BiSearch: ePCR tool for native or bisulfite-treated genomic template

Research output: Chapter in Book/Report/Conference proceedingChapter

17 Citations (Scopus)

Abstract

The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are targets for mispriming and alternative amplification products. Such examples are GC-rich native or bisulfite-treated genomic DNA sequences. Bisulfite treatment leads to the specific conversion of non-methylated cytosines to uracyls. This is the key step of bisulfite genomic sequencing, widely used to determine DNA methylation of a sequence. Here, we describe BiSearch Web server (http://bisearch.enzim.hu), a primer design software created for designing primers to amplify such target sequences. Furthermore, we developed a unique post-design primer analysis module, to carry out genome wide searches to identify genomic mispriming sites and to test by electronic (in silico) PCR (ePCR) for alternative PCR products. This option is currently available on four native or bisulfite-treated mammalian genomes.

Original languageEnglish
Title of host publicationPCR Primer Design
EditorsAnton Yuryev
Pages385-402
Number of pages18
DOIs
Publication statusPublished - Aug 2 2007

Publication series

NameMethods in Molecular Biology
Volume402
ISSN (Print)1064-3745

Keywords

  • DNA methylation
  • Epigenetic control
  • Genomic DNA
  • Methylation-specific PCR (MSP)
  • Mispriming
  • Non-specific amplification
  • Primer design
  • Primer validation
  • Sequence alignment

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Arányi, T., & Tusnády, G. E. (2007). BiSearch: ePCR tool for native or bisulfite-treated genomic template. In A. Yuryev (Ed.), PCR Primer Design (pp. 385-402). (Methods in Molecular Biology; Vol. 402). https://doi.org/10.1385/1-59745-528-8:385