Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana

The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.

Designing and experimental evaluation of gene-specific primers of pea (Pisum sativum) defense proteins

Real-time gene expression analysis by semi-quantitative and quantitative RT-PCR requires a set of gene-specific primers which should have the ability to amplify the gene of interest specifically. In the present study, we have standardized certain parameters for primer design using the freely available Primer3 software. We have designed the primers for defense genes such as ICS (isochorismate synthase), CCoAOMT (caffeoyl CoA O-methyltransferase), C4H (cinnamate 4-hydroxylase), and G-alpha in pea. We have also discussed, the way of sequence retrieval, when the sequence is not reported in the organism of interest. We have evaluated the designed primers using cDNA prepared from mRNA isolated from the pea leaves. By analyzing the results, we have found that primers are perfectly binding with the target and giving single sharp band on a DNA electrophoresis gel. It can be concluded that the parameters used for primer designing by Primer3 play a critical role in the experimental results and parameters defined in the present study resulting in a very good amplification during PCR.

An approach to delineate primers for a group of poorly conserved sequences incorporating the common motif region

Glutathione synthetase (gshB) has previously been reported to confer tolerance to acidic soil condition in Rhizobium species. Cloning the gene coding for this enzyme necessitates the designing of proper primer sets which in turn depends on the identification of high quality sequence similarity in multiple global alignments. In this experiment, a group of homologous gene sequences related to gshB gene (accession no: gi-86355669:327589-328536) of Rhizobium etli CFN 42, were extracted from NCBI nucleotide sequence databases using BLASTN and were analyzed for designing degenerate primers. However, the T-coffee multiple global alignment results did not show any block of conserved region for the above sequence set to design the primers. Therefore, we attempted to identify the location of common motif region based on multiple local alignments employing the MEME algorithm supported with MAST and Primer3. The results revealed some common motif regions that enabled us to design the primer sets for related gshB gene sequences. The result will be validated in wet lab.