Primers (Figure 4). CleanAmp™ Primers greatly improve these systems by reducing or eliminating the off-target amplifications that compete with the desired amplicon.
CleanAmp™ Primers have utility in many high-sensitivity downstream applications, such as single molecule detection.
Product Details
CleanAmp™ Primers are available in two forms that differ in the rate of thermal activation. See table below for application based benefits. CleanAmp™ Primers are supplied cartridge purified. However, for those applications where PCR performance is of the utmost importance, we can RP-HPLC purify your CleanAmp™ Primers on a custom quote basis. Each primer undergoes quality control analysis by PAGE, MS and RP-HPLC to ensure high quality. CleanAmp™ Primers 15-40 bases in length are $250/pair. We guarantee at least a 10 OD final yield from every synthesis.
| CleanAmp™ Turbo Primers |
CleanAmp™ Precision Primers |
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| Fast cycling |
Standard cycling |
| Multiplex PCR |
One-step reverse-transcription PCR |
| Improves amplicon yield |
Improves specificity and limit of detection |
| Reduces mis-priming/primer dimer formation |
Greatest reduction in mis-priming/primer dimer formation |
CleanAmp™ Amidites
CleanAmp™ modified phosphoramidites are available for in-house synthesis of CleanAmp™ Primers.
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