New primer combinations with comparable melting temperatures detecting highest numbers of nosZ sequences from sequence databases | Nove kombinacije zacetnih oligonukleotidov s primerljivimi temperaturami taljenja zaznavajo najvisje stevilo sekvenc nosZ v podatkovnih bazah
2009
Stres, B., Ljubljana Univ. (Slovenia). Biotechnical Fac., Dept. of Animal Science | Murovec, B., Ljubljana Univ. (Slovenia). Fac. of Electrical Engineering
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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