Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR.
BACKGROUND
In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of reverse transcriptase polymerase chain reaction, is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. Given the absence of software available to produce genome suitable tags, a simple tool to fulfill such need was developed.


RESULTS
The program was developed in Perl, with separate use of the basic local alignment search tool, making the tool platform independent (known to run on Windows XP and Linux). In order to test the performance of the generated tags, several molecular experiments were performed. The results show that Tagenerator is capable of generating tags with good priming properties, which will deliberately not result in PCR amplification of genomic DNA.


CONCLUSIONS
The program Tagenerator is capable of generating tag sequences that combine genome absence with good priming properties for RT-PCR based experiments, circumventing the effects of genomic DNA contamination in an RNA sample.
Pinto
Fernando Lopes
FL
Department of Physiological Botany, The Angström Laboratories, Uppsala University, Box 523, SE-75120, Uppsala, Sweden. fernando.lopespinto@ebc.uu.se
Svensson
Håkan
H
Lindblad
Peter
P
D000465:Algorithms; D000818:Animals; D001709:Biotechnology / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000032:analysis; D017931:DNA Primers / Q000737:chemistry; D003627:Data Interpretation, Statistical; D004285:Dogs; D011381:Programming Languages; D012313:RNA / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012984:Software
D017931:DNA Primers; D012313:RNA; D004247:DNA