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Data base for PCR primers
Database
Currently, the complete database contains more than 500 primers, mainly in the 'long single copy' (LSC) region. In our hands, many of the published and newly designed primers can be used in different combinations, and in many species. 'Generic' PCR conditions that favour sucessful amplification for majority of combinations are: 2 mM Mg2+; and a PCR program with 10 cycles @ 70 deg annealing, followed by 32 cycles @ 55 deg annealing ('stepdown PCR'; alternatively, 'touchdown PCR' programs should also work). With these primers and methods, the chloroplast genome of hitherto unexplored species can be scanned in detail, and regions specific for different purposes can be picked.

The graphics accessible under "Maps" (see link on the left) present the positions of primers on the tobacco (Nicotiana tabaccum) chloroplast.
 
The database itself is a large table. It can be displayed by pressing the "Table" button on the left (if it is not fully visible in your browser, try "mark all", "copy" and "paste" it into e.g. Excel or Word). It includes primer names, genes, orientation of the primer towards the tobacco sequence, primer sequences, positions of the primers in 8 fully sequenced chloroplast genomes, and references.

Primer sequence data are presented in a simple tabular format. I suggest you download the table (by simple mark, copy, and paste) into a spreadsheet or database program. Please contact me if you have any further questions.
17.02.06 | Heinze, B.
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