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Herculase II Fusion DNA Polymerases - Details & Specifications

Herculase II Fusion DNA Polymerase provides you with superior yields in both routine and challenging PCR applications, with the additional benefit of allowing the use of fast cycling times. Some PCR targets are problematic to amplify due to their content or structure. Our Herculase II Fusion DNA Polymerase helps you overcome these PCR challenges with successful amplification of complex and GC-rich templates. The Herculase II enzyme also provides fidelity comparable to Pfu DNA Polymerase, which is 6 times more accurate than Taq DNA polymerase.

Superior Yield with Fast Cycles

Herculase II Fusion DNA Polymerase is the most robust PCR enzyme, producing unrivaled amplicon yields across a broad range of target types and lengths. This great performance is a combination of the highly processive Herculase II enzyme, our proprietary ArchaeMaxx PCR enhancing factor and the specially optimized Herculase II buffer.

Figure 1. Robust Yields Achieved with Fast Cycling Times Herculase II Fusion DNA Polymerase produced superior yields of a 6-kb fragment (a) and a 1.7 kb fragment (b) in amplifications employing human genomic DNA and extension times of 15, 30, 45, and 60 sec/kb. Experiments were conducted under identical conditions using each enzyme’s recommended buffer.

Successful Amplification of GC-Rich/Complex Targets

Herculase II Fusion DNA Polymerase is ideal for amplification of difficult targets. The specially engineered enzyme and the optimized buffer system enable the Herculase II enzyme to amplify difficult targets with high yields using fast cycling conditions. Targets that contain as much as 84% GC content are easily amplified while other competitors’ enzymes failed or produced low yield. To enhance amplification of problematic or GC-rich templates, DMSO (provided in a separate tube) can be added (3-10% DMSO; titrated in 1% increments to find optimal performance with your targets).

Figure 2. Herculase II Fusion DNA Polymerase Excels in Amplifying GC-Rich Targets Our Herculase II Fusion DNA Polymerase easily amplifies targets that contain as high as 84% GC content while competitors’ enzymes failed or produced low yield. Fragments of the following human genes were amplified from genomic DNA: IGFB, insulin-like growth factor binding protein 3 (79% GC, 250 bp), FMR1, fragile X mental retardation syndrome protein (84% GC, 300 bp); HTR, hydroxytryptamine receptor C2 fragment (65% GC, 540 bp); MMZ5, ZIC5 – zinc family member 5 protein (68% GC, 562 bp). All reactions were conducted using manufacturers' recommended buffer and cycling conditions for GC-rich targets.

High Sensitivity with Low Abundance Targets

Herculase II Fusion DNA Polymerase amplifies DNA fragments with great sensitivity. A 3.9 kb fragment of the human a1-antitrypsin gene is amplified from as little as 1 ng input human genomic DNA. In comparison, competitors' enzymes were less sensitive and less specific. Herculase II Fusion DNA Polymerase enables you to amplify limited amounts of DNA with great accuracy. (Also see PicoMaxx our most sensitive polymerase.)

Figure 3. Herculase II Fusion DNA Polymerase Exhibits Superior Sensitivity A 3.9-kb fragment of the human a1-antitrypsin gene was amplified from genomic DNA with DNA input amounts varying from 0, 1, 5, 10, 50, 100, 200, and 300 ng, lanes 1 through 8, respectively. Herculase II Fusion DNA Polymerase amplified the specific target DNA fragment from as little as 1 ng input DNA. In comparison, competitors’ enzymes were less sensitive and less specific. All reactions were conducted using manufacturers’ recommended buffer and cycling conditions.

Enhanced Processivity

We have dramatically increased the processivity of the Herculase II fusion enzyme by fusing the DNA polymerase with a high affinity double-stranded DNA binding domain. This domain serves to better anchor the DNA polymerase, preventing early dissociation from the DNA template. This improved processivity leads to higher PCR yields and allows the use of shorter extension times, hence reducing overall run times.  The below image shows the time savings of fusion technology in your total PCR run time.  (PfuUltra II also has the advantage of fusion technology).

All Fusions Are Not Alike

Several archaeal DNA polymerase fusions have been commercialized that differ with respect to DNA polymerase and/or DNA-binding domain employed, and the inclusion of various PCR-enhancing supplements. For example, the PfuUltra II Fusion HS DNA Polymerase is formulated with a Pfu-based DNA polymerase fused to a proprietary double-stranded DNA binding protein (and supplemented with P. furiosus dUTPase, ArchaeMaxx, and hotstart antibody), while PhusionTM DNA Polymerase consists of chimeric DeepVent/Pfu (Pyrococcus sp. GB-D/furiosus) DNA polymerase fused to Sso7d.

Exclusive ArchaeMaxx Factor

Stratagene scientists isolated the ArchaeMaxx factor from Pyrococcus furiosus and added it to our high-fidelity enzyme, where it eliminates a PCR inhibitor and promotes shorter extension times, higher yield and greater target length capability. The ArchaeMaxx factor is a key ingredient in many of Stratagene’s enzyme formulations. The ArchaeMaxx factor improves the yield of products that contain Pfu DNA polymerase by overcoming "dUTP poisoning", which is caused by dUTP accumulation during PCR through dCTP deamination (See citations). This dUTP poisoning inhibits Pfu and many other archaeal proofreading DNA polymerases, such as VentR® and Deep VentR® DNA polymerases, limiting their efficiency. The ArchaeMaxx factor functions as a dUTPase, converting poisonous dUTP to harmless dUMP and inorganic pyrophosphate resulting in greatly enhanced overall PCR performance.

Applications where Herculase II Fusion DNA Polymerase Excels

Herculase II is an ideal polymerase to choose for applications where fidelity is required but may not be the only factor. (If fidelity is the primary concern, PfuUltra II Fusion HS DNA Polymerase would suit the application.) Combine high fidelity with Herculase II’s ability to deliver unrivaled yields, extreme sensitivity, and the ability to amplify difficult samples, and you have an ideal polymerase for routine high fidelity use. In addition, Herculase II is economical enough to be used for high throughput applications.

Herculase II in Next-Gen Sequencing

Our data indicates that Herculase II is a superior polymerase for Next-Gen Sequencing.  The high yields allow for fewer cycles of amplification thereby reducing PCR bias. In addition, during library preparation, Herculase II delivers the best size distribution of any polymerase with the vast majority of amplicons in the ideal sequencing size range. In conjunction with SureSelect, this leads to the need for fewer sequencing reactions and better sets of sequencing data.


For Research Use Only. Not for use in diagnostic procedures