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RNase H-dependent PCR (rhPCR) (CAT#: STEM-MB-0217-WXH)

Introduction

RNase H-dependent PCR (rhPCR) is a nucleic acid amplification method that provides increased target specificity over traditional PCR. Compared to traditional PCR, rhPCR requires an additional enzyme, RNase H2, and uses blocked primers in place of conventional PCR primers.
In rhPCR, the primers are designed with a removable amplification block on the 3’ end. Amplification of the blocked primer is dependent on the cleavage activity of a hyperthermophilic archaeal Type II RNase H enzyme during hybridization to the complementary target sequence. This RNase H enzyme possesses several useful characteristics that enhance the PCR. First, it has very little enzymatic activity at low temperature, enabling a “hot start PCR” without modifications to the DNA polymerase. Second, the cleavage efficiency of the enzyme is reduced in the presence of mismatches near the RNA residue. This allows for reduced primer dimer formation, detection of alternative splicing variants, ability to perform multiplex PCR with higher numbers of PCR primers, and the ability to detect single-nucleotide polymorphisms.
The primer-dimer reducing abilities of rhAmp technology make it ideal for demanding genomics applications like multiplexed amplicon sequencing and SNP genotyping.




Principle

rh PCR technology relies heavily on the unique design of rhPrimers and the inherent characteristics of RNase H2. As opposed to DNA-only primers used in traditional PCR and qPCR, rhPrimers contain a single RNA base and a 3′ blocking group that must be removed by RNase H2 before extension by DNA polymerase can occur. The added specificity achieved by this mechanism consistently yields more amplification of the fragments you are targeting, and less off-target amplification.

Applications

• Gene expression assays
• Alternative splicing
• SNP genotyping
• Multiplex PCR

Procedure

General procedure:
1. Denaturation
2. Annealing
3. Extension

Materials

rhPCR requires an additional enzyme, RNase H2, and uses blocked primers (rhPrimers)
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