Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: method development, evaluation and application

Background

Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples.

Methods

The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep.

Conclusions

The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively.

Significance

The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food.     

Interactions of angiotensin II with membranes using a combination of differential scanning calorimetry and 31P NMR spectroscopy

Summary This study of angiotensin II (ANG II) membrane interactions uses a combination of³¹P NMR spectroscopy and differential scanning calorimetry (DSC), two valuable and complementary techniques which can provide useful information about the thermotropic and dynamic properties of peptide hormones in membranes. The major conclusion from the calorimetric experiments is that ANG II affects the phase properties of hydrated dipalmitoyl-phosphatidylcholine (DPPC) bilayers by mainly broadening the pretransition area. Preliminary³¹P NMR data seem to confirm the DSC results by showing that ANG II produces a lowering of the pretransition temperature but affects only minimally the main phase transition. In combination, the results from the two methods may indicate that the hormone produces its effects on the phospholipid head groups while its effects on the bilayer alkyl chains are not significant. Such results can be interpreted to mean that ANG II closely interacts with the phospholipid head groups perhaps up to the level of the interface, but does not enter deeper into the membrane bilayer.     

A new synthesis of the tripeptide Gly-His-Lys with antimicrobial activity

Summary A new solid phase synthesis of the growth-modulating tripeptide Gly-His-Lys is described. 2-Chlorotrityl chloride resin and 9-fluorenylmethoxycarbonyl-(Fmoc), 4-methyltrityl-(Mtt) protecting groups were used. The synthetic tripeptide was tested for its activity against bacteria, yeast and fungi. The in vitro effect of the tripeptide on DNA, RNA and protein synthesis was studied as well.