A new technique of PCR hot-start using duplex primers has been developed which can decrease the undesirableproducts arising throughout PCR amplification thereby giving better results than a manual hot-start method.

A novel method for duplex probes is designed to simulate theTaqMan probe during polymerase chain reaction (PCR); two single-labelled probes are used for this method, whichrelies on the 5'-exonuclease activity of nucleic acid polymerase.

The application of a new fluorogenic probe-based PCR assay (PCR duplex scorpion primer assay) to the detectionof Hepatitis B virus (HBV) DNA in human sera was described. Duplex scorpion primer is a modified variant ofduplex Amplifluor, and the incorporation of a PCR stopper between probe and primer sequences improve the detectionspecificity and sensitivity. Combined with PCR amplification, this probe can give unambiguous positive resultsfor the reactions initiated with more than 20 HBV molecules. In addition, the particular unimolecular probingmechanism of this probe makes the use of short target-specific probe sequence possible, which will render thisprobe applicable in some specific systems.

A novel method for duplex probes is designed to simulate the TaqMan probe during polymerase chain reaction(PCR). In this method, two partly complementary single-labelled oligonucleotide probes labelled with afluorophore or a quencher, respectively, are used. At lower temperature the two probes can bind to each otherand form a mismatched duplex, in which the fluorophore and quencher are in close proximity and the sameenergy transfer mechanism as in molecular beacons may occur between them; thus, a quenching efficiencybetter than conventional TaqMan probes is acquired. In the anneal-extend step of PCR, one single-labelledprobe hybridises to the predetermined target and is cleaved by Taq DNA polymerase. Increased fluorescentsignal can be observed at lower temperature. The fluorescent data analysis demonstrated that a significantlyhigher level of fluorescent signal and hence higher sensitivity of detection is obtainable using our duplex probesin place of conventional TaqMan probes. Combined with real-time PCR instruments, the assay can be used toquantify the input target molecules and the dynamic linear range is of at least six orders of magnitude.

In our previous paper it was shown that the two C-terminal Gln residues of a C-terminal 15-residue fragment, Mel(12-26)(GLPALISWIKRKRQQ-NH2), of melittin and a series of individual substituted analogues might not involved in the interaction withbacterial membranes. In this paper, peptides with one and two Gln residues deletion, respectively, Mel(12-25) and Mel(12-24), weresynthesized and characterized. Both of the deletion peptides showed higher antimicrobial activities than the parent peptide, Mel(12-26). If both of the Gln residues of Mel(12-26) were respectively replaced by a hydrophilic amino acid Gly, the antimicrobial activity increasedslightly. If the Gln residue of Mel(12-25) was replaced by a hydrophobic amino acid Leu, the antimicrobial activity changed little, althoughthe substituted peptide possessed much higher hydrophobicity and higher α-helical conformation percentage in 1,1,1,3,3,3-hexafluoro-2-propanol/water determined by circular dichroism spectroscopy (CD) than the parent peptide. These results indicated that the two C-terminalresidues might be indeed not involved in the binding to bacterial membranes. The antimicrobial activity increasing with the residue deletionmay be caused by the decrease of the translational and rotational entropic cost of the binding of the peptides to bacterial membranes becauseof the lower molecular weights of the deletion peptides.