AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs.
BACKGROUND
Primer design is a critical step in all types of RT-PCR methods to ensure specificity and efficiency of a target amplicon. However, most traditional primer design programs suggest primers on a single template of limited genetic complexity. To provide researchers with a sufficient number of pre-designed specific RT-PCR primer pairs for whole genes in Arabidopsis, we aimed to construct a genome-wide primer-pair database.


METHODS
We considered the homogeneous physical and chemical properties of each primer (homogeneity) of a gene, non-specific binding against all other known genes (specificity), and other possible amplicons from its corresponding genomic DNA or similar cDNAs (additional information). Then, we evaluated the reliability of our database with selected primer pairs from 15 genes using conventional and real time RT-PCR.


CONCLUSIONS
Approximately 97% of 28,952 genes investigated were finally registered in AtRTPrimer. Unlike other freely available primer databases for Arabidopsis thaliana, AtRTPrimer provides a large number of reliable primer pairs for each gene so that researchers can perform various types of RT-PCR experiments for their specific needs. Furthermore, by experimentally evaluating our database, we made sure that our database provides good starting primer pairs for Arabidopsis researchers to perform various types of RT-PCR experiments.
Department of BioSystems, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea. Sangjo_Han@kaist.ac.kr
Sangjo
S
Han
Dongsup
D
Kim
D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods
D017931:DNA Primers; D018744:DNA, Plant