New primer combinations with comparable melting temperatures detecting highest numbers of nosZ sequences from sequence databases

Authors

  • Blaž STRES Univ. of Ljubljana, Biotechnical Fac., Dept. of Animal Science, Groblje 3, SI-1230 Domžale, Slovenia
  • Boštjan MUROVEC Univ. of Ljubljana, Fac. of Electrical Engineering, Tržaška 25, SI-1000 Ljubljana, Slovenia

DOI:

https://doi.org/10.14720/aas.2009.94.2.14853

Keywords:

microbiology, molecular biology, denitrification, nitrous oxide reductase, melting temperature, detection

Abstract

We explored existing primer sequences targeting nitrous oxide reductase (nosZ) gene in order to explore their capability to recognize variant nosZ sequences. Published nosZ sequences longer than 380 AA residues were obtained from FunctionalGene Database /Repository (http://flyingcloud.cme.msu.edu/fungene/) and used for explorations with PrimerChart program. The numbers of sequences recovered using all possible forward and reverse primer combinations were determined and the stringency of primer site recognition was further varied by allowing 1, 2, or 3 primer mismatches to DNA binding site. We identified novel primer combinations resulting in satisfactory amplicon length (> 500 bp) and increased sequence recognition capabilities at comparable forward and reverse primer melting temperatures. Overall, this study indicates that current state of the art molecular methods can be and should frequently be further refined by the use of targeted bioinformatic approaches.

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Published

11. 12. 2009

Issue

Section

Original Scientific Article

How to Cite

STRES, B., & MUROVEC, B. (2009). New primer combinations with comparable melting temperatures detecting highest numbers of nosZ sequences from sequence databases. Acta Agriculturae Slovenica, 94(2), 139–142. https://doi.org/10.14720/aas.2009.94.2.14853